Multiple sequence alignment - TraesCS2A01G429000

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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 TraesCS2A01G429000 chr2A 100.000 2896 0 0 1 2896 682483417 682480522 0.000000e+00 5349
1 TraesCS2A01G429000 chr2A 100.000 555 0 0 3230 3784 682480188 682479634 0.000000e+00 1026
2 TraesCS2A01G429000 chr2A 83.770 992 144 9 1805 2788 682154055 682153073 0.000000e+00 924
3 TraesCS2A01G429000 chr2A 78.436 946 154 42 1838 2755 682492317 682491394 4.240000e-159 571
4 TraesCS2A01G429000 chr2A 83.333 630 88 9 1805 2425 681997459 681996838 1.970000e-157 566
5 TraesCS2A01G429000 chr2A 77.670 412 63 13 1027 1410 682493422 682493012 1.370000e-54 224
6 TraesCS2A01G429000 chr2D 94.516 1094 43 6 1792 2870 539168325 539167234 0.000000e+00 1672
7 TraesCS2A01G429000 chr2D 89.970 1007 54 16 798 1787 539169542 539168566 0.000000e+00 1256
8 TraesCS2A01G429000 chr2D 85.388 657 96 0 2132 2788 539016457 539015801 0.000000e+00 682
9 TraesCS2A01G429000 chr2D 77.778 945 162 39 1838 2755 539226129 539225206 4.300000e-149 538
10 TraesCS2A01G429000 chr2D 93.103 319 14 4 3230 3546 539167225 539166913 9.580000e-126 460
11 TraesCS2A01G429000 chr2D 83.901 323 44 6 1805 2127 539016937 539016623 6.140000e-78 302
12 TraesCS2A01G429000 chr2D 88.557 201 21 2 3585 3784 69525920 69526119 3.780000e-60 243
13 TraesCS2A01G429000 chr2D 91.892 148 8 3 656 799 539169952 539169805 1.780000e-48 204
14 TraesCS2A01G429000 chr2D 77.513 378 56 15 1061 1410 539227068 539226692 2.310000e-47 200
15 TraesCS2A01G429000 chr2B 90.708 1130 66 13 1763 2874 642978622 642977514 0.000000e+00 1469
16 TraesCS2A01G429000 chr2B 94.576 719 28 3 798 1513 642979759 642979049 0.000000e+00 1101
17 TraesCS2A01G429000 chr2B 89.803 814 56 10 1 799 642980684 642979883 0.000000e+00 1018
18 TraesCS2A01G429000 chr2B 83.280 939 133 17 1803 2741 642782985 642782071 0.000000e+00 843
19 TraesCS2A01G429000 chr2B 78.049 943 157 39 1838 2752 643091936 643091016 1.990000e-152 549
20 TraesCS2A01G429000 chr2B 89.547 287 10 7 3303 3584 642977349 642977078 2.800000e-91 346
21 TraesCS2A01G429000 chr2B 90.094 212 19 2 3573 3784 570887602 570887811 1.340000e-69 274
22 TraesCS2A01G429000 chr2B 89.394 198 20 1 3586 3782 1668120 1667923 8.120000e-62 248
23 TraesCS2A01G429000 chr2B 77.262 409 67 10 1027 1410 643093012 643092605 2.290000e-52 217
24 TraesCS2A01G429000 chr2B 90.345 145 9 3 1577 1721 642978950 642978811 6.450000e-43 185
25 TraesCS2A01G429000 chr2B 91.667 72 6 0 3230 3301 642977507 642977436 2.410000e-17 100
26 TraesCS2A01G429000 chr5B 94.444 198 10 1 3587 3783 476814320 476814123 1.710000e-78 303
27 TraesCS2A01G429000 chr5A 92.965 199 14 0 3586 3784 514775592 514775790 1.330000e-74 291
28 TraesCS2A01G429000 chr7A 91.457 199 16 1 3586 3784 199432077 199431880 4.820000e-69 272
29 TraesCS2A01G429000 chr1A 90.452 199 19 0 3586 3784 565356016 565356214 2.900000e-66 263
30 TraesCS2A01G429000 chr3D 89.109 202 21 1 3584 3784 500659606 500659405 2.260000e-62 250
31 TraesCS2A01G429000 chr3D 88.670 203 22 1 3583 3784 372521508 372521710 2.920000e-61 246


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 TraesCS2A01G429000 chr2A 682479634 682483417 3783 True 3187.500000 5349 100.000000 1 3784 2 chr2A.!!$R3 3783
1 TraesCS2A01G429000 chr2A 682153073 682154055 982 True 924.000000 924 83.770000 1805 2788 1 chr2A.!!$R2 983
2 TraesCS2A01G429000 chr2A 681996838 681997459 621 True 566.000000 566 83.333000 1805 2425 1 chr2A.!!$R1 620
3 TraesCS2A01G429000 chr2A 682491394 682493422 2028 True 397.500000 571 78.053000 1027 2755 2 chr2A.!!$R4 1728
4 TraesCS2A01G429000 chr2D 539166913 539169952 3039 True 898.000000 1672 92.370250 656 3546 4 chr2D.!!$R2 2890
5 TraesCS2A01G429000 chr2D 539015801 539016937 1136 True 492.000000 682 84.644500 1805 2788 2 chr2D.!!$R1 983
6 TraesCS2A01G429000 chr2D 539225206 539227068 1862 True 369.000000 538 77.645500 1061 2755 2 chr2D.!!$R3 1694
7 TraesCS2A01G429000 chr2B 642782071 642782985 914 True 843.000000 843 83.280000 1803 2741 1 chr2B.!!$R2 938
8 TraesCS2A01G429000 chr2B 642977078 642980684 3606 True 703.166667 1469 91.107667 1 3584 6 chr2B.!!$R3 3583
9 TraesCS2A01G429000 chr2B 643091016 643093012 1996 True 383.000000 549 77.655500 1027 2752 2 chr2B.!!$R4 1725

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
932 1219 0.173481 TAGCAGCACCACATCTCGTC 59.827 55.000 0.00 0.0 0.00 4.20 F
1514 1867 0.320683 CACGTGGAGCAGGTCATTCA 60.321 55.000 7.95 0.0 29.69 2.57 F
1515 1868 0.320771 ACGTGGAGCAGGTCATTCAC 60.321 55.000 1.20 0.0 0.00 3.18 F
2076 3240 1.000486 TCCCCTCTTAGCTCAGCGT 60.000 57.895 0.00 0.0 0.00 5.07 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2453 3779 0.176680 CCTCCACCCAGTCGATCAAG 59.823 60.0 0.00 0.00 0.00 3.02 R
2684 4022 0.676466 CATGCACGTACACCACCCAT 60.676 55.0 0.00 0.00 0.00 4.00 R
2759 4097 0.975544 CGAACACGTAGCTGTTCTCG 59.024 55.0 12.93 3.55 42.19 4.04 R
3687 5140 0.106708 ACAGTGTCATGTGGCGTCTT 59.893 50.0 0.00 0.00 30.46 3.01 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
19 20 0.466189 ACGTCCCCCATGATCATTGC 60.466 55.000 5.16 0.00 0.00 3.56
70 71 3.483869 AGAAGGGCGGGGCTCATC 61.484 66.667 0.00 0.00 0.00 2.92
104 105 1.982073 GCGGCTGCGTGCTTAGAAAT 61.982 55.000 0.00 0.00 42.39 2.17
147 148 3.385384 CCGAGCTGGGCAGAGTGA 61.385 66.667 0.21 0.00 0.00 3.41
148 149 2.659016 CGAGCTGGGCAGAGTGAA 59.341 61.111 0.00 0.00 0.00 3.18
175 176 5.246883 GCATGGGGGAAGCAAAATATTATCT 59.753 40.000 0.00 0.00 0.00 1.98
176 177 6.239686 GCATGGGGGAAGCAAAATATTATCTT 60.240 38.462 0.00 0.00 0.00 2.40
188 189 8.765219 GCAAAATATTATCTTGAGAACGAGCTA 58.235 33.333 3.10 0.00 0.00 3.32
193 194 3.677190 TCTTGAGAACGAGCTACGATC 57.323 47.619 11.64 9.39 45.77 3.69
198 199 1.328069 AGAACGAGCTACGATCGAGTG 59.672 52.381 24.34 11.87 45.89 3.51
200 201 1.719425 CGAGCTACGATCGAGTGCG 60.719 63.158 24.34 16.39 45.77 5.34
210 211 2.052157 GATCGAGTGCGTATAAGTGGC 58.948 52.381 0.00 0.00 38.98 5.01
211 212 1.100510 TCGAGTGCGTATAAGTGGCT 58.899 50.000 0.00 0.00 38.98 4.75
228 229 1.506718 CTGCTGACGCGAGGAGTAA 59.493 57.895 15.93 0.00 39.65 2.24
231 232 1.201343 GCTGACGCGAGGAGTAAATC 58.799 55.000 15.93 0.00 0.00 2.17
236 238 3.678072 TGACGCGAGGAGTAAATCTTTTG 59.322 43.478 15.93 0.00 0.00 2.44
266 268 1.959899 GCGCATAATGGATCGGCTCG 61.960 60.000 0.30 0.00 0.00 5.03
286 288 2.477754 CGGTCCGTTTTAACTCCTCAAC 59.522 50.000 2.08 0.00 0.00 3.18
288 290 3.495629 GGTCCGTTTTAACTCCTCAACCT 60.496 47.826 0.00 0.00 0.00 3.50
291 293 4.131596 CCGTTTTAACTCCTCAACCTGAA 58.868 43.478 0.00 0.00 0.00 3.02
292 294 4.577283 CCGTTTTAACTCCTCAACCTGAAA 59.423 41.667 0.00 0.00 0.00 2.69
293 295 5.505159 CCGTTTTAACTCCTCAACCTGAAAC 60.505 44.000 0.00 0.00 0.00 2.78
294 296 5.505159 CGTTTTAACTCCTCAACCTGAAACC 60.505 44.000 0.00 0.00 0.00 3.27
295 297 2.256117 AACTCCTCAACCTGAAACCG 57.744 50.000 0.00 0.00 0.00 4.44
296 298 1.420430 ACTCCTCAACCTGAAACCGA 58.580 50.000 0.00 0.00 0.00 4.69
297 299 1.766496 ACTCCTCAACCTGAAACCGAA 59.234 47.619 0.00 0.00 0.00 4.30
299 301 3.181443 ACTCCTCAACCTGAAACCGAATT 60.181 43.478 0.00 0.00 0.00 2.17
300 302 3.821033 CTCCTCAACCTGAAACCGAATTT 59.179 43.478 0.00 0.00 0.00 1.82
301 303 4.211920 TCCTCAACCTGAAACCGAATTTT 58.788 39.130 0.00 0.00 0.00 1.82
302 304 4.647399 TCCTCAACCTGAAACCGAATTTTT 59.353 37.500 0.00 0.00 0.00 1.94
303 305 4.982295 CCTCAACCTGAAACCGAATTTTTC 59.018 41.667 0.00 0.00 34.16 2.29
304 306 5.221244 CCTCAACCTGAAACCGAATTTTTCT 60.221 40.000 3.46 0.00 34.58 2.52
305 307 6.016610 CCTCAACCTGAAACCGAATTTTTCTA 60.017 38.462 3.46 0.00 34.58 2.10
306 308 6.966021 TCAACCTGAAACCGAATTTTTCTAG 58.034 36.000 3.46 0.00 34.58 2.43
307 309 6.768861 TCAACCTGAAACCGAATTTTTCTAGA 59.231 34.615 0.00 0.00 34.58 2.43
326 328 8.767478 TTCTAGAAGTTAACCGGTTTTATGAG 57.233 34.615 27.64 13.99 0.00 2.90
348 350 5.879763 AGATCTGCTAGAGATGCTCTTAGA 58.120 41.667 1.88 5.51 41.91 2.10
349 351 5.707298 AGATCTGCTAGAGATGCTCTTAGAC 59.293 44.000 1.88 1.93 41.91 2.59
352 354 3.634448 TGCTAGAGATGCTCTTAGACACC 59.366 47.826 1.88 0.00 41.50 4.16
359 361 5.593010 AGATGCTCTTAGACACCGTAAATC 58.407 41.667 0.00 0.00 0.00 2.17
361 363 5.142061 TGCTCTTAGACACCGTAAATCAA 57.858 39.130 0.00 0.00 0.00 2.57
383 385 7.171653 TCAAAATAGACCATTGTCCACATGTA 58.828 34.615 0.00 0.00 42.81 2.29
404 413 2.605837 GCTCCCTAGCTAGTGTTTCC 57.394 55.000 19.31 0.00 45.85 3.13
459 468 4.261656 GCAGTTCATATAGAGTACACGGCT 60.262 45.833 0.00 0.00 0.00 5.52
470 479 2.360165 AGTACACGGCTTTAGGGTATCG 59.640 50.000 0.00 0.00 29.46 2.92
480 489 6.585322 CGGCTTTAGGGTATCGTAAAGATAAG 59.415 42.308 25.24 12.45 46.23 1.73
481 490 6.368243 GGCTTTAGGGTATCGTAAAGATAAGC 59.632 42.308 25.24 13.89 46.23 3.09
484 493 9.843334 CTTTAGGGTATCGTAAAGATAAGCTAG 57.157 37.037 19.06 0.00 46.23 3.42
551 560 1.420514 TCGTATGTCCCAAACCAACCA 59.579 47.619 0.00 0.00 0.00 3.67
624 637 4.595762 ATGCAAACAAAAGCTCATCAGT 57.404 36.364 0.00 0.00 0.00 3.41
629 642 5.922544 GCAAACAAAAGCTCATCAGTATGTT 59.077 36.000 0.00 0.00 37.40 2.71
646 659 9.201989 TCAGTATGTTATCTTCATCTTGGTAGT 57.798 33.333 0.00 0.00 37.40 2.73
647 660 9.823647 CAGTATGTTATCTTCATCTTGGTAGTT 57.176 33.333 0.00 0.00 0.00 2.24
721 738 1.184322 TAACGCCACCCGAACCACTA 61.184 55.000 0.00 0.00 41.02 2.74
839 1123 5.118990 CGAACAGGAACTATGAATGGTGAT 58.881 41.667 0.00 0.00 36.02 3.06
840 1124 5.586243 CGAACAGGAACTATGAATGGTGATT 59.414 40.000 0.00 0.00 36.02 2.57
841 1125 6.761242 CGAACAGGAACTATGAATGGTGATTA 59.239 38.462 0.00 0.00 36.02 1.75
842 1126 7.279981 CGAACAGGAACTATGAATGGTGATTAA 59.720 37.037 0.00 0.00 36.02 1.40
843 1127 7.865706 ACAGGAACTATGAATGGTGATTAAC 57.134 36.000 0.00 0.00 36.02 2.01
844 1128 7.633789 ACAGGAACTATGAATGGTGATTAACT 58.366 34.615 0.00 0.00 36.02 2.24
845 1129 7.770897 ACAGGAACTATGAATGGTGATTAACTC 59.229 37.037 0.00 0.00 36.02 3.01
846 1130 7.770433 CAGGAACTATGAATGGTGATTAACTCA 59.230 37.037 0.00 0.00 36.02 3.41
932 1219 0.173481 TAGCAGCACCACATCTCGTC 59.827 55.000 0.00 0.00 0.00 4.20
1064 1361 4.034258 GTCTGCGACGACGGTGGA 62.034 66.667 9.67 0.00 40.15 4.02
1305 1629 2.963371 GTCGACTTCACCGAGGCT 59.037 61.111 8.70 0.00 36.66 4.58
1481 1810 1.021968 AGGTCCACGTGAAAAACAGC 58.978 50.000 19.30 3.11 0.00 4.40
1513 1866 1.021390 CCACGTGGAGCAGGTCATTC 61.021 60.000 31.31 0.00 37.39 2.67
1514 1867 0.320683 CACGTGGAGCAGGTCATTCA 60.321 55.000 7.95 0.00 29.69 2.57
1515 1868 0.320771 ACGTGGAGCAGGTCATTCAC 60.321 55.000 1.20 0.00 0.00 3.18
1517 1870 1.375908 TGGAGCAGGTCATTCACGC 60.376 57.895 1.20 0.00 0.00 5.34
1518 1871 2.456119 GGAGCAGGTCATTCACGCG 61.456 63.158 3.53 3.53 0.00 6.01
1519 1872 1.738099 GAGCAGGTCATTCACGCGT 60.738 57.895 5.58 5.58 0.00 6.01
1526 1947 1.448893 TCATTCACGCGTTAGGCCC 60.449 57.895 10.22 0.00 38.94 5.80
1528 1949 1.003112 ATTCACGCGTTAGGCCCAA 60.003 52.632 10.22 0.00 38.94 4.12
1559 1980 3.990469 CGTGGCAGCCTTCTGTATTATAG 59.010 47.826 14.15 0.00 42.29 1.31
1560 1981 4.319177 GTGGCAGCCTTCTGTATTATAGG 58.681 47.826 14.15 0.00 42.29 2.57
1561 1982 4.040461 GTGGCAGCCTTCTGTATTATAGGA 59.960 45.833 14.15 0.00 42.29 2.94
1562 1983 4.284490 TGGCAGCCTTCTGTATTATAGGAG 59.716 45.833 14.15 0.00 42.29 3.69
1563 1984 4.284746 GGCAGCCTTCTGTATTATAGGAGT 59.715 45.833 3.29 0.00 42.29 3.85
1564 1985 5.480772 GGCAGCCTTCTGTATTATAGGAGTA 59.519 44.000 3.29 0.00 42.29 2.59
1565 1986 6.391537 GCAGCCTTCTGTATTATAGGAGTAC 58.608 44.000 0.00 0.00 42.29 2.73
1566 1987 6.015350 GCAGCCTTCTGTATTATAGGAGTACA 60.015 42.308 0.00 0.00 42.29 2.90
1567 1988 7.371936 CAGCCTTCTGTATTATAGGAGTACAC 58.628 42.308 0.00 0.00 35.61 2.90
1568 1989 7.231722 CAGCCTTCTGTATTATAGGAGTACACT 59.768 40.741 0.00 0.00 35.61 3.55
1569 1990 8.446394 AGCCTTCTGTATTATAGGAGTACACTA 58.554 37.037 0.00 0.00 0.00 2.74
1694 2115 8.278729 AGATGCTCTAAAGATTCTTTTTCCAG 57.721 34.615 16.39 8.34 0.00 3.86
1738 2160 7.577979 TCTTTTGTCGAAAATGCTAAACGTAT 58.422 30.769 0.00 0.00 30.59 3.06
1749 2171 7.435068 AATGCTAAACGTATGGATCATTACC 57.565 36.000 0.00 0.00 0.00 2.85
1824 2979 1.996898 CTAATTCCGTTGCGTGCTACA 59.003 47.619 7.18 0.00 0.00 2.74
1825 2980 1.448985 AATTCCGTTGCGTGCTACAT 58.551 45.000 7.18 0.00 0.00 2.29
2076 3240 1.000486 TCCCCTCTTAGCTCAGCGT 60.000 57.895 0.00 0.00 0.00 5.07
2233 3558 1.804372 GCAACTCTGCTCTATGTCGGG 60.804 57.143 0.00 0.00 45.74 5.14
2359 3685 2.543777 ACTTACGGTGTCAACAGCAT 57.456 45.000 12.33 0.00 44.00 3.79
2567 3905 1.969589 GTCGTCGGGCATGGGTTTT 60.970 57.895 0.00 0.00 0.00 2.43
2666 4004 2.202932 GTGATGCCGATGCCGAGT 60.203 61.111 0.00 0.00 38.22 4.18
2705 4043 1.963855 GGTGGTGTACGTGCATGCA 60.964 57.895 18.46 18.46 0.00 3.96
2759 4097 3.312697 AGCCGACTGTTTTCAAAGTTCTC 59.687 43.478 0.00 0.00 0.00 2.87
2810 4159 4.518970 ACAGTTGTGGTGCCTGTTATTTAG 59.481 41.667 0.00 0.00 36.03 1.85
2812 4161 5.003804 AGTTGTGGTGCCTGTTATTTAGAG 58.996 41.667 0.00 0.00 0.00 2.43
3257 4618 2.638480 AGTTGTTGCTCTACAAGGCA 57.362 45.000 0.00 0.00 39.50 4.75
3275 4636 8.723942 ACAAGGCATTTTGTGTGTAAAAATAA 57.276 26.923 0.42 0.00 39.68 1.40
3298 4659 7.617533 AATGTAAAAACGTGTGATTGCTAAC 57.382 32.000 0.00 0.00 0.00 2.34
3301 4747 7.569297 TGTAAAAACGTGTGATTGCTAACTAG 58.431 34.615 0.00 0.00 0.00 2.57
3370 4820 4.621038 GCTCCATCAGATGTGATCGATCAT 60.621 45.833 29.53 16.00 41.85 2.45
3371 4821 5.069501 TCCATCAGATGTGATCGATCATC 57.930 43.478 29.53 22.98 41.85 2.92
3451 4903 6.371271 TCGCTCATAAATGTCATCTGTTTTCA 59.629 34.615 0.00 0.00 0.00 2.69
3503 4955 2.028658 CGGATGGGATCGATCATCAGTT 60.029 50.000 25.93 10.09 40.94 3.16
3533 4985 5.796350 AATATCGGGTGATAAAATAGCGC 57.204 39.130 0.00 0.00 40.37 5.92
3584 5037 6.570378 GCTTATAATGTGTCACCTGCTTTTGT 60.570 38.462 0.00 0.00 0.00 2.83
3585 5038 3.441496 AATGTGTCACCTGCTTTTGTG 57.559 42.857 0.00 0.00 0.00 3.33
3586 5039 1.102154 TGTGTCACCTGCTTTTGTGG 58.898 50.000 0.00 0.00 33.29 4.17
3587 5040 0.249031 GTGTCACCTGCTTTTGTGGC 60.249 55.000 0.00 0.00 37.60 5.01
3588 5041 0.682532 TGTCACCTGCTTTTGTGGCA 60.683 50.000 0.00 0.00 44.19 4.92
3589 5042 0.459489 GTCACCTGCTTTTGTGGCAA 59.541 50.000 0.00 0.00 39.30 4.52
3590 5043 1.134848 GTCACCTGCTTTTGTGGCAAA 60.135 47.619 0.00 0.00 39.30 3.68
3591 5044 1.761784 TCACCTGCTTTTGTGGCAAAT 59.238 42.857 0.00 0.00 39.30 2.32
3592 5045 2.170187 TCACCTGCTTTTGTGGCAAATT 59.830 40.909 0.00 0.00 39.30 1.82
3593 5046 2.944349 CACCTGCTTTTGTGGCAAATTT 59.056 40.909 0.00 0.00 39.30 1.82
3594 5047 2.944349 ACCTGCTTTTGTGGCAAATTTG 59.056 40.909 14.03 14.03 39.30 2.32
3595 5048 3.204526 CCTGCTTTTGTGGCAAATTTGA 58.795 40.909 22.31 0.00 39.30 2.69
3596 5049 3.816523 CCTGCTTTTGTGGCAAATTTGAT 59.183 39.130 22.31 0.00 39.30 2.57
3597 5050 4.996122 CCTGCTTTTGTGGCAAATTTGATA 59.004 37.500 22.31 6.54 39.30 2.15
3598 5051 5.469421 CCTGCTTTTGTGGCAAATTTGATAA 59.531 36.000 22.31 3.81 39.30 1.75
3599 5052 6.149807 CCTGCTTTTGTGGCAAATTTGATAAT 59.850 34.615 22.31 0.00 39.30 1.28
3600 5053 7.308710 CCTGCTTTTGTGGCAAATTTGATAATT 60.309 33.333 22.31 0.00 39.30 1.40
3601 5054 7.938715 TGCTTTTGTGGCAAATTTGATAATTT 58.061 26.923 22.31 0.00 43.09 1.82
3602 5055 8.411683 TGCTTTTGTGGCAAATTTGATAATTTT 58.588 25.926 22.31 0.00 40.97 1.82
3603 5056 8.692615 GCTTTTGTGGCAAATTTGATAATTTTG 58.307 29.630 22.31 6.76 40.97 2.44
3604 5057 9.947669 CTTTTGTGGCAAATTTGATAATTTTGA 57.052 25.926 22.31 0.00 40.97 2.69
3605 5058 9.727627 TTTTGTGGCAAATTTGATAATTTTGAC 57.272 25.926 22.31 9.31 40.97 3.18
3606 5059 7.432350 TGTGGCAAATTTGATAATTTTGACC 57.568 32.000 22.31 9.40 40.97 4.02
3607 5060 7.222872 TGTGGCAAATTTGATAATTTTGACCT 58.777 30.769 22.31 0.00 40.97 3.85
3608 5061 7.172875 TGTGGCAAATTTGATAATTTTGACCTG 59.827 33.333 22.31 0.00 40.97 4.00
3609 5062 7.173047 GTGGCAAATTTGATAATTTTGACCTGT 59.827 33.333 22.31 0.00 40.97 4.00
3610 5063 7.172875 TGGCAAATTTGATAATTTTGACCTGTG 59.827 33.333 22.31 0.00 40.97 3.66
3611 5064 7.387397 GGCAAATTTGATAATTTTGACCTGTGA 59.613 33.333 22.31 0.00 40.97 3.58
3612 5065 8.772705 GCAAATTTGATAATTTTGACCTGTGAA 58.227 29.630 22.31 0.00 40.97 3.18
3619 5072 9.859427 TGATAATTTTGACCTGTGAATGAAATC 57.141 29.630 0.00 0.00 0.00 2.17
3620 5073 9.859427 GATAATTTTGACCTGTGAATGAAATCA 57.141 29.630 0.00 0.00 0.00 2.57
3623 5076 9.563748 AATTTTGACCTGTGAATGAAATCATTT 57.436 25.926 9.82 0.00 45.72 2.32
3624 5077 8.592105 TTTTGACCTGTGAATGAAATCATTTC 57.408 30.769 9.82 2.87 45.72 2.17
3639 5092 8.772705 TGAAATCATTTCACAAAATAAACTGCC 58.227 29.630 8.85 0.00 44.21 4.85
3640 5093 7.671495 AATCATTTCACAAAATAAACTGCCC 57.329 32.000 0.00 0.00 33.27 5.36
3641 5094 6.418057 TCATTTCACAAAATAAACTGCCCT 57.582 33.333 0.00 0.00 33.27 5.19
3642 5095 6.825610 TCATTTCACAAAATAAACTGCCCTT 58.174 32.000 0.00 0.00 33.27 3.95
3643 5096 7.957002 TCATTTCACAAAATAAACTGCCCTTA 58.043 30.769 0.00 0.00 33.27 2.69
3644 5097 8.424918 TCATTTCACAAAATAAACTGCCCTTAA 58.575 29.630 0.00 0.00 33.27 1.85
3645 5098 9.050601 CATTTCACAAAATAAACTGCCCTTAAA 57.949 29.630 0.00 0.00 33.27 1.52
3646 5099 9.620259 ATTTCACAAAATAAACTGCCCTTAAAA 57.380 25.926 0.00 0.00 33.27 1.52
3647 5100 9.449719 TTTCACAAAATAAACTGCCCTTAAAAA 57.550 25.926 0.00 0.00 0.00 1.94
3671 5124 9.447157 AAAAATTCACTCAAATGACCTTTTTGA 57.553 25.926 0.00 0.00 39.96 2.69
3676 5129 4.320608 TCAAATGACCTTTTTGAGTGGC 57.679 40.909 0.00 0.00 37.97 5.01
3677 5130 3.052036 CAAATGACCTTTTTGAGTGGCG 58.948 45.455 0.00 0.00 36.40 5.69
3678 5131 0.598065 ATGACCTTTTTGAGTGGCGC 59.402 50.000 0.00 0.00 0.00 6.53
3679 5132 1.285950 GACCTTTTTGAGTGGCGCC 59.714 57.895 22.73 22.73 0.00 6.53
3680 5133 2.142357 GACCTTTTTGAGTGGCGCCC 62.142 60.000 26.77 15.80 0.00 6.13
3681 5134 2.255252 CTTTTTGAGTGGCGCCCG 59.745 61.111 26.77 0.00 0.00 6.13
3682 5135 2.203224 TTTTTGAGTGGCGCCCGA 60.203 55.556 26.77 2.06 0.00 5.14
3683 5136 1.586154 CTTTTTGAGTGGCGCCCGAT 61.586 55.000 26.77 9.83 0.00 4.18
3684 5137 0.321741 TTTTTGAGTGGCGCCCGATA 60.322 50.000 26.77 0.59 0.00 2.92
3685 5138 1.022451 TTTTGAGTGGCGCCCGATAC 61.022 55.000 26.77 15.91 0.00 2.24
3686 5139 3.709880 TTGAGTGGCGCCCGATACG 62.710 63.158 26.77 0.00 0.00 3.06
3687 5140 3.896133 GAGTGGCGCCCGATACGA 61.896 66.667 26.77 0.00 0.00 3.43
3688 5141 3.420214 GAGTGGCGCCCGATACGAA 62.420 63.158 26.77 0.00 0.00 3.85
3689 5142 2.960129 GTGGCGCCCGATACGAAG 60.960 66.667 26.77 0.00 0.00 3.79
3690 5143 3.142162 TGGCGCCCGATACGAAGA 61.142 61.111 26.77 0.00 0.00 2.87
3691 5144 2.657620 GGCGCCCGATACGAAGAC 60.658 66.667 18.11 0.00 0.00 3.01
3692 5145 3.022914 GCGCCCGATACGAAGACG 61.023 66.667 0.00 0.00 45.75 4.18
3693 5146 3.022914 CGCCCGATACGAAGACGC 61.023 66.667 0.00 0.00 43.96 5.19
3694 5147 2.657620 GCCCGATACGAAGACGCC 60.658 66.667 0.00 0.00 43.96 5.68
3695 5148 2.802792 CCCGATACGAAGACGCCA 59.197 61.111 0.00 0.00 43.96 5.69
3696 5149 1.588139 CCCGATACGAAGACGCCAC 60.588 63.158 0.00 0.00 43.96 5.01
3697 5150 1.138036 CCGATACGAAGACGCCACA 59.862 57.895 0.00 0.00 43.96 4.17
3698 5151 0.248907 CCGATACGAAGACGCCACAT 60.249 55.000 0.00 0.00 43.96 3.21
3699 5152 0.846401 CGATACGAAGACGCCACATG 59.154 55.000 0.00 0.00 43.96 3.21
3700 5153 1.533129 CGATACGAAGACGCCACATGA 60.533 52.381 0.00 0.00 43.96 3.07
3701 5154 1.852895 GATACGAAGACGCCACATGAC 59.147 52.381 0.00 0.00 43.96 3.06
3702 5155 0.599060 TACGAAGACGCCACATGACA 59.401 50.000 0.00 0.00 43.96 3.58
3703 5156 0.944311 ACGAAGACGCCACATGACAC 60.944 55.000 0.00 0.00 43.96 3.67
3704 5157 0.667487 CGAAGACGCCACATGACACT 60.667 55.000 0.00 0.00 0.00 3.55
3705 5158 0.792640 GAAGACGCCACATGACACTG 59.207 55.000 0.00 0.00 0.00 3.66
3706 5159 0.106708 AAGACGCCACATGACACTGT 59.893 50.000 0.00 0.00 0.00 3.55
3707 5160 0.601046 AGACGCCACATGACACTGTG 60.601 55.000 6.19 6.19 44.92 3.66
3708 5161 0.880278 GACGCCACATGACACTGTGT 60.880 55.000 14.23 14.23 44.04 3.72
3709 5162 0.391228 ACGCCACATGACACTGTGTA 59.609 50.000 14.31 3.14 44.04 2.90
3710 5163 1.070821 CGCCACATGACACTGTGTAG 58.929 55.000 14.31 9.43 44.04 2.74
3711 5164 0.798776 GCCACATGACACTGTGTAGC 59.201 55.000 14.31 2.92 44.04 3.58
3712 5165 1.070821 CCACATGACACTGTGTAGCG 58.929 55.000 14.31 7.36 44.04 4.26
3713 5166 0.439985 CACATGACACTGTGTAGCGC 59.560 55.000 14.31 0.00 41.29 5.92
3714 5167 0.670546 ACATGACACTGTGTAGCGCC 60.671 55.000 14.31 1.37 0.00 6.53
3715 5168 0.390340 CATGACACTGTGTAGCGCCT 60.390 55.000 14.31 0.00 0.00 5.52
3716 5169 0.390340 ATGACACTGTGTAGCGCCTG 60.390 55.000 14.31 0.00 0.00 4.85
3717 5170 1.289066 GACACTGTGTAGCGCCTGA 59.711 57.895 14.31 0.00 0.00 3.86
3718 5171 1.006102 ACACTGTGTAGCGCCTGAC 60.006 57.895 12.53 0.00 0.00 3.51
3719 5172 1.290324 CACTGTGTAGCGCCTGACT 59.710 57.895 2.29 0.00 0.00 3.41
3720 5173 1.010935 CACTGTGTAGCGCCTGACTG 61.011 60.000 2.29 4.68 0.00 3.51
3721 5174 1.179174 ACTGTGTAGCGCCTGACTGA 61.179 55.000 2.29 0.00 0.00 3.41
3722 5175 0.734253 CTGTGTAGCGCCTGACTGAC 60.734 60.000 2.29 0.00 0.00 3.51
3723 5176 1.289066 GTGTAGCGCCTGACTGACA 59.711 57.895 2.29 0.00 0.00 3.58
3724 5177 0.734253 GTGTAGCGCCTGACTGACAG 60.734 60.000 2.29 0.00 45.36 3.51
3731 5184 3.248029 CTGACTGACAGGCGTTGC 58.752 61.111 7.51 0.00 42.39 4.17
3732 5185 1.595109 CTGACTGACAGGCGTTGCA 60.595 57.895 7.51 0.00 42.39 4.08
3733 5186 1.835483 CTGACTGACAGGCGTTGCAC 61.835 60.000 7.51 0.00 42.39 4.57
3734 5187 2.943345 GACTGACAGGCGTTGCACG 61.943 63.158 7.51 4.61 45.88 5.34
3743 5196 3.490759 CGTTGCACGCCTAGCCAG 61.491 66.667 0.00 0.00 33.65 4.85
3744 5197 3.804193 GTTGCACGCCTAGCCAGC 61.804 66.667 0.00 0.00 0.00 4.85
3753 5206 4.135153 CTAGCCAGCGTCGCACCT 62.135 66.667 21.09 13.95 0.00 4.00
3754 5207 4.435436 TAGCCAGCGTCGCACCTG 62.435 66.667 21.09 9.03 0.00 4.00
3757 5210 4.969196 CCAGCGTCGCACCTGTGT 62.969 66.667 21.09 0.00 0.00 3.72
3758 5211 3.705638 CAGCGTCGCACCTGTGTG 61.706 66.667 21.09 2.74 45.65 3.82
3759 5212 3.911698 AGCGTCGCACCTGTGTGA 61.912 61.111 21.09 9.34 45.76 3.58
3763 5216 2.261361 TCGCACCTGTGTGATCCG 59.739 61.111 9.34 0.00 45.76 4.18
3764 5217 2.261361 CGCACCTGTGTGATCCGA 59.739 61.111 4.88 0.00 45.76 4.55
3765 5218 1.374125 CGCACCTGTGTGATCCGAA 60.374 57.895 4.88 0.00 45.76 4.30
3766 5219 0.948623 CGCACCTGTGTGATCCGAAA 60.949 55.000 4.88 0.00 45.76 3.46
3767 5220 1.234821 GCACCTGTGTGATCCGAAAA 58.765 50.000 0.00 0.00 45.76 2.29
3768 5221 1.812571 GCACCTGTGTGATCCGAAAAT 59.187 47.619 0.00 0.00 45.76 1.82
3769 5222 2.228822 GCACCTGTGTGATCCGAAAATT 59.771 45.455 0.00 0.00 45.76 1.82
3770 5223 3.438781 GCACCTGTGTGATCCGAAAATTA 59.561 43.478 0.00 0.00 45.76 1.40
3771 5224 4.671766 GCACCTGTGTGATCCGAAAATTAC 60.672 45.833 0.00 0.00 45.76 1.89
3772 5225 4.695455 CACCTGTGTGATCCGAAAATTACT 59.305 41.667 0.00 0.00 45.76 2.24
3773 5226 5.872617 CACCTGTGTGATCCGAAAATTACTA 59.127 40.000 0.00 0.00 45.76 1.82
3774 5227 6.370442 CACCTGTGTGATCCGAAAATTACTAA 59.630 38.462 0.00 0.00 45.76 2.24
3775 5228 6.594159 ACCTGTGTGATCCGAAAATTACTAAG 59.406 38.462 0.00 0.00 0.00 2.18
3776 5229 6.594159 CCTGTGTGATCCGAAAATTACTAAGT 59.406 38.462 0.00 0.00 0.00 2.24
3777 5230 7.201530 CCTGTGTGATCCGAAAATTACTAAGTC 60.202 40.741 0.00 0.00 0.00 3.01
3778 5231 7.156000 TGTGTGATCCGAAAATTACTAAGTCA 58.844 34.615 0.00 0.00 0.00 3.41
3779 5232 7.330946 TGTGTGATCCGAAAATTACTAAGTCAG 59.669 37.037 0.00 0.00 0.00 3.51
3780 5233 7.331193 GTGTGATCCGAAAATTACTAAGTCAGT 59.669 37.037 0.00 0.00 41.62 3.41
3781 5234 7.330946 TGTGATCCGAAAATTACTAAGTCAGTG 59.669 37.037 0.00 0.00 38.24 3.66
3782 5235 7.331193 GTGATCCGAAAATTACTAAGTCAGTGT 59.669 37.037 0.00 0.00 38.24 3.55
3783 5236 7.330946 TGATCCGAAAATTACTAAGTCAGTGTG 59.669 37.037 0.00 0.00 38.24 3.82
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
10 11 3.507924 GGCGTGCGGCAATGATCA 61.508 61.111 3.23 0.00 46.16 2.92
19 20 2.435938 AAGTACCATGGCGTGCGG 60.436 61.111 13.04 0.00 0.00 5.69
99 100 1.160137 GAGTTGCAGCCGACATTTCT 58.840 50.000 0.00 0.00 0.00 2.52
104 105 1.830587 ATCAGGAGTTGCAGCCGACA 61.831 55.000 0.00 0.00 0.00 4.35
140 141 1.077212 CCCCATGCCCTTCACTCTG 60.077 63.158 0.00 0.00 0.00 3.35
141 142 2.311854 CCCCCATGCCCTTCACTCT 61.312 63.158 0.00 0.00 0.00 3.24
142 143 1.863155 TTCCCCCATGCCCTTCACTC 61.863 60.000 0.00 0.00 0.00 3.51
143 144 1.856873 TTCCCCCATGCCCTTCACT 60.857 57.895 0.00 0.00 0.00 3.41
144 145 1.380380 CTTCCCCCATGCCCTTCAC 60.380 63.158 0.00 0.00 0.00 3.18
145 146 3.099171 CTTCCCCCATGCCCTTCA 58.901 61.111 0.00 0.00 0.00 3.02
146 147 2.442830 GCTTCCCCCATGCCCTTC 60.443 66.667 0.00 0.00 0.00 3.46
147 148 2.399600 TTTGCTTCCCCCATGCCCTT 62.400 55.000 0.00 0.00 0.00 3.95
148 149 2.399600 TTTTGCTTCCCCCATGCCCT 62.400 55.000 0.00 0.00 0.00 5.19
175 176 2.004733 TCGATCGTAGCTCGTTCTCAA 58.995 47.619 15.94 0.00 40.80 3.02
176 177 1.593469 CTCGATCGTAGCTCGTTCTCA 59.407 52.381 15.94 0.00 40.80 3.27
188 189 2.286831 CCACTTATACGCACTCGATCGT 60.287 50.000 15.94 11.26 42.09 3.73
189 190 2.307929 CCACTTATACGCACTCGATCG 58.692 52.381 9.36 9.36 39.41 3.69
190 191 2.052157 GCCACTTATACGCACTCGATC 58.948 52.381 0.00 0.00 39.41 3.69
193 194 1.200483 CAGCCACTTATACGCACTCG 58.800 55.000 0.00 0.00 42.43 4.18
198 199 0.931005 GTCAGCAGCCACTTATACGC 59.069 55.000 0.00 0.00 0.00 4.42
200 201 0.931005 GCGTCAGCAGCCACTTATAC 59.069 55.000 0.00 0.00 44.35 1.47
210 211 0.109272 TTTACTCCTCGCGTCAGCAG 60.109 55.000 5.77 0.00 45.49 4.24
211 212 0.530744 ATTTACTCCTCGCGTCAGCA 59.469 50.000 5.77 0.00 45.49 4.41
228 229 4.518970 TGCGCTTTAACTCCTCAAAAGATT 59.481 37.500 9.73 0.00 33.05 2.40
231 232 3.896648 TGCGCTTTAACTCCTCAAAAG 57.103 42.857 9.73 0.00 34.14 2.27
236 238 4.127171 TCCATTATGCGCTTTAACTCCTC 58.873 43.478 9.73 0.00 0.00 3.71
266 268 2.810274 GGTTGAGGAGTTAAAACGGACC 59.190 50.000 0.00 0.00 0.00 4.46
272 274 4.577283 CGGTTTCAGGTTGAGGAGTTAAAA 59.423 41.667 0.00 0.00 0.00 1.52
286 288 7.203255 ACTTCTAGAAAAATTCGGTTTCAGG 57.797 36.000 6.63 0.00 37.43 3.86
288 290 9.940166 GTTAACTTCTAGAAAAATTCGGTTTCA 57.060 29.630 6.63 0.00 37.43 2.69
291 293 7.308169 CCGGTTAACTTCTAGAAAAATTCGGTT 60.308 37.037 6.63 7.77 34.02 4.44
292 294 6.148315 CCGGTTAACTTCTAGAAAAATTCGGT 59.852 38.462 6.63 0.00 34.02 4.69
293 295 6.148315 ACCGGTTAACTTCTAGAAAAATTCGG 59.852 38.462 20.97 20.97 36.71 4.30
294 296 7.125536 ACCGGTTAACTTCTAGAAAAATTCG 57.874 36.000 0.00 6.70 34.02 3.34
295 297 9.740239 AAAACCGGTTAACTTCTAGAAAAATTC 57.260 29.630 22.60 0.00 0.00 2.17
299 301 9.558396 TCATAAAACCGGTTAACTTCTAGAAAA 57.442 29.630 22.60 0.00 0.00 2.29
300 302 9.211485 CTCATAAAACCGGTTAACTTCTAGAAA 57.789 33.333 22.60 0.00 0.00 2.52
301 303 8.587608 TCTCATAAAACCGGTTAACTTCTAGAA 58.412 33.333 22.60 4.81 0.00 2.10
302 304 8.125978 TCTCATAAAACCGGTTAACTTCTAGA 57.874 34.615 22.60 14.29 0.00 2.43
303 305 8.943909 ATCTCATAAAACCGGTTAACTTCTAG 57.056 34.615 22.60 12.25 0.00 2.43
304 306 8.755977 AGATCTCATAAAACCGGTTAACTTCTA 58.244 33.333 22.60 5.23 0.00 2.10
305 307 7.549488 CAGATCTCATAAAACCGGTTAACTTCT 59.451 37.037 22.60 11.68 0.00 2.85
306 308 7.676572 GCAGATCTCATAAAACCGGTTAACTTC 60.677 40.741 22.60 9.66 0.00 3.01
307 309 6.093633 GCAGATCTCATAAAACCGGTTAACTT 59.906 38.462 22.60 14.15 0.00 2.66
348 350 7.175990 ACAATGGTCTATTTTGATTTACGGTGT 59.824 33.333 0.00 0.00 0.00 4.16
349 351 7.535139 ACAATGGTCTATTTTGATTTACGGTG 58.465 34.615 0.00 0.00 0.00 4.94
352 354 7.696453 GTGGACAATGGTCTATTTTGATTTACG 59.304 37.037 0.00 0.00 43.77 3.18
359 361 6.271488 ACATGTGGACAATGGTCTATTTTG 57.729 37.500 0.00 0.00 43.77 2.44
361 363 6.039717 GCATACATGTGGACAATGGTCTATTT 59.960 38.462 9.11 0.00 43.77 1.40
383 385 4.141483 TGGAAACACTAGCTAGGGAGCAT 61.141 47.826 29.71 11.65 43.92 3.79
435 444 4.547532 CCGTGTACTCTATATGAACTGCC 58.452 47.826 0.00 0.00 0.00 4.85
459 468 8.800332 CCTAGCTTATCTTTACGATACCCTAAA 58.200 37.037 0.00 0.00 34.40 1.85
484 493 6.319911 GCCCATTGCTATAGGATTTCTTATCC 59.680 42.308 1.04 0.00 36.31 2.59
601 610 6.276832 ACTGATGAGCTTTTGTTTGCATAT 57.723 33.333 0.00 0.00 0.00 1.78
605 614 5.464168 ACATACTGATGAGCTTTTGTTTGC 58.536 37.500 0.00 0.00 36.48 3.68
606 615 9.282247 GATAACATACTGATGAGCTTTTGTTTG 57.718 33.333 0.00 0.00 36.48 2.93
615 628 8.710551 CAAGATGAAGATAACATACTGATGAGC 58.289 37.037 0.00 0.00 36.48 4.26
645 658 8.590719 AAGTTCACTGTCTAGCTACTAAAAAC 57.409 34.615 0.00 0.00 0.00 2.43
647 660 9.909644 CTTAAGTTCACTGTCTAGCTACTAAAA 57.090 33.333 0.00 0.00 0.00 1.52
713 730 4.546570 GCATTTGTCTGGTTTAGTGGTTC 58.453 43.478 0.00 0.00 0.00 3.62
721 738 1.786937 TGGTGGCATTTGTCTGGTTT 58.213 45.000 0.00 0.00 0.00 3.27
808 1092 5.183228 TCATAGTTCCTGTTCGGGAAAATC 58.817 41.667 13.80 3.61 45.55 2.17
839 1123 6.415702 GCGTAATGCGATGTTAATGAGTTAA 58.584 36.000 0.00 0.00 44.77 2.01
840 1124 5.969741 GCGTAATGCGATGTTAATGAGTTA 58.030 37.500 0.00 0.00 44.77 2.24
841 1125 4.833126 GCGTAATGCGATGTTAATGAGTT 58.167 39.130 0.00 0.00 44.77 3.01
842 1126 4.452890 GCGTAATGCGATGTTAATGAGT 57.547 40.909 0.00 0.00 44.77 3.41
932 1219 2.257894 GAGTGCATGTCTGAAGTCGAG 58.742 52.381 0.00 0.00 0.00 4.04
1092 1389 1.591703 CAGGTTAGACAGCGGCAGA 59.408 57.895 1.45 0.00 0.00 4.26
1335 1659 3.645660 TCCACAATGCCCAGCCGA 61.646 61.111 0.00 0.00 0.00 5.54
1481 1810 1.656652 CACGTGGGGCTTATCTTCAG 58.343 55.000 7.95 0.00 0.00 3.02
1513 1866 3.124921 CCTTGGGCCTAACGCGTG 61.125 66.667 14.98 0.24 38.94 5.34
1559 1980 8.915057 TTGTCCATATACTAGTAGTGTACTCC 57.085 38.462 13.29 1.56 40.14 3.85
1560 1981 9.775854 TCTTGTCCATATACTAGTAGTGTACTC 57.224 37.037 13.29 3.67 40.14 2.59
1703 2124 9.502145 GCATTTTCGACAAAAGAACATCATATA 57.498 29.630 0.00 0.00 34.92 0.86
1704 2125 8.246180 AGCATTTTCGACAAAAGAACATCATAT 58.754 29.630 0.00 0.00 34.92 1.78
1705 2126 7.592938 AGCATTTTCGACAAAAGAACATCATA 58.407 30.769 0.00 0.00 34.92 2.15
1738 2160 2.116827 AAAACGGCGGTAATGATCCA 57.883 45.000 13.24 0.00 0.00 3.41
1790 2366 7.477494 CAACGGAATTAGTAAAAGTTATGGGG 58.523 38.462 0.00 0.00 0.00 4.96
2233 3558 1.447489 AGACGCTGATGTGCTGAGC 60.447 57.895 0.00 0.00 0.00 4.26
2453 3779 0.176680 CCTCCACCCAGTCGATCAAG 59.823 60.000 0.00 0.00 0.00 3.02
2454 3780 1.899437 GCCTCCACCCAGTCGATCAA 61.899 60.000 0.00 0.00 0.00 2.57
2558 3896 3.585856 CGGACCGGAAAACCCATG 58.414 61.111 9.46 0.00 34.14 3.66
2645 3983 1.664649 CGGCATCGGCATCACGTAT 60.665 57.895 0.00 0.00 43.71 3.06
2674 4012 3.712907 CCACCCATTCCCCGTCGT 61.713 66.667 0.00 0.00 0.00 4.34
2675 4013 3.712907 ACCACCCATTCCCCGTCG 61.713 66.667 0.00 0.00 0.00 5.12
2684 4022 0.676466 CATGCACGTACACCACCCAT 60.676 55.000 0.00 0.00 0.00 4.00
2759 4097 0.975544 CGAACACGTAGCTGTTCTCG 59.024 55.000 12.93 3.55 42.19 4.04
2771 4109 1.336887 ACTGTCCTTCATCCGAACACG 60.337 52.381 0.00 0.00 0.00 4.49
3275 4636 6.966021 AGTTAGCAATCACACGTTTTTACAT 58.034 32.000 0.00 0.00 0.00 2.29
3383 4833 9.620259 GACCAAATCCTCTATTTTATCACTCTT 57.380 33.333 0.00 0.00 35.54 2.85
3385 4835 8.964476 TGACCAAATCCTCTATTTTATCACTC 57.036 34.615 0.00 0.00 35.54 3.51
3386 4836 8.772250 TCTGACCAAATCCTCTATTTTATCACT 58.228 33.333 0.00 0.00 35.54 3.41
3451 4903 8.863872 ACAAGCTAATTAACTAAATGGTGAGT 57.136 30.769 0.00 0.00 0.00 3.41
3533 4985 7.578310 ATCATACTTCCATTCTGACCAAATG 57.422 36.000 0.00 0.00 34.55 2.32
3567 5020 1.102154 CCACAAAAGCAGGTGACACA 58.898 50.000 8.08 0.00 37.18 3.72
3584 5037 7.172875 CACAGGTCAAAATTATCAAATTTGCCA 59.827 33.333 13.54 0.47 43.04 4.92
3585 5038 7.387397 TCACAGGTCAAAATTATCAAATTTGCC 59.613 33.333 13.54 4.85 43.04 4.52
3586 5039 8.309163 TCACAGGTCAAAATTATCAAATTTGC 57.691 30.769 13.54 0.00 43.04 3.68
3593 5046 9.859427 GATTTCATTCACAGGTCAAAATTATCA 57.141 29.630 0.00 0.00 0.00 2.15
3594 5047 9.859427 TGATTTCATTCACAGGTCAAAATTATC 57.141 29.630 0.00 0.00 0.00 1.75
3597 5050 9.563748 AAATGATTTCATTCACAGGTCAAAATT 57.436 25.926 6.27 0.00 45.06 1.82
3598 5051 9.211485 GAAATGATTTCATTCACAGGTCAAAAT 57.789 29.630 12.73 0.00 45.06 1.82
3599 5052 8.202811 TGAAATGATTTCATTCACAGGTCAAAA 58.797 29.630 16.04 0.00 45.06 2.44
3600 5053 7.724287 TGAAATGATTTCATTCACAGGTCAAA 58.276 30.769 16.04 0.00 45.06 2.69
3601 5054 7.287512 TGAAATGATTTCATTCACAGGTCAA 57.712 32.000 16.04 0.00 45.06 3.18
3602 5055 6.897706 TGAAATGATTTCATTCACAGGTCA 57.102 33.333 16.04 3.31 45.06 4.02
3613 5066 8.772705 GGCAGTTTATTTTGTGAAATGATTTCA 58.227 29.630 16.04 16.04 46.68 2.69
3614 5067 8.229811 GGGCAGTTTATTTTGTGAAATGATTTC 58.770 33.333 10.85 10.85 36.22 2.17
3615 5068 7.938490 AGGGCAGTTTATTTTGTGAAATGATTT 59.062 29.630 0.00 0.00 36.22 2.17
3616 5069 7.452562 AGGGCAGTTTATTTTGTGAAATGATT 58.547 30.769 0.00 0.00 36.22 2.57
3617 5070 7.008021 AGGGCAGTTTATTTTGTGAAATGAT 57.992 32.000 0.00 0.00 36.22 2.45
3618 5071 6.418057 AGGGCAGTTTATTTTGTGAAATGA 57.582 33.333 0.00 0.00 36.22 2.57
3619 5072 8.600449 TTAAGGGCAGTTTATTTTGTGAAATG 57.400 30.769 0.00 0.00 36.22 2.32
3620 5073 9.620259 TTTTAAGGGCAGTTTATTTTGTGAAAT 57.380 25.926 0.00 0.00 38.88 2.17
3621 5074 9.449719 TTTTTAAGGGCAGTTTATTTTGTGAAA 57.550 25.926 0.00 0.00 0.00 2.69
3645 5098 9.447157 TCAAAAAGGTCATTTGAGTGAATTTTT 57.553 25.926 0.00 0.00 40.75 1.94
3655 5108 3.243367 CGCCACTCAAAAAGGTCATTTGA 60.243 43.478 2.19 2.19 42.73 2.69
3656 5109 3.052036 CGCCACTCAAAAAGGTCATTTG 58.948 45.455 0.00 0.00 38.76 2.32
3657 5110 2.545742 GCGCCACTCAAAAAGGTCATTT 60.546 45.455 0.00 0.00 0.00 2.32
3658 5111 1.000274 GCGCCACTCAAAAAGGTCATT 60.000 47.619 0.00 0.00 0.00 2.57
3659 5112 0.598065 GCGCCACTCAAAAAGGTCAT 59.402 50.000 0.00 0.00 0.00 3.06
3660 5113 1.452145 GGCGCCACTCAAAAAGGTCA 61.452 55.000 24.80 0.00 0.00 4.02
3661 5114 1.285950 GGCGCCACTCAAAAAGGTC 59.714 57.895 24.80 0.00 0.00 3.85
3662 5115 2.200337 GGGCGCCACTCAAAAAGGT 61.200 57.895 30.85 0.00 0.00 3.50
3663 5116 2.650778 GGGCGCCACTCAAAAAGG 59.349 61.111 30.85 0.00 0.00 3.11
3664 5117 1.586154 ATCGGGCGCCACTCAAAAAG 61.586 55.000 30.85 7.24 0.00 2.27
3665 5118 0.321741 TATCGGGCGCCACTCAAAAA 60.322 50.000 30.85 3.67 0.00 1.94
3666 5119 1.022451 GTATCGGGCGCCACTCAAAA 61.022 55.000 30.85 4.85 0.00 2.44
3667 5120 1.448893 GTATCGGGCGCCACTCAAA 60.449 57.895 30.85 6.43 0.00 2.69
3668 5121 2.185867 GTATCGGGCGCCACTCAA 59.814 61.111 30.85 8.44 0.00 3.02
3669 5122 4.201679 CGTATCGGGCGCCACTCA 62.202 66.667 30.85 8.71 0.00 3.41
3670 5123 3.420214 TTCGTATCGGGCGCCACTC 62.420 63.158 30.85 10.33 0.00 3.51
3671 5124 3.426117 CTTCGTATCGGGCGCCACT 62.426 63.158 30.85 14.46 0.00 4.00
3672 5125 2.960129 CTTCGTATCGGGCGCCAC 60.960 66.667 30.85 17.05 0.00 5.01
3673 5126 3.142162 TCTTCGTATCGGGCGCCA 61.142 61.111 30.85 9.36 0.00 5.69
3674 5127 2.657620 GTCTTCGTATCGGGCGCC 60.658 66.667 21.18 21.18 0.00 6.53
3675 5128 3.022914 CGTCTTCGTATCGGGCGC 61.023 66.667 0.00 0.00 0.00 6.53
3676 5129 3.022914 GCGTCTTCGTATCGGGCG 61.023 66.667 0.00 0.00 39.49 6.13
3677 5130 2.657620 GGCGTCTTCGTATCGGGC 60.658 66.667 0.00 0.00 39.49 6.13
3678 5131 1.588139 GTGGCGTCTTCGTATCGGG 60.588 63.158 0.00 0.00 39.49 5.14
3679 5132 0.248907 ATGTGGCGTCTTCGTATCGG 60.249 55.000 0.00 0.00 39.49 4.18
3680 5133 0.846401 CATGTGGCGTCTTCGTATCG 59.154 55.000 0.00 0.00 39.49 2.92
3681 5134 1.852895 GTCATGTGGCGTCTTCGTATC 59.147 52.381 0.00 0.00 39.49 2.24
3682 5135 1.203758 TGTCATGTGGCGTCTTCGTAT 59.796 47.619 0.00 0.00 39.49 3.06
3683 5136 0.599060 TGTCATGTGGCGTCTTCGTA 59.401 50.000 0.00 0.00 39.49 3.43
3684 5137 0.944311 GTGTCATGTGGCGTCTTCGT 60.944 55.000 0.00 0.00 39.49 3.85
3685 5138 0.667487 AGTGTCATGTGGCGTCTTCG 60.667 55.000 0.00 0.00 40.37 3.79
3686 5139 0.792640 CAGTGTCATGTGGCGTCTTC 59.207 55.000 0.00 0.00 0.00 2.87
3687 5140 0.106708 ACAGTGTCATGTGGCGTCTT 59.893 50.000 0.00 0.00 30.46 3.01
3688 5141 0.601046 CACAGTGTCATGTGGCGTCT 60.601 55.000 0.00 0.00 45.53 4.18
3689 5142 1.862123 CACAGTGTCATGTGGCGTC 59.138 57.895 0.00 0.00 45.53 5.19
3690 5143 4.047834 CACAGTGTCATGTGGCGT 57.952 55.556 0.00 0.00 45.53 5.68
3695 5148 0.670546 GGCGCTACACAGTGTCATGT 60.671 55.000 10.23 0.00 36.86 3.21
3696 5149 0.390340 AGGCGCTACACAGTGTCATG 60.390 55.000 10.23 3.23 39.44 3.07
3697 5150 0.390340 CAGGCGCTACACAGTGTCAT 60.390 55.000 10.23 0.00 39.44 3.06
3698 5151 1.006220 CAGGCGCTACACAGTGTCA 60.006 57.895 10.23 0.00 39.44 3.58
3699 5152 1.009389 GTCAGGCGCTACACAGTGTC 61.009 60.000 10.23 0.00 37.15 3.67
3700 5153 1.006102 GTCAGGCGCTACACAGTGT 60.006 57.895 11.87 11.87 34.60 3.55
3701 5154 1.010935 CAGTCAGGCGCTACACAGTG 61.011 60.000 7.64 0.00 35.26 3.66
3702 5155 1.179174 TCAGTCAGGCGCTACACAGT 61.179 55.000 7.64 0.00 0.00 3.55
3703 5156 0.734253 GTCAGTCAGGCGCTACACAG 60.734 60.000 7.64 0.00 0.00 3.66
3704 5157 1.289066 GTCAGTCAGGCGCTACACA 59.711 57.895 7.64 0.00 0.00 3.72
3705 5158 0.734253 CTGTCAGTCAGGCGCTACAC 60.734 60.000 7.64 0.64 40.23 2.90
3706 5159 1.586541 CTGTCAGTCAGGCGCTACA 59.413 57.895 7.64 0.06 40.23 2.74
3707 5160 4.485554 CTGTCAGTCAGGCGCTAC 57.514 61.111 7.64 3.42 40.23 3.58
3714 5167 1.595109 TGCAACGCCTGTCAGTCAG 60.595 57.895 0.00 0.00 43.27 3.51
3715 5168 1.887242 GTGCAACGCCTGTCAGTCA 60.887 57.895 0.00 0.00 0.00 3.41
3716 5169 2.939022 GTGCAACGCCTGTCAGTC 59.061 61.111 0.00 0.00 0.00 3.51
3727 5180 3.804193 GCTGGCTAGGCGTGCAAC 61.804 66.667 22.76 2.61 0.00 4.17
3736 5189 4.135153 AGGTGCGACGCTGGCTAG 62.135 66.667 22.08 0.00 0.00 3.42
3737 5190 4.435436 CAGGTGCGACGCTGGCTA 62.435 66.667 22.08 0.00 0.00 3.93
3740 5193 4.969196 ACACAGGTGCGACGCTGG 62.969 66.667 22.08 9.93 0.00 4.85
3741 5194 3.705638 CACACAGGTGCGACGCTG 61.706 66.667 22.08 13.56 38.37 5.18
3742 5195 3.226429 ATCACACAGGTGCGACGCT 62.226 57.895 22.08 0.00 44.87 5.07
3743 5196 2.730672 GATCACACAGGTGCGACGC 61.731 63.158 14.19 14.19 44.87 5.19
3744 5197 2.094659 GGATCACACAGGTGCGACG 61.095 63.158 0.00 0.00 44.87 5.12
3745 5198 2.094659 CGGATCACACAGGTGCGAC 61.095 63.158 0.00 0.00 44.87 5.19
3746 5199 1.811645 TTCGGATCACACAGGTGCGA 61.812 55.000 0.00 0.00 44.87 5.10
3747 5200 0.948623 TTTCGGATCACACAGGTGCG 60.949 55.000 0.00 0.00 44.87 5.34
3748 5201 1.234821 TTTTCGGATCACACAGGTGC 58.765 50.000 0.00 0.00 44.87 5.01
3749 5202 4.695455 AGTAATTTTCGGATCACACAGGTG 59.305 41.667 0.00 0.00 46.66 4.00
3750 5203 4.906618 AGTAATTTTCGGATCACACAGGT 58.093 39.130 0.00 0.00 0.00 4.00
3751 5204 6.594159 ACTTAGTAATTTTCGGATCACACAGG 59.406 38.462 0.00 0.00 0.00 4.00
3752 5205 7.330946 TGACTTAGTAATTTTCGGATCACACAG 59.669 37.037 0.00 0.00 0.00 3.66
3753 5206 7.156000 TGACTTAGTAATTTTCGGATCACACA 58.844 34.615 0.00 0.00 0.00 3.72
3754 5207 7.331193 ACTGACTTAGTAATTTTCGGATCACAC 59.669 37.037 0.00 0.00 38.04 3.82
3755 5208 7.330946 CACTGACTTAGTAATTTTCGGATCACA 59.669 37.037 0.00 0.00 37.60 3.58
3756 5209 7.331193 ACACTGACTTAGTAATTTTCGGATCAC 59.669 37.037 0.00 0.00 37.60 3.06
3757 5210 7.330946 CACACTGACTTAGTAATTTTCGGATCA 59.669 37.037 0.00 0.00 37.60 2.92
3758 5211 7.676393 CACACTGACTTAGTAATTTTCGGATC 58.324 38.462 0.00 0.00 37.60 3.36
3759 5212 7.596749 CACACTGACTTAGTAATTTTCGGAT 57.403 36.000 0.00 0.00 37.60 4.18


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

AutoCloner maintained by Alex Coulton.