Multiple sequence alignment - TraesCS2A01G580100

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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 TraesCS2A01G580100 chr2A 100.000 4435 0 0 1 4435 772439406 772434972 0.000000e+00 8191
1 TraesCS2A01G580100 chr2A 81.560 423 59 12 1467 1882 480059637 480060047 9.190000e-87 331
2 TraesCS2A01G580100 chr2A 90.000 160 15 1 4224 4383 779975418 779975260 5.810000e-49 206
3 TraesCS2A01G580100 chr2A 82.710 214 12 8 4224 4435 772375250 772375440 2.740000e-37 167
4 TraesCS2A01G580100 chr2D 87.901 2959 234 61 943 3831 650780234 650777330 0.000000e+00 3367
5 TraesCS2A01G580100 chr2D 86.314 3003 264 73 685 3588 647836501 647839455 0.000000e+00 3133
6 TraesCS2A01G580100 chr2D 83.902 528 54 13 3886 4411 650777310 650776812 4.010000e-130 475
7 TraesCS2A01G580100 chr2D 86.174 311 23 14 302 595 647859803 647860110 7.160000e-83 318
8 TraesCS2A01G580100 chr2D 91.324 219 14 2 3583 3801 647839688 647839901 1.210000e-75 294
9 TraesCS2A01G580100 chr2D 89.916 119 12 0 410 528 647836186 647836304 2.140000e-33 154
10 TraesCS2A01G580100 chr2B 87.441 2564 210 55 1902 4411 787957654 787960159 0.000000e+00 2848
11 TraesCS2A01G580100 chr2B 85.150 2761 268 58 943 3628 787980564 787977871 0.000000e+00 2697
12 TraesCS2A01G580100 chr2B 86.255 1004 79 23 943 1903 787956563 787957550 0.000000e+00 1035
13 TraesCS2A01G580100 chr2B 90.071 282 16 7 248 528 787981409 787981139 5.460000e-94 355
14 TraesCS2A01G580100 chr2B 89.720 214 20 2 4198 4411 787977290 787977079 5.650000e-69 272
15 TraesCS2A01G580100 chr2B 81.703 317 32 19 609 912 787980991 787980688 1.590000e-59 241
16 TraesCS2A01G580100 chr2B 83.590 195 16 7 3637 3831 787977597 787977419 7.630000e-38 169
17 TraesCS2A01G580100 chr2B 93.103 87 6 0 1051 1137 787982845 787982759 1.290000e-25 128


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 TraesCS2A01G580100 chr2A 772434972 772439406 4434 True 8191.000000 8191 100.000000 1 4435 1 chr2A.!!$R1 4434
1 TraesCS2A01G580100 chr2D 650776812 650780234 3422 True 1921.000000 3367 85.901500 943 4411 2 chr2D.!!$R1 3468
2 TraesCS2A01G580100 chr2D 647836186 647839901 3715 False 1193.666667 3133 89.184667 410 3801 3 chr2D.!!$F2 3391
3 TraesCS2A01G580100 chr2B 787956563 787960159 3596 False 1941.500000 2848 86.848000 943 4411 2 chr2B.!!$F1 3468
4 TraesCS2A01G580100 chr2B 787977079 787982845 5766 True 643.666667 2697 87.222833 248 4411 6 chr2B.!!$R1 4163

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
249 250 0.108329 CGGGCCTGATACTTTCACGT 60.108 55.0 5.28 0.0 0.00 4.49 F
772 2054 0.174389 ACTCAGGACACTATGCGCTG 59.826 55.0 9.73 0.0 0.00 5.18 F
1626 3054 0.392998 CATCACCCTTGGAGGTTCGG 60.393 60.0 0.00 0.0 38.39 4.30 F
1939 3502 0.753262 AGTGACCACTGACCACTGAC 59.247 55.0 1.31 0.0 40.75 3.51 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1608 3036 0.546747 TCCGAACCTCCAAGGGTGAT 60.547 55.000 0.0 0.0 33.59 3.06 R
2666 4275 0.105760 AAGGCCCACCAACATGTCAA 60.106 50.000 0.0 0.0 39.06 3.18 R
2669 4278 1.416030 GAAAAAGGCCCACCAACATGT 59.584 47.619 0.0 0.0 39.06 3.21 R
3732 5854 1.137872 CAGGGCTACATGGTCAGAGTC 59.862 57.143 0.0 0.0 0.00 3.36 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
22 23 4.836125 AACATTTTTCAGACGCATGACT 57.164 36.364 0.00 0.00 0.00 3.41
23 24 5.940192 AACATTTTTCAGACGCATGACTA 57.060 34.783 0.00 0.00 0.00 2.59
24 25 6.500684 AACATTTTTCAGACGCATGACTAT 57.499 33.333 0.00 0.00 0.00 2.12
25 26 7.609760 AACATTTTTCAGACGCATGACTATA 57.390 32.000 0.00 0.00 0.00 1.31
27 28 8.213518 ACATTTTTCAGACGCATGACTATATT 57.786 30.769 0.00 0.00 0.00 1.28
28 29 8.677300 ACATTTTTCAGACGCATGACTATATTT 58.323 29.630 0.00 0.00 0.00 1.40
29 30 9.507280 CATTTTTCAGACGCATGACTATATTTT 57.493 29.630 0.00 0.00 0.00 1.82
31 32 6.844696 TTCAGACGCATGACTATATTTTCC 57.155 37.500 0.00 0.00 0.00 3.13
32 33 5.297547 TCAGACGCATGACTATATTTTCCC 58.702 41.667 0.00 0.00 0.00 3.97
33 34 4.452455 CAGACGCATGACTATATTTTCCCC 59.548 45.833 0.00 0.00 0.00 4.81
35 36 4.985538 ACGCATGACTATATTTTCCCCAT 58.014 39.130 0.00 0.00 0.00 4.00
36 37 5.385198 ACGCATGACTATATTTTCCCCATT 58.615 37.500 0.00 0.00 0.00 3.16
37 38 5.833131 ACGCATGACTATATTTTCCCCATTT 59.167 36.000 0.00 0.00 0.00 2.32
38 39 6.323739 ACGCATGACTATATTTTCCCCATTTT 59.676 34.615 0.00 0.00 0.00 1.82
39 40 7.147742 ACGCATGACTATATTTTCCCCATTTTT 60.148 33.333 0.00 0.00 0.00 1.94
195 196 4.814234 TCAACTGCTCGAGTAACATTGTTT 59.186 37.500 15.13 0.00 33.09 2.83
196 197 5.986741 TCAACTGCTCGAGTAACATTGTTTA 59.013 36.000 15.13 0.00 33.09 2.01
197 198 6.480651 TCAACTGCTCGAGTAACATTGTTTAA 59.519 34.615 15.13 0.00 33.09 1.52
199 200 7.435068 ACTGCTCGAGTAACATTGTTTAAAT 57.565 32.000 15.13 0.00 30.86 1.40
200 201 8.542497 ACTGCTCGAGTAACATTGTTTAAATA 57.458 30.769 15.13 0.00 30.86 1.40
201 202 9.162764 ACTGCTCGAGTAACATTGTTTAAATAT 57.837 29.630 15.13 0.00 30.86 1.28
225 226 5.757850 ATTCTCAACTTCTTTCACACACC 57.242 39.130 0.00 0.00 0.00 4.16
226 227 4.214986 TCTCAACTTCTTTCACACACCA 57.785 40.909 0.00 0.00 0.00 4.17
227 228 4.191544 TCTCAACTTCTTTCACACACCAG 58.808 43.478 0.00 0.00 0.00 4.00
228 229 3.278574 TCAACTTCTTTCACACACCAGG 58.721 45.455 0.00 0.00 0.00 4.45
229 230 1.680338 ACTTCTTTCACACACCAGGC 58.320 50.000 0.00 0.00 0.00 4.85
231 232 0.817634 TTCTTTCACACACCAGGCCG 60.818 55.000 0.00 0.00 0.00 6.13
233 234 3.783362 TTTCACACACCAGGCCGGG 62.783 63.158 21.67 21.67 40.22 5.73
244 245 2.595655 GGCCGGGCCTGATACTTT 59.404 61.111 30.86 0.00 46.69 2.66
245 246 1.526225 GGCCGGGCCTGATACTTTC 60.526 63.158 30.86 0.00 46.69 2.62
247 248 1.095807 GCCGGGCCTGATACTTTCAC 61.096 60.000 15.09 0.00 0.00 3.18
248 249 0.810031 CCGGGCCTGATACTTTCACG 60.810 60.000 15.09 0.00 0.00 4.35
249 250 0.108329 CGGGCCTGATACTTTCACGT 60.108 55.000 5.28 0.00 0.00 4.49
250 251 1.135527 CGGGCCTGATACTTTCACGTA 59.864 52.381 5.28 0.00 0.00 3.57
322 1518 2.824041 CCGGGCCGGTCAATTCTG 60.824 66.667 36.52 7.82 42.73 3.02
323 1519 2.824041 CGGGCCGGTCAATTCTGG 60.824 66.667 20.56 0.00 36.96 3.86
324 1520 2.355115 GGGCCGGTCAATTCTGGT 59.645 61.111 9.07 0.00 36.33 4.00
325 1521 1.605453 GGGCCGGTCAATTCTGGTA 59.395 57.895 9.07 0.00 36.33 3.25
326 1522 0.746923 GGGCCGGTCAATTCTGGTAC 60.747 60.000 9.07 0.00 36.33 3.34
327 1523 0.252197 GGCCGGTCAATTCTGGTACT 59.748 55.000 0.00 0.00 36.33 2.73
328 1524 1.653151 GCCGGTCAATTCTGGTACTC 58.347 55.000 1.90 0.00 36.33 2.59
329 1525 1.207329 GCCGGTCAATTCTGGTACTCT 59.793 52.381 1.90 0.00 36.33 3.24
330 1526 2.738964 GCCGGTCAATTCTGGTACTCTC 60.739 54.545 1.90 0.00 36.33 3.20
331 1527 2.761208 CCGGTCAATTCTGGTACTCTCT 59.239 50.000 0.00 0.00 0.00 3.10
332 1528 3.181485 CCGGTCAATTCTGGTACTCTCTC 60.181 52.174 0.00 0.00 0.00 3.20
333 1529 3.181485 CGGTCAATTCTGGTACTCTCTCC 60.181 52.174 0.00 0.00 0.00 3.71
334 1530 4.027437 GGTCAATTCTGGTACTCTCTCCT 58.973 47.826 0.00 0.00 0.00 3.69
335 1531 4.468153 GGTCAATTCTGGTACTCTCTCCTT 59.532 45.833 0.00 0.00 0.00 3.36
336 1532 5.394773 GGTCAATTCTGGTACTCTCTCCTTC 60.395 48.000 0.00 0.00 0.00 3.46
337 1533 5.186021 GTCAATTCTGGTACTCTCTCCTTCA 59.814 44.000 0.00 0.00 0.00 3.02
338 1534 5.420421 TCAATTCTGGTACTCTCTCCTTCAG 59.580 44.000 0.00 0.00 0.00 3.02
458 1654 1.078709 CAAGCCGAGCGAAGATTCAA 58.921 50.000 0.00 0.00 0.00 2.69
466 1662 1.067565 AGCGAAGATTCAACTCGAGCA 60.068 47.619 13.61 0.00 0.00 4.26
528 1724 0.633921 CCAGAGAGGAGGAGGAGGAA 59.366 60.000 0.00 0.00 41.22 3.36
598 1836 2.167398 AACATGGCGACCGTACTGCT 62.167 55.000 0.00 0.00 0.00 4.24
601 1839 4.735132 GGCGACCGTACTGCTGCA 62.735 66.667 0.88 0.88 0.00 4.41
602 1840 3.479269 GCGACCGTACTGCTGCAC 61.479 66.667 0.00 0.00 0.00 4.57
603 1841 2.049526 CGACCGTACTGCTGCACA 60.050 61.111 0.00 0.00 0.00 4.57
618 1889 1.374758 CACAGTCGCCCTTGGTCTC 60.375 63.158 0.00 0.00 0.00 3.36
638 1909 4.469586 TCTCCATTACTGTTGCCATGACTA 59.530 41.667 0.00 0.00 0.00 2.59
646 1917 4.024048 ACTGTTGCCATGACTAAAACTTCG 60.024 41.667 0.00 0.00 0.00 3.79
648 1919 2.432444 TGCCATGACTAAAACTTCGGG 58.568 47.619 0.00 0.00 0.00 5.14
651 1922 3.886123 CCATGACTAAAACTTCGGGGAT 58.114 45.455 0.00 0.00 0.00 3.85
665 1936 3.541632 TCGGGGATCTTCAAACTATTGC 58.458 45.455 0.00 0.00 36.45 3.56
669 1940 3.242870 GGGATCTTCAAACTATTGCAGCG 60.243 47.826 0.00 0.00 36.45 5.18
695 1977 6.318648 CAGCAGGAAACTTGGTATTAGCATAA 59.681 38.462 0.00 0.00 40.21 1.90
743 2025 9.618890 AGCATCAAACTATTTTAGCTTGATAGA 57.381 29.630 11.01 0.00 45.05 1.98
772 2054 0.174389 ACTCAGGACACTATGCGCTG 59.826 55.000 9.73 0.00 0.00 5.18
773 2055 0.457443 CTCAGGACACTATGCGCTGA 59.543 55.000 9.73 0.00 0.00 4.26
774 2056 1.068281 CTCAGGACACTATGCGCTGAT 59.932 52.381 9.73 0.00 0.00 2.90
791 2073 5.735324 CGCTGATTGACTGAATAATGTGAG 58.265 41.667 0.00 0.00 0.00 3.51
825 2110 9.623000 ACTACCATTTACAGACCAAAATATACC 57.377 33.333 0.00 0.00 0.00 2.73
848 2133 4.271533 CGGTAAATAAGCGCAGGAAATACA 59.728 41.667 11.47 0.00 42.92 2.29
851 2140 4.882671 AATAAGCGCAGGAAATACACAG 57.117 40.909 11.47 0.00 0.00 3.66
862 2151 4.451096 AGGAAATACACAGTGTAGCAAACG 59.549 41.667 18.30 0.00 36.14 3.60
894 2186 5.139727 ACATGTTTCCTTCTGTCATTTCCA 58.860 37.500 0.00 0.00 0.00 3.53
917 2296 5.367945 TGGTTGGATCCATAAGAGGTAAC 57.632 43.478 17.06 7.09 31.96 2.50
989 2378 1.825474 TCTGTAGGCTGTAACCTCTGC 59.175 52.381 0.00 0.00 41.50 4.26
1077 2491 2.425829 CCTCCACCAGTACTATGCCCTA 60.426 54.545 0.00 0.00 0.00 3.53
1137 2551 2.988800 GCTGCCTTCCTGCTCTCT 59.011 61.111 0.00 0.00 35.71 3.10
1146 2560 1.990060 CCTGCTCTCTTCCCCGGAA 60.990 63.158 0.73 0.00 0.00 4.30
1165 2579 1.585651 AAACCCACTGAACCCCACCA 61.586 55.000 0.00 0.00 0.00 4.17
1170 2584 1.285280 CACTGAACCCCACCATCCTA 58.715 55.000 0.00 0.00 0.00 2.94
1389 2803 2.125685 CAGCTGCATCTCTACATCACG 58.874 52.381 0.00 0.00 0.00 4.35
1419 2844 5.714806 CCCCTGTATGTTTATGGTGTTCTTT 59.285 40.000 0.00 0.00 0.00 2.52
1432 2857 5.350633 TGGTGTTCTTTCAAAGCTGAATTG 58.649 37.500 0.00 0.00 41.22 2.32
1443 2868 3.083122 AGCTGAATTGTCCTCTGCATT 57.917 42.857 0.00 0.00 39.47 3.56
1517 2943 1.731160 GACTGCTGCAGTGATGTCTTC 59.269 52.381 37.29 17.70 45.44 2.87
1529 2955 5.628193 CAGTGATGTCTTCTGATTTGTTTGC 59.372 40.000 0.00 0.00 0.00 3.68
1626 3054 0.392998 CATCACCCTTGGAGGTTCGG 60.393 60.000 0.00 0.00 38.39 4.30
1716 3146 4.695455 GCAGAAGTTGTTAGTTCATGCCTA 59.305 41.667 0.00 0.00 36.37 3.93
1786 3222 3.328931 AGACTGTCTGAATTGGACCATGT 59.671 43.478 10.00 0.00 33.22 3.21
1882 3332 1.391157 TTGCTTTGGGTGGTGCTGTC 61.391 55.000 0.00 0.00 0.00 3.51
1896 3346 1.343142 TGCTGTCGAAGTGTGGTACAT 59.657 47.619 0.00 0.00 44.52 2.29
1935 3498 3.244078 TGACATTAGTGACCACTGACCAC 60.244 47.826 12.54 0.00 42.52 4.16
1938 3501 2.375014 TAGTGACCACTGACCACTGA 57.625 50.000 12.54 0.00 42.52 3.41
1939 3502 0.753262 AGTGACCACTGACCACTGAC 59.247 55.000 1.31 0.00 40.75 3.51
1943 3508 2.180276 GACCACTGACCACTGACCTAT 58.820 52.381 0.00 0.00 0.00 2.57
2027 3596 4.335315 CACTTTGGACTCTGCAAGTGTTTA 59.665 41.667 6.31 0.00 41.37 2.01
2028 3597 4.576463 ACTTTGGACTCTGCAAGTGTTTAG 59.424 41.667 6.31 2.90 41.37 1.85
2065 3634 5.465532 TGGACTGCTCATTTTTATTTGCA 57.534 34.783 0.00 0.00 0.00 4.08
2086 3655 8.888332 TTGCATTGTTACTAATTCGTTACATG 57.112 30.769 3.21 0.00 0.00 3.21
2241 3811 5.070847 AGGTTGTTTTCCAGAATCATTTGCT 59.929 36.000 0.00 0.00 0.00 3.91
2253 3823 7.598869 CCAGAATCATTTGCTGATCCATATTTG 59.401 37.037 0.00 0.00 44.03 2.32
2254 3824 8.141909 CAGAATCATTTGCTGATCCATATTTGT 58.858 33.333 0.00 0.00 44.03 2.83
2255 3825 8.141909 AGAATCATTTGCTGATCCATATTTGTG 58.858 33.333 0.00 0.00 44.03 3.33
2256 3826 7.591421 ATCATTTGCTGATCCATATTTGTGA 57.409 32.000 0.00 0.00 40.77 3.58
2258 3828 7.430441 TCATTTGCTGATCCATATTTGTGATG 58.570 34.615 0.00 0.00 0.00 3.07
2259 3829 5.777850 TTGCTGATCCATATTTGTGATGG 57.222 39.130 0.00 0.00 44.59 3.51
2260 3830 4.795469 TGCTGATCCATATTTGTGATGGT 58.205 39.130 1.78 0.00 43.79 3.55
2261 3831 5.939447 TGCTGATCCATATTTGTGATGGTA 58.061 37.500 1.78 0.00 43.79 3.25
2262 3832 6.545567 TGCTGATCCATATTTGTGATGGTAT 58.454 36.000 1.78 0.00 43.79 2.73
2263 3833 7.005902 TGCTGATCCATATTTGTGATGGTATT 58.994 34.615 1.78 0.00 43.79 1.89
2264 3834 8.162746 TGCTGATCCATATTTGTGATGGTATTA 58.837 33.333 1.78 0.00 43.79 0.98
2314 3906 7.915397 CCAATATATGGTGCAGACACTTTTAAC 59.085 37.037 0.00 0.00 46.57 2.01
2333 3925 9.921637 CTTTTAACTGCCAACCATTTCTTATTA 57.078 29.630 0.00 0.00 0.00 0.98
2340 3932 8.593945 TGCCAACCATTTCTTATTATTCTCTT 57.406 30.769 0.00 0.00 0.00 2.85
2341 3933 8.686334 TGCCAACCATTTCTTATTATTCTCTTC 58.314 33.333 0.00 0.00 0.00 2.87
2342 3934 8.138074 GCCAACCATTTCTTATTATTCTCTTCC 58.862 37.037 0.00 0.00 0.00 3.46
2343 3935 9.189156 CCAACCATTTCTTATTATTCTCTTCCA 57.811 33.333 0.00 0.00 0.00 3.53
2357 3949 5.705609 TCTCTTCCAGTTATGTTTTTGCC 57.294 39.130 0.00 0.00 0.00 4.52
2358 3950 5.385198 TCTCTTCCAGTTATGTTTTTGCCT 58.615 37.500 0.00 0.00 0.00 4.75
2359 3951 5.473504 TCTCTTCCAGTTATGTTTTTGCCTC 59.526 40.000 0.00 0.00 0.00 4.70
2361 3953 5.833131 TCTTCCAGTTATGTTTTTGCCTCTT 59.167 36.000 0.00 0.00 0.00 2.85
2362 3954 5.705609 TCCAGTTATGTTTTTGCCTCTTC 57.294 39.130 0.00 0.00 0.00 2.87
2488 4096 4.650588 CCACCATTACCATTGGACAATCAT 59.349 41.667 10.37 0.00 37.69 2.45
2566 4174 2.166664 GCTCGTTTGTCCTGTCTATCCT 59.833 50.000 0.00 0.00 0.00 3.24
2568 4176 3.162666 TCGTTTGTCCTGTCTATCCTGT 58.837 45.455 0.00 0.00 0.00 4.00
2569 4177 4.338012 TCGTTTGTCCTGTCTATCCTGTA 58.662 43.478 0.00 0.00 0.00 2.74
2570 4178 4.768448 TCGTTTGTCCTGTCTATCCTGTAA 59.232 41.667 0.00 0.00 0.00 2.41
2571 4179 5.421056 TCGTTTGTCCTGTCTATCCTGTAAT 59.579 40.000 0.00 0.00 0.00 1.89
2628 4236 4.767409 GGTTACCTGCTTTTCATTCCTTCT 59.233 41.667 0.00 0.00 0.00 2.85
2629 4237 5.944007 GGTTACCTGCTTTTCATTCCTTCTA 59.056 40.000 0.00 0.00 0.00 2.10
2630 4238 6.127980 GGTTACCTGCTTTTCATTCCTTCTAC 60.128 42.308 0.00 0.00 0.00 2.59
2631 4239 4.003648 ACCTGCTTTTCATTCCTTCTACG 58.996 43.478 0.00 0.00 0.00 3.51
2632 4240 3.375299 CCTGCTTTTCATTCCTTCTACGG 59.625 47.826 0.00 0.00 0.00 4.02
2633 4241 4.253685 CTGCTTTTCATTCCTTCTACGGA 58.746 43.478 0.00 0.00 0.00 4.69
2634 4242 4.253685 TGCTTTTCATTCCTTCTACGGAG 58.746 43.478 0.00 0.00 33.89 4.63
2666 4275 7.896811 TGTAGTGAGACAGTACATTCTTCATT 58.103 34.615 13.24 0.00 42.89 2.57
2667 4276 8.367911 TGTAGTGAGACAGTACATTCTTCATTT 58.632 33.333 13.24 0.00 42.89 2.32
2669 4278 7.445121 AGTGAGACAGTACATTCTTCATTTGA 58.555 34.615 0.00 0.00 0.00 2.69
2681 4290 3.573538 TCTTCATTTGACATGTTGGTGGG 59.426 43.478 0.00 0.00 0.00 4.61
2688 4297 1.416030 GACATGTTGGTGGGCCTTTTT 59.584 47.619 4.53 0.00 35.27 1.94
2689 4298 1.416030 ACATGTTGGTGGGCCTTTTTC 59.584 47.619 4.53 0.00 35.27 2.29
2693 4302 3.515562 TGTTGGTGGGCCTTTTTCATAT 58.484 40.909 4.53 0.00 35.27 1.78
2694 4303 3.906846 TGTTGGTGGGCCTTTTTCATATT 59.093 39.130 4.53 0.00 35.27 1.28
2800 4413 6.460953 GGGTAGTTATATGGTTTGTTGCCATG 60.461 42.308 7.05 0.00 45.47 3.66
2839 4452 9.497030 TCATTTTGTTCGTATTGTATTGTATGC 57.503 29.630 0.00 0.00 0.00 3.14
2866 4480 5.529581 TTTTTGGTTGACCTCCTCATTTC 57.470 39.130 1.34 0.00 36.82 2.17
2876 4490 1.328680 CTCCTCATTTCGCCGTTCATG 59.671 52.381 0.00 0.00 0.00 3.07
2997 4611 1.678123 CCCTCCACTGAGTCATTGCTG 60.678 57.143 4.98 0.57 36.86 4.41
3029 4645 6.432403 AGAGAGTTTCCTTTCTCATTCTGT 57.568 37.500 4.53 0.00 41.78 3.41
3030 4646 6.463360 AGAGAGTTTCCTTTCTCATTCTGTC 58.537 40.000 4.53 0.00 41.78 3.51
3031 4647 6.042552 AGAGAGTTTCCTTTCTCATTCTGTCA 59.957 38.462 4.53 0.00 41.78 3.58
3032 4648 6.777782 AGAGTTTCCTTTCTCATTCTGTCAT 58.222 36.000 0.00 0.00 33.63 3.06
3053 4669 6.939163 GTCATTCCTAGCATCCTGATGTAAAT 59.061 38.462 8.79 0.73 40.80 1.40
3072 4688 8.146479 TGTAAATCTGTCATGATAATCTGTGC 57.854 34.615 0.00 0.00 0.00 4.57
3100 4716 2.105477 GGCAGGATAAGATTGGCAGAGA 59.895 50.000 0.00 0.00 37.35 3.10
3117 4733 5.049167 GCAGAGACCTTCATATCACTTGAG 58.951 45.833 0.00 0.00 0.00 3.02
3135 4751 5.413833 ACTTGAGCATCCATTAGTCACAAAG 59.586 40.000 0.00 0.00 0.00 2.77
3139 4755 5.564550 AGCATCCATTAGTCACAAAGTTCT 58.435 37.500 0.00 0.00 0.00 3.01
3144 4760 5.758296 TCCATTAGTCACAAAGTTCTGTCAC 59.242 40.000 0.00 0.00 0.00 3.67
3148 4764 2.540101 GTCACAAAGTTCTGTCACGAGG 59.460 50.000 0.00 0.00 0.00 4.63
3153 4769 2.802787 AGTTCTGTCACGAGGAACTG 57.197 50.000 9.03 0.00 45.06 3.16
3178 4794 8.952278 TGTCTTATCGTGCAATTAAGGTATTTT 58.048 29.630 10.14 0.00 0.00 1.82
3271 4890 3.127548 TGATTTCTGATTCTTTGCGAGCC 59.872 43.478 0.00 0.00 0.00 4.70
3313 4932 8.877195 AGAAGTGAAGGTTTAAGGTGTCTTATA 58.123 33.333 0.00 0.00 35.61 0.98
3492 5111 2.287849 GCTGGTTCTTGAAGTTCCTTGC 60.288 50.000 0.00 9.12 0.00 4.01
3510 5129 8.303876 GTTCCTTGCTTTCACCATAATTTTAGA 58.696 33.333 0.00 0.00 0.00 2.10
3657 5779 7.559897 AGGTGGGTGTTTATATGGATTGTTAAG 59.440 37.037 0.00 0.00 0.00 1.85
3712 5834 9.480053 GAGAGAATAAGAAGAGATGAAGGAATG 57.520 37.037 0.00 0.00 0.00 2.67
3732 5854 5.581126 ATGGGCACACAGTAAATATGTTG 57.419 39.130 0.00 0.00 0.00 3.33
3796 5918 6.070824 CCCCAAAATAGTTAAGACTTTGCCAT 60.071 38.462 0.00 0.00 37.33 4.40
3836 5975 5.297547 CACTTAGTTGTCTGAAGTGGCTAA 58.702 41.667 6.17 0.00 44.08 3.09
3837 5976 5.934625 CACTTAGTTGTCTGAAGTGGCTAAT 59.065 40.000 6.17 0.00 44.08 1.73
3859 5998 2.414994 ACTGCATCCTTCATGTCTGG 57.585 50.000 0.00 0.00 34.56 3.86
3871 6010 5.183713 CCTTCATGTCTGGTCAAATTAGCAA 59.816 40.000 0.00 0.00 0.00 3.91
3874 6013 6.472016 TCATGTCTGGTCAAATTAGCAAGTA 58.528 36.000 0.00 0.00 0.00 2.24
3895 6034 7.045126 AGTAATAATGCTCAGTACCACTCTC 57.955 40.000 0.00 0.00 0.00 3.20
3896 6035 4.946478 ATAATGCTCAGTACCACTCTCC 57.054 45.455 0.00 0.00 0.00 3.71
3966 6105 1.863155 TTCCCAATCCTGGACAGGCC 61.863 60.000 13.51 0.00 46.92 5.19
3999 6142 0.907486 AGCTCTGAGTGCAGGCATTA 59.093 50.000 9.33 0.00 42.53 1.90
4004 6147 2.133553 CTGAGTGCAGGCATTATCGAG 58.866 52.381 0.00 0.00 38.51 4.04
4046 6189 3.135712 TGACAGTTGAGCTTGGGTTTCTA 59.864 43.478 0.00 0.00 0.00 2.10
4065 6208 2.391616 AGCTGATTTGCTCATCACGA 57.608 45.000 0.00 0.00 39.34 4.35
4144 6287 4.805719 TCATCAAGATCCTCGTTCAAATCG 59.194 41.667 0.00 0.00 0.00 3.34
4175 6318 3.814842 TGGCATAATTTATCACGCCTGAG 59.185 43.478 14.11 0.00 40.27 3.35
4188 6331 3.974401 CACGCCTGAGTTAAACATGTTTG 59.026 43.478 29.72 14.54 34.23 2.93
4226 6370 3.136626 AGTGCCAGTCAGGTCTAACTTTT 59.863 43.478 0.00 0.00 40.61 2.27
4235 6379 6.931840 AGTCAGGTCTAACTTTTCAAGCTTAG 59.068 38.462 0.00 0.00 0.00 2.18
4268 6412 2.094675 GTGGACCTATTGCAAGCACAT 58.905 47.619 4.94 0.00 0.00 3.21
4285 6429 8.292448 GCAAGCACATTATTGTTAGCACTATAT 58.708 33.333 3.75 0.00 32.34 0.86
4300 6444 6.279123 AGCACTATATATCCAAGATCATGCG 58.721 40.000 0.00 0.00 33.51 4.73
4313 6457 2.538512 TCATGCGATGATTCAGAGGG 57.461 50.000 0.00 0.00 33.59 4.30
4321 6465 0.694771 TGATTCAGAGGGCTTGCTGT 59.305 50.000 0.00 0.00 33.90 4.40
4322 6466 1.093159 GATTCAGAGGGCTTGCTGTG 58.907 55.000 0.00 0.00 33.90 3.66
4327 6471 0.475906 AGAGGGCTTGCTGTGAAACT 59.524 50.000 0.00 0.00 38.04 2.66
4360 6505 0.888619 TGGCGTGGTTTGTCACAAAA 59.111 45.000 4.02 0.00 37.50 2.44
4363 6508 2.933260 GGCGTGGTTTGTCACAAAATTT 59.067 40.909 4.02 0.00 37.50 1.82
4364 6509 3.000825 GGCGTGGTTTGTCACAAAATTTC 59.999 43.478 4.02 0.00 37.50 2.17
4365 6510 3.862845 GCGTGGTTTGTCACAAAATTTCT 59.137 39.130 4.02 0.00 37.50 2.52
4366 6511 4.259770 GCGTGGTTTGTCACAAAATTTCTG 60.260 41.667 4.02 0.00 37.50 3.02
4367 6512 4.862018 CGTGGTTTGTCACAAAATTTCTGT 59.138 37.500 4.02 0.00 37.50 3.41
4370 6515 5.047021 TGGTTTGTCACAAAATTTCTGTGGA 60.047 36.000 22.19 13.06 43.60 4.02
4373 6518 4.681744 TGTCACAAAATTTCTGTGGAAGC 58.318 39.130 22.19 14.94 43.60 3.86
4380 6525 0.878523 TTTCTGTGGAAGCGGTCACG 60.879 55.000 2.53 0.00 44.63 4.35
4426 6571 5.762179 ACCTGAAGTAGTTCCATGAATGA 57.238 39.130 7.84 0.00 0.00 2.57
4427 6572 6.319048 ACCTGAAGTAGTTCCATGAATGAT 57.681 37.500 7.84 0.00 0.00 2.45
4428 6573 6.352516 ACCTGAAGTAGTTCCATGAATGATC 58.647 40.000 7.84 0.00 0.00 2.92
4429 6574 6.157645 ACCTGAAGTAGTTCCATGAATGATCT 59.842 38.462 7.84 0.00 0.00 2.75
4430 6575 7.052873 CCTGAAGTAGTTCCATGAATGATCTT 58.947 38.462 7.84 0.00 0.00 2.40
4431 6576 7.555554 CCTGAAGTAGTTCCATGAATGATCTTT 59.444 37.037 7.84 0.00 0.00 2.52
4432 6577 8.868522 TGAAGTAGTTCCATGAATGATCTTTT 57.131 30.769 7.84 0.00 0.00 2.27
4433 6578 9.300681 TGAAGTAGTTCCATGAATGATCTTTTT 57.699 29.630 7.84 0.00 0.00 1.94
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 5.940192 AGTCATGCGTCTGAAAAATGTTA 57.060 34.783 0.00 0.00 0.00 2.41
1 2 4.836125 AGTCATGCGTCTGAAAAATGTT 57.164 36.364 0.00 0.00 0.00 2.71
2 3 7.792374 ATATAGTCATGCGTCTGAAAAATGT 57.208 32.000 0.00 0.00 0.00 2.71
4 5 9.722056 GAAAATATAGTCATGCGTCTGAAAAAT 57.278 29.630 0.00 0.00 0.00 1.82
5 6 8.181573 GGAAAATATAGTCATGCGTCTGAAAAA 58.818 33.333 0.00 0.00 0.00 1.94
6 7 7.201696 GGGAAAATATAGTCATGCGTCTGAAAA 60.202 37.037 0.00 0.00 0.00 2.29
7 8 6.260050 GGGAAAATATAGTCATGCGTCTGAAA 59.740 38.462 0.00 0.00 0.00 2.69
9 10 5.297547 GGGAAAATATAGTCATGCGTCTGA 58.702 41.667 0.00 0.00 0.00 3.27
11 12 4.102524 TGGGGAAAATATAGTCATGCGTCT 59.897 41.667 0.00 0.00 0.00 4.18
12 13 4.385825 TGGGGAAAATATAGTCATGCGTC 58.614 43.478 0.00 0.00 0.00 5.19
13 14 4.431416 TGGGGAAAATATAGTCATGCGT 57.569 40.909 0.00 0.00 0.00 5.24
14 15 5.964958 AATGGGGAAAATATAGTCATGCG 57.035 39.130 0.00 0.00 0.00 4.73
168 169 6.183360 ACAATGTTACTCGAGCAGTTGAAAAA 60.183 34.615 13.61 0.00 36.43 1.94
170 171 4.814234 ACAATGTTACTCGAGCAGTTGAAA 59.186 37.500 13.61 0.00 36.43 2.69
171 172 4.377021 ACAATGTTACTCGAGCAGTTGAA 58.623 39.130 13.61 0.00 36.43 2.69
173 174 4.732285 AACAATGTTACTCGAGCAGTTG 57.268 40.909 13.61 12.73 36.43 3.16
174 175 6.854496 TTAAACAATGTTACTCGAGCAGTT 57.146 33.333 13.61 4.28 36.43 3.16
175 176 6.854496 TTTAAACAATGTTACTCGAGCAGT 57.146 33.333 13.61 0.00 39.41 4.40
199 200 8.999431 GGTGTGTGAAAGAAGTTGAGAATTATA 58.001 33.333 0.00 0.00 0.00 0.98
200 201 7.502226 TGGTGTGTGAAAGAAGTTGAGAATTAT 59.498 33.333 0.00 0.00 0.00 1.28
201 202 6.826231 TGGTGTGTGAAAGAAGTTGAGAATTA 59.174 34.615 0.00 0.00 0.00 1.40
204 205 4.584874 TGGTGTGTGAAAGAAGTTGAGAA 58.415 39.130 0.00 0.00 0.00 2.87
205 206 4.191544 CTGGTGTGTGAAAGAAGTTGAGA 58.808 43.478 0.00 0.00 0.00 3.27
206 207 3.313526 CCTGGTGTGTGAAAGAAGTTGAG 59.686 47.826 0.00 0.00 0.00 3.02
207 208 3.278574 CCTGGTGTGTGAAAGAAGTTGA 58.721 45.455 0.00 0.00 0.00 3.18
208 209 2.223572 GCCTGGTGTGTGAAAGAAGTTG 60.224 50.000 0.00 0.00 0.00 3.16
210 211 1.680338 GCCTGGTGTGTGAAAGAAGT 58.320 50.000 0.00 0.00 0.00 3.01
211 212 0.954452 GGCCTGGTGTGTGAAAGAAG 59.046 55.000 0.00 0.00 0.00 2.85
212 213 0.817634 CGGCCTGGTGTGTGAAAGAA 60.818 55.000 0.00 0.00 0.00 2.52
213 214 1.227823 CGGCCTGGTGTGTGAAAGA 60.228 57.895 0.00 0.00 0.00 2.52
214 215 2.260869 CCGGCCTGGTGTGTGAAAG 61.261 63.158 0.00 0.00 0.00 2.62
215 216 2.203280 CCGGCCTGGTGTGTGAAA 60.203 61.111 0.00 0.00 0.00 2.69
216 217 4.263572 CCCGGCCTGGTGTGTGAA 62.264 66.667 4.74 0.00 35.15 3.18
228 229 1.095807 GTGAAAGTATCAGGCCCGGC 61.096 60.000 0.00 0.00 39.19 6.13
229 230 0.810031 CGTGAAAGTATCAGGCCCGG 60.810 60.000 0.00 0.00 39.19 5.73
231 232 2.973694 TACGTGAAAGTATCAGGCCC 57.026 50.000 0.00 0.00 45.66 5.80
233 234 2.608090 GCCTTACGTGAAAGTATCAGGC 59.392 50.000 0.00 4.18 45.66 4.85
234 235 3.195661 GGCCTTACGTGAAAGTATCAGG 58.804 50.000 0.00 0.00 46.82 3.86
235 236 3.857052 TGGCCTTACGTGAAAGTATCAG 58.143 45.455 3.32 0.00 39.19 2.90
236 237 3.369052 CCTGGCCTTACGTGAAAGTATCA 60.369 47.826 3.32 0.00 35.05 2.15
237 238 3.195661 CCTGGCCTTACGTGAAAGTATC 58.804 50.000 3.32 0.00 0.00 2.24
238 239 2.679930 GCCTGGCCTTACGTGAAAGTAT 60.680 50.000 7.66 0.00 0.00 2.12
239 240 1.338389 GCCTGGCCTTACGTGAAAGTA 60.338 52.381 7.66 0.00 0.00 2.24
240 241 0.605589 GCCTGGCCTTACGTGAAAGT 60.606 55.000 7.66 0.00 0.00 2.66
241 242 1.305930 GGCCTGGCCTTACGTGAAAG 61.306 60.000 30.42 0.00 46.69 2.62
242 243 1.302993 GGCCTGGCCTTACGTGAAA 60.303 57.895 30.42 0.00 46.69 2.69
243 244 2.349755 GGCCTGGCCTTACGTGAA 59.650 61.111 30.42 0.00 46.69 3.18
289 1479 2.534019 CGGTGTATGCGGACATGGC 61.534 63.158 0.00 0.00 37.04 4.40
293 1483 4.460683 GCCCGGTGTATGCGGACA 62.461 66.667 0.00 0.00 0.00 4.02
321 1517 3.308545 GGAGACTGAAGGAGAGAGTACCA 60.309 52.174 0.00 0.00 0.00 3.25
322 1518 3.284617 GGAGACTGAAGGAGAGAGTACC 58.715 54.545 0.00 0.00 0.00 3.34
323 1519 3.284617 GGGAGACTGAAGGAGAGAGTAC 58.715 54.545 0.00 0.00 0.00 2.73
324 1520 2.242708 GGGGAGACTGAAGGAGAGAGTA 59.757 54.545 0.00 0.00 0.00 2.59
325 1521 1.006639 GGGGAGACTGAAGGAGAGAGT 59.993 57.143 0.00 0.00 0.00 3.24
326 1522 1.687996 GGGGGAGACTGAAGGAGAGAG 60.688 61.905 0.00 0.00 0.00 3.20
327 1523 0.336737 GGGGGAGACTGAAGGAGAGA 59.663 60.000 0.00 0.00 0.00 3.10
328 1524 0.041833 TGGGGGAGACTGAAGGAGAG 59.958 60.000 0.00 0.00 0.00 3.20
329 1525 0.252284 GTGGGGGAGACTGAAGGAGA 60.252 60.000 0.00 0.00 0.00 3.71
330 1526 0.252467 AGTGGGGGAGACTGAAGGAG 60.252 60.000 0.00 0.00 0.00 3.69
331 1527 0.545309 CAGTGGGGGAGACTGAAGGA 60.545 60.000 0.00 0.00 43.04 3.36
332 1528 1.986413 CAGTGGGGGAGACTGAAGG 59.014 63.158 0.00 0.00 43.04 3.46
333 1529 1.298014 GCAGTGGGGGAGACTGAAG 59.702 63.158 0.00 0.00 43.04 3.02
334 1530 2.224159 GGCAGTGGGGGAGACTGAA 61.224 63.158 0.00 0.00 43.04 3.02
335 1531 2.607750 GGCAGTGGGGGAGACTGA 60.608 66.667 0.00 0.00 43.04 3.41
336 1532 3.721706 GGGCAGTGGGGGAGACTG 61.722 72.222 0.00 0.00 43.22 3.51
442 1638 0.647925 GAGTTGAATCTTCGCTCGGC 59.352 55.000 0.00 0.00 0.00 5.54
450 1646 1.673033 CCGGTGCTCGAGTTGAATCTT 60.673 52.381 15.13 0.00 42.43 2.40
573 1811 1.813753 CGGTCGCCATGTTACCTGG 60.814 63.158 2.20 2.20 36.81 4.45
598 1836 3.825160 GACCAAGGGCGACTGTGCA 62.825 63.158 0.00 0.00 36.28 4.57
601 1839 2.584391 GGAGACCAAGGGCGACTGT 61.584 63.158 0.00 0.00 0.00 3.55
602 1840 1.903877 ATGGAGACCAAGGGCGACTG 61.904 60.000 0.00 0.00 36.95 3.51
603 1841 1.201429 AATGGAGACCAAGGGCGACT 61.201 55.000 0.00 0.00 36.95 4.18
604 1842 0.539986 TAATGGAGACCAAGGGCGAC 59.460 55.000 0.00 0.00 36.95 5.19
605 1843 0.539986 GTAATGGAGACCAAGGGCGA 59.460 55.000 0.00 0.00 36.95 5.54
607 1845 1.282157 ACAGTAATGGAGACCAAGGGC 59.718 52.381 0.00 0.00 36.95 5.19
638 1909 4.470602 AGTTTGAAGATCCCCGAAGTTTT 58.529 39.130 0.00 0.00 0.00 2.43
646 1917 3.067320 GCTGCAATAGTTTGAAGATCCCC 59.933 47.826 0.00 0.00 40.53 4.81
648 1919 3.790123 GCGCTGCAATAGTTTGAAGATCC 60.790 47.826 0.00 0.00 40.53 3.36
651 1922 2.150390 TGCGCTGCAATAGTTTGAAGA 58.850 42.857 9.73 0.00 40.53 2.87
665 1936 1.081641 CAAGTTTCCTGCTGCGCTG 60.082 57.895 9.73 10.04 0.00 5.18
669 1940 3.181496 GCTAATACCAAGTTTCCTGCTGC 60.181 47.826 0.00 0.00 0.00 5.25
712 1994 8.668353 CAAGCTAAAATAGTTTGATGCTACAGA 58.332 33.333 7.87 0.00 46.07 3.41
741 2023 9.442047 CATAGTGTCCTGAGTTAAAATTCTTCT 57.558 33.333 0.00 0.00 0.00 2.85
742 2024 8.178313 GCATAGTGTCCTGAGTTAAAATTCTTC 58.822 37.037 0.00 0.00 0.00 2.87
743 2025 7.148407 CGCATAGTGTCCTGAGTTAAAATTCTT 60.148 37.037 0.00 0.00 0.00 2.52
772 2054 7.904094 GTGAGACTCACATTATTCAGTCAATC 58.096 38.462 27.15 0.00 46.22 2.67
773 2055 7.840342 GTGAGACTCACATTATTCAGTCAAT 57.160 36.000 27.15 0.00 46.22 2.57
791 2073 5.169295 GTCTGTAAATGGTAGTGGTGAGAC 58.831 45.833 0.00 0.00 0.00 3.36
825 2110 3.963383 ATTTCCTGCGCTTATTTACCG 57.037 42.857 9.73 0.00 0.00 4.02
848 2133 5.243426 ACAAAAATCGTTTGCTACACTGT 57.757 34.783 0.00 0.00 32.93 3.55
851 2140 6.635239 ACATGTACAAAAATCGTTTGCTACAC 59.365 34.615 0.00 3.34 33.40 2.90
862 2151 8.134895 TGACAGAAGGAAACATGTACAAAAATC 58.865 33.333 0.00 0.00 0.00 2.17
894 2186 6.183361 GAGTTACCTCTTATGGATCCAACCAT 60.183 42.308 20.67 4.42 42.31 3.55
912 2208 9.233232 CAACTGTTAAACAAAATGAGAGTTACC 57.767 33.333 0.00 0.00 0.00 2.85
917 2296 8.971321 CATTCCAACTGTTAAACAAAATGAGAG 58.029 33.333 0.00 0.00 0.00 3.20
921 2300 8.877779 TGAACATTCCAACTGTTAAACAAAATG 58.122 29.630 0.00 1.03 36.98 2.32
989 2378 2.589492 CGGAGCATTTAGGCGAGCG 61.589 63.158 0.00 0.00 39.27 5.03
1137 2551 1.151908 CAGTGGGTTTTCCGGGGAA 59.848 57.895 0.00 0.00 41.82 3.97
1146 2560 1.231928 GGTGGGGTTCAGTGGGTTT 59.768 57.895 0.00 0.00 0.00 3.27
1165 2579 0.833834 CCAGTGGCGAGGGATAGGAT 60.834 60.000 0.00 0.00 0.00 3.24
1389 2803 2.710096 TAAACATACAGGGGAGCTGC 57.290 50.000 0.00 0.00 0.00 5.25
1419 2844 2.816087 GCAGAGGACAATTCAGCTTTGA 59.184 45.455 3.66 0.00 0.00 2.69
1432 2857 6.107901 AGTATTATCAGGAATGCAGAGGAC 57.892 41.667 0.00 0.00 0.00 3.85
1517 2943 2.512485 TGCTGTGGCAAACAAATCAG 57.488 45.000 0.00 0.00 46.36 2.90
1529 2955 6.093909 TCAATTGTTCATACTATGTGCTGTGG 59.906 38.462 5.13 0.00 0.00 4.17
1608 3036 0.546747 TCCGAACCTCCAAGGGTGAT 60.547 55.000 0.00 0.00 33.59 3.06
1626 3054 3.545703 CATGGTATCCAGTTGTTCCCTC 58.454 50.000 0.00 0.00 36.75 4.30
1716 3146 1.211456 AAATAGCAGCTCCAGCCTCT 58.789 50.000 0.00 0.00 43.38 3.69
1786 3222 8.770010 ATTATCCAAAAACATTTATACCGGGA 57.230 30.769 6.32 0.00 0.00 5.14
1882 3332 6.864685 TCAACTAGTAAATGTACCACACTTCG 59.135 38.462 0.00 0.00 0.00 3.79
1896 3346 9.772973 ACTAATGTCATGTTGTCAACTAGTAAA 57.227 29.630 16.45 0.00 0.00 2.01
2027 3596 4.130118 CAGTCCAACTTCAAAGCTGTACT 58.870 43.478 0.00 0.00 0.00 2.73
2028 3597 3.304057 GCAGTCCAACTTCAAAGCTGTAC 60.304 47.826 0.00 0.00 0.00 2.90
2086 3655 0.800012 TGGTGCGCCGATTAGAAAAC 59.200 50.000 12.58 0.00 37.67 2.43
2263 3833 9.002600 GGCATACATCACATGATTGATAGTTTA 57.997 33.333 0.00 0.00 34.29 2.01
2264 3834 7.503230 TGGCATACATCACATGATTGATAGTTT 59.497 33.333 0.00 0.00 34.29 2.66
2266 3836 6.536447 TGGCATACATCACATGATTGATAGT 58.464 36.000 0.00 3.64 34.29 2.12
2271 3863 9.730420 CATATATTGGCATACATCACATGATTG 57.270 33.333 0.00 0.00 31.21 2.67
2306 3898 5.869649 AGAAATGGTTGGCAGTTAAAAGT 57.130 34.783 0.00 0.00 0.00 2.66
2307 3899 8.831715 AATAAGAAATGGTTGGCAGTTAAAAG 57.168 30.769 0.00 0.00 0.00 2.27
2314 3906 8.230472 AGAGAATAATAAGAAATGGTTGGCAG 57.770 34.615 0.00 0.00 0.00 4.85
2317 3909 9.189156 TGGAAGAGAATAATAAGAAATGGTTGG 57.811 33.333 0.00 0.00 0.00 3.77
2333 3925 6.494835 AGGCAAAAACATAACTGGAAGAGAAT 59.505 34.615 0.00 0.00 37.43 2.40
2336 3928 5.474876 AGAGGCAAAAACATAACTGGAAGAG 59.525 40.000 0.00 0.00 37.43 2.85
2340 3932 5.009610 GTGAAGAGGCAAAAACATAACTGGA 59.990 40.000 0.00 0.00 0.00 3.86
2341 3933 5.222631 GTGAAGAGGCAAAAACATAACTGG 58.777 41.667 0.00 0.00 0.00 4.00
2342 3934 4.911610 CGTGAAGAGGCAAAAACATAACTG 59.088 41.667 0.00 0.00 0.00 3.16
2343 3935 4.819630 TCGTGAAGAGGCAAAAACATAACT 59.180 37.500 0.00 0.00 0.00 2.24
2344 3936 5.103290 TCGTGAAGAGGCAAAAACATAAC 57.897 39.130 0.00 0.00 0.00 1.89
2347 3939 3.632145 ACTTCGTGAAGAGGCAAAAACAT 59.368 39.130 16.10 0.00 40.79 2.71
2349 3941 3.181500 ACACTTCGTGAAGAGGCAAAAAC 60.181 43.478 16.10 0.00 40.79 2.43
2354 3946 1.138069 TGAACACTTCGTGAAGAGGCA 59.862 47.619 16.10 8.28 40.79 4.75
2355 3947 1.865865 TGAACACTTCGTGAAGAGGC 58.134 50.000 16.10 6.05 40.79 4.70
2357 3949 6.719365 AGAAAATTGAACACTTCGTGAAGAG 58.281 36.000 16.10 10.65 40.79 2.85
2358 3950 6.677781 AGAAAATTGAACACTTCGTGAAGA 57.322 33.333 16.10 0.00 40.79 2.87
2359 3951 8.122952 AGTAAGAAAATTGAACACTTCGTGAAG 58.877 33.333 8.04 8.04 43.79 3.02
2361 3953 7.279090 TGAGTAAGAAAATTGAACACTTCGTGA 59.721 33.333 0.38 0.00 36.96 4.35
2362 3954 7.406553 TGAGTAAGAAAATTGAACACTTCGTG 58.593 34.615 0.00 0.00 39.75 4.35
2488 4096 0.325933 CCTTCAGGTGCACCATCAGA 59.674 55.000 36.39 24.10 38.89 3.27
2566 4174 6.795590 TGAAAGGGTCAGGGAATTTATTACA 58.204 36.000 0.00 0.00 0.00 2.41
2568 4176 7.179516 GGTTTGAAAGGGTCAGGGAATTTATTA 59.820 37.037 0.00 0.00 37.61 0.98
2569 4177 6.013725 GGTTTGAAAGGGTCAGGGAATTTATT 60.014 38.462 0.00 0.00 37.61 1.40
2570 4178 5.483937 GGTTTGAAAGGGTCAGGGAATTTAT 59.516 40.000 0.00 0.00 37.61 1.40
2571 4179 4.836175 GGTTTGAAAGGGTCAGGGAATTTA 59.164 41.667 0.00 0.00 37.61 1.40
2611 4219 4.253685 TCCGTAGAAGGAATGAAAAGCAG 58.746 43.478 0.00 0.00 37.36 4.24
2614 4222 6.631962 ACTACTCCGTAGAAGGAATGAAAAG 58.368 40.000 7.94 0.00 40.25 2.27
2628 4236 5.174395 GTCTCACTACAGAACTACTCCGTA 58.826 45.833 0.00 0.00 0.00 4.02
2629 4237 4.002316 GTCTCACTACAGAACTACTCCGT 58.998 47.826 0.00 0.00 0.00 4.69
2630 4238 4.001652 TGTCTCACTACAGAACTACTCCG 58.998 47.826 0.00 0.00 0.00 4.63
2643 4251 8.585018 TCAAATGAAGAATGTACTGTCTCACTA 58.415 33.333 0.00 0.00 0.00 2.74
2666 4275 0.105760 AAGGCCCACCAACATGTCAA 60.106 50.000 0.00 0.00 39.06 3.18
2667 4276 0.105760 AAAGGCCCACCAACATGTCA 60.106 50.000 0.00 0.00 39.06 3.58
2669 4278 1.416030 GAAAAAGGCCCACCAACATGT 59.584 47.619 0.00 0.00 39.06 3.21
2681 4290 3.371898 GTGGCTGCAAATATGAAAAAGGC 59.628 43.478 0.50 0.00 0.00 4.35
2735 4344 8.207545 GGTATATCTCCTGAAGTCTGTTGAAAT 58.792 37.037 0.00 0.00 0.00 2.17
2800 4413 5.173854 CGAACAAAATGAAAAGGAGCTCAAC 59.826 40.000 17.19 0.00 0.00 3.18
2866 4480 3.973657 AGTACCTAATACATGAACGGCG 58.026 45.455 4.80 4.80 36.09 6.46
2940 4554 7.684428 GCCTTTGAAGATGTACCTTGTTTTCTT 60.684 37.037 0.00 0.00 0.00 2.52
2997 4611 5.760743 AGAAAGGAAACTCTCTTACTTGCAC 59.239 40.000 0.00 0.00 32.48 4.57
3029 4645 6.499106 TTTACATCAGGATGCTAGGAATGA 57.501 37.500 9.12 0.63 42.39 2.57
3030 4646 7.119407 CAGATTTACATCAGGATGCTAGGAATG 59.881 40.741 9.12 0.00 42.39 2.67
3031 4647 7.166851 CAGATTTACATCAGGATGCTAGGAAT 58.833 38.462 9.12 3.39 42.39 3.01
3032 4648 6.100279 ACAGATTTACATCAGGATGCTAGGAA 59.900 38.462 9.12 0.00 42.39 3.36
3053 4669 6.408869 TCAAAGCACAGATTATCATGACAGA 58.591 36.000 0.00 0.00 0.00 3.41
3072 4688 4.261909 GCCAATCTTATCCTGCCATCAAAG 60.262 45.833 0.00 0.00 0.00 2.77
3100 4716 4.164796 TGGATGCTCAAGTGATATGAAGGT 59.835 41.667 0.00 0.00 0.00 3.50
3117 4733 5.182001 ACAGAACTTTGTGACTAATGGATGC 59.818 40.000 0.00 0.00 0.00 3.91
3135 4751 2.034812 AGACAGTTCCTCGTGACAGAAC 59.965 50.000 2.90 2.90 40.14 3.01
3139 4755 3.119955 CGATAAGACAGTTCCTCGTGACA 60.120 47.826 0.00 0.00 0.00 3.58
3144 4760 2.186076 GCACGATAAGACAGTTCCTCG 58.814 52.381 0.00 0.00 0.00 4.63
3148 4764 6.092259 ACCTTAATTGCACGATAAGACAGTTC 59.908 38.462 11.87 0.00 0.00 3.01
3313 4932 3.220110 CAAGCCATATCCTGCAACAGAT 58.780 45.455 0.00 0.00 32.44 2.90
3408 5027 4.377022 CCGTGGAACTGTAAACGAATCAAG 60.377 45.833 10.28 0.00 38.27 3.02
3510 5129 4.947388 TGAAAGAGCTGGTACACAAAACTT 59.053 37.500 0.00 0.00 0.00 2.66
3561 5180 6.751888 ACAACTGTTCAAAACTTCAGTATTGC 59.248 34.615 0.00 0.00 39.72 3.56
3657 5779 9.783256 ACAATTAAAAGAACAAGAGTTACACAC 57.217 29.630 0.00 0.00 38.30 3.82
3685 5807 8.601047 TTCCTTCATCTCTTCTTATTCTCTCA 57.399 34.615 0.00 0.00 0.00 3.27
3693 5815 4.474651 TGCCCATTCCTTCATCTCTTCTTA 59.525 41.667 0.00 0.00 0.00 2.10
3699 5821 2.019984 GTGTGCCCATTCCTTCATCTC 58.980 52.381 0.00 0.00 0.00 2.75
3712 5834 4.700213 AGTCAACATATTTACTGTGTGCCC 59.300 41.667 0.00 0.00 0.00 5.36
3732 5854 1.137872 CAGGGCTACATGGTCAGAGTC 59.862 57.143 0.00 0.00 0.00 3.36
3796 5918 6.184789 ACTAAGTGGACTGTTCCTTGAAAAA 58.815 36.000 1.48 0.00 43.31 1.94
3836 5975 5.309020 ACCAGACATGAAGGATGCAGTATAT 59.691 40.000 0.00 0.00 35.15 0.86
3837 5976 4.655649 ACCAGACATGAAGGATGCAGTATA 59.344 41.667 0.00 0.00 35.15 1.47
3871 6010 6.041069 GGAGAGTGGTACTGAGCATTATTACT 59.959 42.308 0.00 0.00 35.06 2.24
3874 6013 4.716784 TGGAGAGTGGTACTGAGCATTATT 59.283 41.667 0.00 0.00 35.06 1.40
3895 6034 9.530633 GTATCTTAACAGGTCATAAAGTACTGG 57.469 37.037 0.00 0.00 33.63 4.00
3939 6078 3.110705 TCCAGGATTGGGAAGAGAAGAG 58.889 50.000 0.00 0.00 45.10 2.85
3966 6105 4.969196 AGCTGCACCGGTGTCACG 62.969 66.667 33.92 23.01 0.00 4.35
3999 6142 4.215908 TCTGATAGCCAAGTTACCTCGAT 58.784 43.478 0.00 0.00 0.00 3.59
4004 6147 4.870991 GTCAGTTCTGATAGCCAAGTTACC 59.129 45.833 5.80 0.00 0.00 2.85
4015 6158 5.233225 CAAGCTCAACTGTCAGTTCTGATA 58.767 41.667 15.48 2.70 36.03 2.15
4049 6192 2.635714 AGCATCGTGATGAGCAAATCA 58.364 42.857 13.83 0.00 43.70 2.57
4065 6208 0.604578 ACGCTGCCAAAATGAAGCAT 59.395 45.000 0.00 0.00 35.64 3.79
4099 6242 0.878961 GCCATTCGCCTAGGGTAACG 60.879 60.000 11.72 5.48 37.60 3.18
4111 6254 2.486982 GGATCTTGATGATGGCCATTCG 59.513 50.000 21.84 2.89 35.17 3.34
4164 6307 3.674997 ACATGTTTAACTCAGGCGTGAT 58.325 40.909 9.94 0.00 30.18 3.06
4188 6331 7.094377 TGACTGGCACTTGTTATCCTTTAATTC 60.094 37.037 0.00 0.00 0.00 2.17
4235 6379 3.686916 AGGTCCACAAAGAAGCTACTC 57.313 47.619 0.00 0.00 0.00 2.59
4300 6444 1.948145 CAGCAAGCCCTCTGAATCATC 59.052 52.381 0.00 0.00 32.26 2.92
4313 6457 0.661483 GGCGAAGTTTCACAGCAAGC 60.661 55.000 0.00 0.00 0.00 4.01
4321 6465 0.316360 GTTTTCGCGGCGAAGTTTCA 60.316 50.000 32.64 18.53 46.43 2.69
4322 6466 0.041576 AGTTTTCGCGGCGAAGTTTC 60.042 50.000 32.64 23.41 46.43 2.78
4327 6471 4.020378 GCCAGTTTTCGCGGCGAA 62.020 61.111 31.54 31.54 44.28 4.70
4360 6505 1.523758 GTGACCGCTTCCACAGAAAT 58.476 50.000 0.00 0.00 33.72 2.17
4363 6508 2.142357 CTCGTGACCGCTTCCACAGA 62.142 60.000 0.00 0.00 33.13 3.41
4364 6509 1.734477 CTCGTGACCGCTTCCACAG 60.734 63.158 0.00 0.00 33.13 3.66
4365 6510 2.338620 CTCGTGACCGCTTCCACA 59.661 61.111 0.00 0.00 33.13 4.17
4366 6511 2.432628 CCTCGTGACCGCTTCCAC 60.433 66.667 0.00 0.00 0.00 4.02
4367 6512 3.691342 CCCTCGTGACCGCTTCCA 61.691 66.667 0.00 0.00 0.00 3.53
4370 6515 1.477553 TATTACCCTCGTGACCGCTT 58.522 50.000 0.00 0.00 0.00 4.68
4373 6518 1.477700 TGGTTATTACCCTCGTGACCG 59.522 52.381 0.00 0.00 44.35 4.79
4380 6525 2.431782 TGCGTACCTGGTTATTACCCTC 59.568 50.000 3.84 0.00 44.35 4.30


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

AutoCloner maintained by Alex Coulton.