Multiple sequence alignment - TraesCS5B01G415100

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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 TraesCS5B01G415100 chr5B 100.000 6443 0 0 1 6443 589376616 589370174 0.000000e+00 11899.0
1 TraesCS5B01G415100 chr5B 78.495 186 33 6 406 588 10338354 10338173 1.470000e-21 115.0
2 TraesCS5B01G415100 chr5B 94.000 50 3 0 6394 6443 418150935 418150984 6.930000e-10 76.8
3 TraesCS5B01G415100 chr5A 93.682 5081 206 55 773 5780 600070673 600065635 0.000000e+00 7498.0
4 TraesCS5B01G415100 chr5A 83.060 549 64 12 15 548 600071303 600070769 7.560000e-129 472.0
5 TraesCS5B01G415100 chr5D 91.398 4150 192 63 2077 6165 480858433 480854388 0.000000e+00 5533.0
6 TraesCS5B01G415100 chr5D 89.031 1641 131 26 466 2073 480860186 480858562 0.000000e+00 1988.0
7 TraesCS5B01G415100 chr5D 91.340 485 26 3 1 470 480904971 480904488 0.000000e+00 649.0
8 TraesCS5B01G415100 chr5D 91.213 239 16 5 6175 6412 480854327 480854093 2.900000e-83 320.0
9 TraesCS5B01G415100 chr5D 96.875 32 0 1 5970 6001 499659491 499659461 1.200000e-02 52.8
10 TraesCS5B01G415100 chr6D 76.923 169 28 8 426 590 286784299 286784460 1.150000e-12 86.1
11 TraesCS5B01G415100 chr1B 91.935 62 2 2 529 589 587182039 587182098 4.140000e-12 84.2
12 TraesCS5B01G415100 chr1A 90.164 61 3 2 530 589 532271855 532271913 6.930000e-10 76.8
13 TraesCS5B01G415100 chr7A 97.561 41 1 0 6403 6443 646092490 646092450 3.220000e-08 71.3
14 TraesCS5B01G415100 chr4B 95.349 43 2 0 6401 6443 583472190 583472232 1.160000e-07 69.4
15 TraesCS5B01G415100 chr4B 90.196 51 2 3 6393 6443 514611464 514611511 5.390000e-06 63.9
16 TraesCS5B01G415100 chr4A 93.617 47 2 1 6397 6443 586567388 586567343 1.160000e-07 69.4
17 TraesCS5B01G415100 chr4A 93.333 45 3 0 6399 6443 583133273 583133229 4.170000e-07 67.6
18 TraesCS5B01G415100 chr2A 91.837 49 4 0 6395 6443 114544797 114544749 1.160000e-07 69.4
19 TraesCS5B01G415100 chr6A 93.478 46 1 2 6399 6443 109377476 109377520 4.170000e-07 67.6
20 TraesCS5B01G415100 chr7B 93.182 44 3 0 6400 6443 307638104 307638061 1.500000e-06 65.8
21 TraesCS5B01G415100 chr7B 100.000 28 0 0 5972 5999 711212254 711212281 1.200000e-02 52.8


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

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS5B01G415100 chr5B 589370174 589376616 6442 True 11899.000000 11899 100.000000 1 6443 1 chr5B.!!$R2 6442
1 TraesCS5B01G415100 chr5A 600065635 600071303 5668 True 3985.000000 7498 88.371000 15 5780 2 chr5A.!!$R1 5765
2 TraesCS5B01G415100 chr5D 480854093 480860186 6093 True 2613.666667 5533 90.547333 466 6412 3 chr5D.!!$R3 5946

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
28 29 0.677414 TGCATGCATGACCATGACGT 60.677 50.000 30.64 0.0 44.12 4.34 F
1382 1445 0.322906 AGGGCAAGGTAAAGCAGAGC 60.323 55.000 0.00 0.0 0.00 4.09 F
1543 1610 0.033228 CAGCTATCAGAGGCTTCGGG 59.967 60.000 0.00 0.0 36.59 5.14 F
3435 3661 1.340405 ACCTGATGGAGGATGTGCAAC 60.340 52.381 0.00 0.0 46.33 4.17 F
4507 4765 0.250770 GGGGACACACCTTGTTCTCC 60.251 60.000 0.00 0.0 39.17 3.71 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1543 1610 1.001633 TCTTGACTCACCGGCTTAACC 59.998 52.381 0.00 0.0 0.00 2.85 R
3015 3241 0.247814 CACATTCACGCTCGATTGCC 60.248 55.000 0.00 0.0 0.00 4.52 R
3519 3745 1.414158 TGCGGTGGGAATTTTGGAAA 58.586 45.000 0.00 0.0 0.00 3.13 R
5038 5298 0.105039 GGATGTACCTCCTCGCCTTG 59.895 60.000 9.76 0.0 35.41 3.61 R
5570 5849 0.744771 GCTGGATCCGGGTCTTGAAC 60.745 60.000 22.38 0.0 0.00 3.18 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
28 29 0.677414 TGCATGCATGACCATGACGT 60.677 50.000 30.64 0.00 44.12 4.34
39 40 1.623311 ACCATGACGTGAGATTCCACA 59.377 47.619 0.00 0.00 36.89 4.17
67 68 3.036577 CCATGCCCGCATAAGCAG 58.963 61.111 1.04 0.00 43.38 4.24
74 75 1.102809 CCCGCATAAGCAGGCAATCA 61.103 55.000 0.00 0.00 42.27 2.57
77 78 1.268896 CGCATAAGCAGGCAATCAAGG 60.269 52.381 0.00 0.00 42.27 3.61
89 90 1.639298 AATCAAGGCGCGACAAGAGC 61.639 55.000 17.71 0.00 45.31 4.09
105 106 4.043200 GCTGCCCGCCACTCAAAC 62.043 66.667 0.00 0.00 0.00 2.93
122 123 5.872617 ACTCAAACCGTCGAATGATGAAATA 59.127 36.000 0.00 0.00 32.56 1.40
134 135 7.169813 TCGAATGATGAAATATCCTTTGACGAG 59.830 37.037 0.00 0.00 0.00 4.18
141 142 6.889722 TGAAATATCCTTTGACGAGGGAAAAT 59.110 34.615 0.00 0.00 37.41 1.82
147 148 3.485463 TTGACGAGGGAAAATGTCACT 57.515 42.857 0.00 0.00 45.37 3.41
149 150 4.188247 TGACGAGGGAAAATGTCACTAG 57.812 45.455 0.00 0.00 41.45 2.57
155 156 3.445096 AGGGAAAATGTCACTAGCATTGC 59.555 43.478 0.00 0.00 38.66 3.56
157 158 3.429085 GAAAATGTCACTAGCATTGCCG 58.571 45.455 4.70 0.00 36.75 5.69
160 161 2.401583 TGTCACTAGCATTGCCGATT 57.598 45.000 4.70 0.00 0.00 3.34
165 166 4.273480 GTCACTAGCATTGCCGATTTATGT 59.727 41.667 4.70 0.00 0.00 2.29
170 171 7.535258 CACTAGCATTGCCGATTTATGTAATTC 59.465 37.037 4.70 0.00 0.00 2.17
171 172 6.639632 AGCATTGCCGATTTATGTAATTCT 57.360 33.333 4.70 0.00 0.00 2.40
172 173 7.744087 AGCATTGCCGATTTATGTAATTCTA 57.256 32.000 4.70 0.00 0.00 2.10
181 182 8.141909 CCGATTTATGTAATTCTAGACACTCCA 58.858 37.037 0.00 0.00 0.00 3.86
182 183 9.529325 CGATTTATGTAATTCTAGACACTCCAA 57.471 33.333 0.00 0.00 0.00 3.53
187 188 7.166691 TGTAATTCTAGACACTCCAACCTAC 57.833 40.000 0.00 0.00 0.00 3.18
193 194 4.021102 AGACACTCCAACCTACAAATGG 57.979 45.455 0.00 0.00 35.49 3.16
229 230 8.347004 TCTCAAAATATACATCAACCAAAGCA 57.653 30.769 0.00 0.00 0.00 3.91
230 231 8.243426 TCTCAAAATATACATCAACCAAAGCAC 58.757 33.333 0.00 0.00 0.00 4.40
233 234 7.701539 AAATATACATCAACCAAAGCACTGA 57.298 32.000 0.00 0.00 0.00 3.41
234 235 7.886629 AATATACATCAACCAAAGCACTGAT 57.113 32.000 0.00 0.00 0.00 2.90
235 236 3.928727 ACATCAACCAAAGCACTGATG 57.071 42.857 8.88 8.88 46.88 3.07
248 249 4.220533 GCACTGATGCCATAGAAACATC 57.779 45.455 0.00 0.00 46.97 3.06
289 290 9.887406 ATTAAAAGTAATGTAGTTCAAACGTGG 57.113 29.630 0.00 0.00 0.00 4.94
318 319 8.438513 CAGAAGAAAGTGTAGTAACATGTGATG 58.561 37.037 0.00 0.00 38.08 3.07
328 329 5.762045 AGTAACATGTGATGCAGTTGAAAC 58.238 37.500 0.00 0.00 0.00 2.78
330 331 3.968649 ACATGTGATGCAGTTGAAACAC 58.031 40.909 0.00 0.00 0.00 3.32
331 332 3.380954 ACATGTGATGCAGTTGAAACACA 59.619 39.130 5.76 5.76 41.28 3.72
332 333 3.419264 TGTGATGCAGTTGAAACACAC 57.581 42.857 0.00 0.00 34.19 3.82
333 334 2.223226 TGTGATGCAGTTGAAACACACG 60.223 45.455 0.00 0.00 34.19 4.49
335 336 2.877786 TGATGCAGTTGAAACACACGAT 59.122 40.909 0.00 0.00 0.00 3.73
336 337 2.753989 TGCAGTTGAAACACACGATG 57.246 45.000 0.00 0.00 0.00 3.84
337 338 1.268488 TGCAGTTGAAACACACGATGC 60.268 47.619 0.00 0.00 34.28 3.91
338 339 1.268488 GCAGTTGAAACACACGATGCA 60.268 47.619 0.00 0.00 34.04 3.96
340 341 3.631144 CAGTTGAAACACACGATGCAAT 58.369 40.909 0.00 0.00 0.00 3.56
384 400 9.528018 AAAAATGTGTAGTTAAAACATGTGAGG 57.472 29.630 0.00 0.00 34.82 3.86
385 401 6.817765 ATGTGTAGTTAAAACATGTGAGGG 57.182 37.500 0.00 0.00 33.37 4.30
404 420 8.160765 TGTGAGGGAGTTGATAAAATGAAGTTA 58.839 33.333 0.00 0.00 0.00 2.24
410 426 4.868450 TGATAAAATGAAGTTACCGCCG 57.132 40.909 0.00 0.00 0.00 6.46
414 430 2.005971 AATGAAGTTACCGCCGAGAC 57.994 50.000 0.00 0.00 0.00 3.36
435 451 0.750850 GAGGTATAGAGGCGGCAACA 59.249 55.000 13.08 0.00 0.00 3.33
641 663 6.564709 AAAATTGTAAAACGGTACTCCCTC 57.435 37.500 0.00 0.00 0.00 4.30
642 664 4.895668 ATTGTAAAACGGTACTCCCTCA 57.104 40.909 0.00 0.00 0.00 3.86
678 702 8.578151 AGTTTATCCCTCGAATAGATGTCTAAC 58.422 37.037 0.00 0.00 31.39 2.34
684 708 5.980116 CCTCGAATAGATGTCTAACACCAAG 59.020 44.000 0.00 0.00 31.39 3.61
708 732 2.241176 TGGGACAACCTTGAGACAAACT 59.759 45.455 0.00 0.00 41.11 2.66
709 733 2.618709 GGGACAACCTTGAGACAAACTG 59.381 50.000 0.00 0.00 35.85 3.16
718 742 4.440112 CCTTGAGACAAACTGTTTTGGACC 60.440 45.833 2.41 0.00 45.65 4.46
740 764 4.970611 CCGAGTGAGTAATATTGAGTGACG 59.029 45.833 0.00 0.00 0.00 4.35
741 765 5.448768 CCGAGTGAGTAATATTGAGTGACGT 60.449 44.000 0.00 0.00 0.00 4.34
858 907 1.603455 CAACCTTCGCCACCACCAT 60.603 57.895 0.00 0.00 0.00 3.55
1005 1056 1.410882 GGAGAGGAAGGTTCGATGGAG 59.589 57.143 0.00 0.00 0.00 3.86
1098 1149 1.069765 CCGGAGCATCTACGCCAAT 59.930 57.895 0.00 0.00 36.34 3.16
1253 1314 1.294659 GAGCGCTGAAGGTGTTGAGG 61.295 60.000 18.48 0.00 0.00 3.86
1310 1373 1.736645 CGTACGTTCCTGCAGTGGG 60.737 63.158 13.81 0.00 0.00 4.61
1382 1445 0.322906 AGGGCAAGGTAAAGCAGAGC 60.323 55.000 0.00 0.00 0.00 4.09
1477 1544 5.045942 TGAAATTCAGGCTGGTGACTATGTA 60.046 40.000 15.73 0.00 0.00 2.29
1543 1610 0.033228 CAGCTATCAGAGGCTTCGGG 59.967 60.000 0.00 0.00 36.59 5.14
1589 1656 1.796459 GCTCTGTCTTTAAACGCCGAA 59.204 47.619 0.00 0.00 0.00 4.30
1590 1657 2.222445 GCTCTGTCTTTAAACGCCGAAA 59.778 45.455 0.00 0.00 0.00 3.46
1595 1662 5.910723 TCTGTCTTTAAACGCCGAAAAATTC 59.089 36.000 0.00 0.00 0.00 2.17
1600 1667 6.757478 TCTTTAAACGCCGAAAAATTCCTTTT 59.243 30.769 0.00 0.00 40.03 2.27
1605 1672 4.233789 CGCCGAAAAATTCCTTTTGATCA 58.766 39.130 0.00 0.00 37.36 2.92
1608 1675 5.446340 GCCGAAAAATTCCTTTTGATCATGC 60.446 40.000 0.00 0.00 37.36 4.06
1609 1676 5.638657 CCGAAAAATTCCTTTTGATCATGCA 59.361 36.000 0.00 0.00 37.36 3.96
1610 1677 6.147492 CCGAAAAATTCCTTTTGATCATGCAA 59.853 34.615 0.00 0.00 37.36 4.08
1615 1682 8.857694 AAATTCCTTTTGATCATGCAAAATCT 57.142 26.923 10.45 0.00 44.14 2.40
1736 1804 8.021973 GCAGGTGAGAATTCATGATATTCATTC 58.978 37.037 21.90 16.19 34.28 2.67
1737 1805 9.063615 CAGGTGAGAATTCATGATATTCATTCA 57.936 33.333 21.90 17.23 34.28 2.57
1762 1840 5.705609 TTAACAAGGCTTCAGGAACATTC 57.294 39.130 0.00 0.00 0.00 2.67
1766 1844 4.202461 ACAAGGCTTCAGGAACATTCTGTA 60.202 41.667 0.00 0.00 34.15 2.74
1785 1864 8.853077 TTCTGTAAACTGATGTGAGATTTCAT 57.147 30.769 0.00 0.00 35.39 2.57
1927 2006 2.950433 GTGAATGCACAAGGGTTCATG 58.050 47.619 0.00 0.00 44.51 3.07
1928 2007 2.297033 GTGAATGCACAAGGGTTCATGT 59.703 45.455 0.00 0.00 44.51 3.21
1929 2008 2.557924 TGAATGCACAAGGGTTCATGTC 59.442 45.455 0.00 0.00 31.09 3.06
1964 2043 9.875691 GAGCACTTTTTATTTGGGAGAATAATT 57.124 29.630 0.00 0.00 33.01 1.40
2273 2499 4.142249 TGCGTGGCGTCATATATATTAGCT 60.142 41.667 0.00 0.00 0.00 3.32
2282 2508 7.923344 GCGTCATATATATTAGCTTGTCTCCAT 59.077 37.037 0.00 0.00 0.00 3.41
2293 2519 5.749462 AGCTTGTCTCCATTAAATGCTACT 58.251 37.500 0.00 0.00 0.00 2.57
2294 2520 5.587844 AGCTTGTCTCCATTAAATGCTACTG 59.412 40.000 0.00 0.00 0.00 2.74
2295 2521 5.355350 GCTTGTCTCCATTAAATGCTACTGT 59.645 40.000 0.00 0.00 0.00 3.55
2296 2522 6.676456 GCTTGTCTCCATTAAATGCTACTGTG 60.676 42.308 0.00 0.00 0.00 3.66
2297 2523 4.635765 TGTCTCCATTAAATGCTACTGTGC 59.364 41.667 0.00 0.00 0.00 4.57
2356 2582 6.995091 AGATACAATAAAAGCTAGCCCTGAAG 59.005 38.462 12.13 0.00 0.00 3.02
2537 2763 3.045634 TCCGGACATCAACTATTCCCAT 58.954 45.455 0.00 0.00 0.00 4.00
2542 2768 6.265577 CGGACATCAACTATTCCCATTTTTC 58.734 40.000 0.00 0.00 0.00 2.29
2574 2800 7.851822 AATTTCTTACTTTATGTGTGCAACG 57.148 32.000 0.00 0.00 42.39 4.10
2613 2839 4.025040 TGGAGATGTGACAATTGAGCTT 57.975 40.909 13.59 0.03 0.00 3.74
2758 2984 5.304686 TGCTCTTTTAACAGGGAGAAGAA 57.695 39.130 0.00 0.00 0.00 2.52
2760 2986 5.531287 TGCTCTTTTAACAGGGAGAAGAAAC 59.469 40.000 0.00 0.00 0.00 2.78
2762 2988 6.935208 GCTCTTTTAACAGGGAGAAGAAACTA 59.065 38.462 0.00 0.00 0.00 2.24
2795 3021 7.218614 TCCTAAGAAACAAAAGGACGACATTA 58.781 34.615 0.00 0.00 33.18 1.90
2809 3035 7.952671 AGGACGACATTAGTACAATCATGTAT 58.047 34.615 0.00 0.00 43.60 2.29
2965 3191 3.849527 AGAATTTCAGTGGGGCTTTTCT 58.150 40.909 0.00 0.00 0.00 2.52
2993 3219 3.253432 CAGGTCTCCCTTTTTCTTTTCGG 59.747 47.826 0.00 0.00 39.89 4.30
3014 3240 9.438228 TTTCGGAAAAGGTTTAAACAAAAGAAT 57.562 25.926 19.57 0.00 0.00 2.40
3015 3241 8.413899 TCGGAAAAGGTTTAAACAAAAGAATG 57.586 30.769 19.57 3.77 0.00 2.67
3026 3252 2.179589 CAAAAGAATGGCAATCGAGCG 58.820 47.619 0.00 0.00 34.64 5.03
3126 3352 2.811431 GTGGTCATGGTTTGTTCATCGA 59.189 45.455 0.00 0.00 0.00 3.59
3275 3501 6.103330 TCACATTTTCGATCAAGTAATCGGA 58.897 36.000 6.46 0.00 46.59 4.55
3375 3601 2.210116 TGTCGCTTTTCTGTGACTTCC 58.790 47.619 9.16 0.00 44.87 3.46
3435 3661 1.340405 ACCTGATGGAGGATGTGCAAC 60.340 52.381 0.00 0.00 46.33 4.17
3512 3738 5.360714 CACAGGTATTATGCAAACCTCCATT 59.639 40.000 9.68 0.00 41.75 3.16
3519 3745 9.816354 GTATTATGCAAACCTCCATTATTGTTT 57.184 29.630 0.00 0.00 0.00 2.83
3537 3763 2.535012 TTTTCCAAAATTCCCACCGC 57.465 45.000 0.00 0.00 0.00 5.68
3541 3767 1.974236 TCCAAAATTCCCACCGCATTT 59.026 42.857 0.00 0.00 0.00 2.32
3545 3771 2.453983 AATTCCCACCGCATTTTGTG 57.546 45.000 0.00 0.00 0.00 3.33
3569 3795 7.663081 GTGCTCCATCATAATTGAGGAATCTTA 59.337 37.037 0.00 0.00 35.69 2.10
3611 3837 2.503895 AAATTCAGTCTGGAGGGCTG 57.496 50.000 0.00 0.00 0.00 4.85
3905 4133 9.821662 AGCAAAGTACGTAAAATATTTGAAGTC 57.178 29.630 7.33 1.63 31.01 3.01
4002 4230 3.272334 CTTGGAGGCCGCATACGC 61.272 66.667 9.31 0.00 38.22 4.42
4014 4242 1.363744 GCATACGCCTCATGCTATCC 58.636 55.000 4.93 0.00 44.35 2.59
4077 4305 0.764890 TTACCAGCTGCAGTGTCCTT 59.235 50.000 16.64 0.00 0.00 3.36
4099 4327 4.030216 TGCACAAGGATATGGTGAGACTA 58.970 43.478 0.00 0.00 34.52 2.59
4138 4366 5.586243 ACAACTGTGCTCATCATAACCATAC 59.414 40.000 0.00 0.00 0.00 2.39
4140 4368 5.363101 ACTGTGCTCATCATAACCATACTG 58.637 41.667 0.00 0.00 0.00 2.74
4173 4401 3.891366 CCTTGGTTCTTTGGTCATGACTT 59.109 43.478 24.50 0.00 0.00 3.01
4180 4408 4.136796 TCTTTGGTCATGACTTGGTTCAG 58.863 43.478 24.50 11.32 0.00 3.02
4181 4409 1.896220 TGGTCATGACTTGGTTCAGC 58.104 50.000 24.50 5.96 0.00 4.26
4182 4410 1.142667 TGGTCATGACTTGGTTCAGCA 59.857 47.619 24.50 8.50 0.00 4.41
4183 4411 2.224843 TGGTCATGACTTGGTTCAGCAT 60.225 45.455 24.50 0.00 0.00 3.79
4190 4426 6.939730 TCATGACTTGGTTCAGCATTTAACTA 59.060 34.615 0.00 0.00 0.00 2.24
4206 4442 8.913656 GCATTTAACTAGTTATGGACTACGATC 58.086 37.037 15.92 0.00 39.86 3.69
4216 4452 7.439356 AGTTATGGACTACGATCATGTGAAATG 59.561 37.037 0.00 0.00 36.65 2.32
4220 4456 6.258507 TGGACTACGATCATGTGAAATGAATG 59.741 38.462 0.00 0.00 0.00 2.67
4228 4464 8.177013 CGATCATGTGAAATGAATGTCAGTAAA 58.823 33.333 0.00 0.00 0.00 2.01
4276 4526 9.563748 CTAGTATCCTAGCAGTCTAGTTACTTT 57.436 37.037 12.94 0.98 40.51 2.66
4310 4568 4.593597 ATGATAAACTGTTAACCGTGCG 57.406 40.909 3.24 0.00 0.00 5.34
4372 4630 0.497265 CGTCGATCGCCAACGTTATC 59.503 55.000 16.88 0.00 41.18 1.75
4507 4765 0.250770 GGGGACACACCTTGTTCTCC 60.251 60.000 0.00 0.00 39.17 3.71
4552 4810 3.821600 TCACAGAGGAAGTGTACTCAGAC 59.178 47.826 0.00 0.00 38.16 3.51
4555 4813 1.473278 GAGGAAGTGTACTCAGACGGG 59.527 57.143 0.00 0.00 33.95 5.28
4601 4859 4.920640 TCTCTTCCATTCCTAAGCGTAG 57.079 45.455 0.00 0.00 0.00 3.51
4686 4946 0.986019 ATATCGGGGAGTGGCAACCA 60.986 55.000 12.78 0.00 0.00 3.67
4780 5040 0.392461 GGTCCTGGAAAGCGCATACA 60.392 55.000 11.47 3.65 0.00 2.29
4800 5060 1.488957 GCAGTCTCAACTCGTTGCG 59.511 57.895 4.95 0.00 40.24 4.85
4899 5159 2.524306 ACTGACCAAGAGTCTCTCCTG 58.476 52.381 1.96 0.00 46.46 3.86
5038 5298 1.446907 CTGAGTTGTGCAGTGATCCC 58.553 55.000 0.00 0.00 0.00 3.85
5044 5304 2.046023 TGCAGTGATCCCAAGGCG 60.046 61.111 0.00 0.00 0.00 5.52
5080 5340 1.672881 GATGAGCTGAATCAAACCGGG 59.327 52.381 6.32 0.00 31.76 5.73
5098 5358 0.605083 GGAAGAAACTCGGGGTACGT 59.395 55.000 0.00 0.00 44.69 3.57
5100 5360 0.242017 AAGAAACTCGGGGTACGTCG 59.758 55.000 0.00 0.00 44.69 5.12
5146 5406 8.992835 TTAGCAAGCTATGATATGTATCTGTG 57.007 34.615 2.16 0.00 33.88 3.66
5155 5415 6.638096 TGATATGTATCTGTGCCCATTTTG 57.362 37.500 2.08 0.00 33.88 2.44
5157 5417 7.286313 TGATATGTATCTGTGCCCATTTTGTA 58.714 34.615 2.08 0.00 33.88 2.41
5159 5419 8.710749 ATATGTATCTGTGCCCATTTTGTATT 57.289 30.769 0.00 0.00 0.00 1.89
5180 5440 4.686839 TCCATCATAAGCTACGATCTCG 57.313 45.455 0.00 0.00 46.33 4.04
5236 5496 4.021925 GCCGTTCACCTGGAGCCT 62.022 66.667 0.00 0.00 0.00 4.58
5346 5606 4.151258 ACAAACTTGATCATGCTCGTTG 57.849 40.909 8.45 9.82 0.00 4.10
5361 5622 3.488553 GCTCGTTGCAGTTAGTGGTTTTT 60.489 43.478 0.00 0.00 42.31 1.94
5372 5633 5.066505 AGTTAGTGGTTTTTGCTCACAAGAG 59.933 40.000 0.00 0.00 44.96 2.85
5412 5673 2.515926 ATCGCGTTGATCAGCTGTAT 57.484 45.000 14.67 5.98 28.49 2.29
5431 5692 3.803186 ATAAGGATGCCAAGATGGGAG 57.197 47.619 0.00 0.00 42.59 4.30
5550 5829 4.148825 GGCTCGAGGCGGTGACAT 62.149 66.667 24.18 0.00 42.94 3.06
5552 5831 2.167861 GCTCGAGGCGGTGACATTC 61.168 63.158 15.58 0.00 0.00 2.67
5570 5849 4.142447 ACATTCTGTACCACTACTACTGCG 60.142 45.833 0.00 0.00 0.00 5.18
5780 6065 2.099098 ACAAAGTTGCCGGTTTTGAGAG 59.901 45.455 21.31 4.11 36.09 3.20
5846 6131 5.879237 TGGTCACGTAGTATAAAAGTACCG 58.121 41.667 0.00 0.00 41.61 4.02
5882 6167 6.609237 ATGTGACATTGGAAGACATATTCG 57.391 37.500 0.00 0.00 0.00 3.34
5994 6287 8.918961 AAATTGTTCAACGTGTATCTGAAAAA 57.081 26.923 5.28 5.28 32.33 1.94
5995 6288 9.528018 AAATTGTTCAACGTGTATCTGAAAAAT 57.472 25.926 8.78 8.78 38.21 1.82
5996 6289 7.906611 TTGTTCAACGTGTATCTGAAAAATG 57.093 32.000 1.37 0.00 31.21 2.32
6002 6295 9.440784 TCAACGTGTATCTGAAAAATGTTTAAC 57.559 29.630 0.00 0.00 0.00 2.01
6003 6296 9.227490 CAACGTGTATCTGAAAAATGTTTAACA 57.773 29.630 0.00 0.00 0.00 2.41
6004 6297 8.776680 ACGTGTATCTGAAAAATGTTTAACAC 57.223 30.769 0.00 0.00 0.00 3.32
6005 6298 7.914092 CGTGTATCTGAAAAATGTTTAACACG 58.086 34.615 0.00 13.58 46.64 4.49
6006 6299 7.584847 CGTGTATCTGAAAAATGTTTAACACGT 59.415 33.333 16.61 0.00 46.63 4.49
6007 6300 9.866936 GTGTATCTGAAAAATGTTTAACACGTA 57.133 29.630 0.00 0.00 0.00 3.57
6144 6442 7.973601 AGAAATGTGTTGAACAAATGGAAAAC 58.026 30.769 1.02 0.00 43.61 2.43
6148 6446 7.126726 TGTGTTGAACAAATGGAAAACAAAG 57.873 32.000 0.00 0.00 35.24 2.77
6157 6455 9.454859 AACAAATGGAAAACAAAGAAAACCATA 57.545 25.926 0.00 0.00 35.93 2.74
6167 6465 9.936759 AAACAAAGAAAACCATAGAAGAAAACA 57.063 25.926 0.00 0.00 0.00 2.83
6168 6466 9.586435 AACAAAGAAAACCATAGAAGAAAACAG 57.414 29.630 0.00 0.00 0.00 3.16
6169 6467 8.197439 ACAAAGAAAACCATAGAAGAAAACAGG 58.803 33.333 0.00 0.00 0.00 4.00
6170 6468 7.898014 AAGAAAACCATAGAAGAAAACAGGT 57.102 32.000 0.00 0.00 0.00 4.00
6185 6523 7.518188 AGAAAACAGGTGAAGAAATAAGAGGA 58.482 34.615 0.00 0.00 0.00 3.71
6196 6542 9.696917 TGAAGAAATAAGAGGAAAAATTTGAGC 57.303 29.630 0.00 0.00 0.00 4.26
6203 6549 4.082125 GAGGAAAAATTTGAGCCAGAGGA 58.918 43.478 0.00 0.00 0.00 3.71
6209 6555 1.644509 TTTGAGCCAGAGGAGCTACA 58.355 50.000 0.00 0.00 41.75 2.74
6220 6566 2.365941 GAGGAGCTACAGTATTGGGACC 59.634 54.545 0.00 0.00 0.00 4.46
6221 6567 2.022918 AGGAGCTACAGTATTGGGACCT 60.023 50.000 0.00 0.00 0.00 3.85
6256 6602 0.608640 CAGGAGGCGTGAGTTAGGTT 59.391 55.000 0.00 0.00 0.00 3.50
6282 6628 3.125573 GGCGAGAAAAGGCCCGAC 61.126 66.667 0.00 0.00 43.64 4.79
6283 6629 3.488090 GCGAGAAAAGGCCCGACG 61.488 66.667 0.00 0.00 0.00 5.12
6284 6630 2.048503 CGAGAAAAGGCCCGACGT 60.049 61.111 0.00 0.00 0.00 4.34
6285 6631 2.092882 CGAGAAAAGGCCCGACGTC 61.093 63.158 5.18 5.18 0.00 4.34
6286 6632 1.005394 GAGAAAAGGCCCGACGTCA 60.005 57.895 17.16 0.00 0.00 4.35
6287 6633 0.391263 GAGAAAAGGCCCGACGTCAT 60.391 55.000 17.16 0.00 0.00 3.06
6336 6682 4.627035 GCTTTTGCAATGTGGAAGATAACC 59.373 41.667 11.17 0.00 46.58 2.85
6348 6694 4.276431 TGGAAGATAACCGTGTGTTTTTCC 59.724 41.667 0.00 0.00 39.13 3.13
6350 6696 3.469739 AGATAACCGTGTGTTTTTCCGT 58.530 40.909 0.00 0.00 38.42 4.69
6361 6707 6.251801 CGTGTGTTTTTCCGTGAAACTAAAAT 59.748 34.615 6.95 0.00 37.75 1.82
6416 6762 9.845214 ATTTCTTACATATATCTAGACCCCTGT 57.155 33.333 0.00 0.00 0.00 4.00
6417 6763 9.670442 TTTCTTACATATATCTAGACCCCTGTT 57.330 33.333 0.00 0.00 0.00 3.16
6418 6764 8.880991 TCTTACATATATCTAGACCCCTGTTC 57.119 38.462 0.00 0.00 0.00 3.18
6419 6765 8.453681 TCTTACATATATCTAGACCCCTGTTCA 58.546 37.037 0.00 0.00 0.00 3.18
6420 6766 9.090103 CTTACATATATCTAGACCCCTGTTCAA 57.910 37.037 0.00 0.00 0.00 2.69
6421 6767 7.546250 ACATATATCTAGACCCCTGTTCAAG 57.454 40.000 0.00 0.00 0.00 3.02
6422 6768 7.306013 ACATATATCTAGACCCCTGTTCAAGA 58.694 38.462 0.00 0.00 0.00 3.02
6423 6769 7.789831 ACATATATCTAGACCCCTGTTCAAGAA 59.210 37.037 0.00 0.00 0.00 2.52
6424 6770 8.820831 CATATATCTAGACCCCTGTTCAAGAAT 58.179 37.037 0.00 0.00 0.00 2.40
6425 6771 7.698163 ATATCTAGACCCCTGTTCAAGAATT 57.302 36.000 0.00 0.00 0.00 2.17
6426 6772 5.422214 TCTAGACCCCTGTTCAAGAATTC 57.578 43.478 0.00 0.00 0.00 2.17
6427 6773 4.844085 TCTAGACCCCTGTTCAAGAATTCA 59.156 41.667 8.44 0.00 0.00 2.57
6428 6774 4.664688 AGACCCCTGTTCAAGAATTCAT 57.335 40.909 8.44 0.00 0.00 2.57
6429 6775 4.593956 AGACCCCTGTTCAAGAATTCATC 58.406 43.478 8.44 0.00 0.00 2.92
6430 6776 3.696548 GACCCCTGTTCAAGAATTCATCC 59.303 47.826 8.44 0.00 0.00 3.51
6431 6777 2.684881 CCCCTGTTCAAGAATTCATCCG 59.315 50.000 8.44 0.00 0.00 4.18
6432 6778 3.609853 CCCTGTTCAAGAATTCATCCGA 58.390 45.455 8.44 0.00 0.00 4.55
6433 6779 4.202441 CCCTGTTCAAGAATTCATCCGAT 58.798 43.478 8.44 0.00 0.00 4.18
6434 6780 4.641989 CCCTGTTCAAGAATTCATCCGATT 59.358 41.667 8.44 0.00 0.00 3.34
6435 6781 5.822519 CCCTGTTCAAGAATTCATCCGATTA 59.177 40.000 8.44 0.00 0.00 1.75
6436 6782 6.318648 CCCTGTTCAAGAATTCATCCGATTAA 59.681 38.462 8.44 0.00 0.00 1.40
6437 6783 7.189512 CCTGTTCAAGAATTCATCCGATTAAC 58.810 38.462 8.44 1.74 0.00 2.01
6438 6784 7.083875 TGTTCAAGAATTCATCCGATTAACC 57.916 36.000 8.44 0.00 0.00 2.85
6439 6785 6.657117 TGTTCAAGAATTCATCCGATTAACCA 59.343 34.615 8.44 0.00 0.00 3.67
6440 6786 6.925610 TCAAGAATTCATCCGATTAACCAG 57.074 37.500 8.44 0.00 0.00 4.00
6441 6787 6.414732 TCAAGAATTCATCCGATTAACCAGT 58.585 36.000 8.44 0.00 0.00 4.00
6442 6788 6.884295 TCAAGAATTCATCCGATTAACCAGTT 59.116 34.615 8.44 0.00 0.00 3.16
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
1 2 1.535896 GGTCATGCATGCATCTAGCTG 59.464 52.381 30.07 19.30 45.94 4.24
2 3 1.142262 TGGTCATGCATGCATCTAGCT 59.858 47.619 30.07 6.83 45.94 3.32
3 4 1.601166 TGGTCATGCATGCATCTAGC 58.399 50.000 30.07 26.82 45.96 3.42
4 5 3.188667 GTCATGGTCATGCATGCATCTAG 59.811 47.826 30.07 19.04 38.65 2.43
5 6 3.143728 GTCATGGTCATGCATGCATCTA 58.856 45.455 30.07 18.02 38.65 1.98
9 10 0.677414 ACGTCATGGTCATGCATGCA 60.677 50.000 25.04 25.04 38.65 3.96
10 11 0.248336 CACGTCATGGTCATGCATGC 60.248 55.000 22.25 11.82 38.65 4.06
11 12 1.329599 CTCACGTCATGGTCATGCATG 59.670 52.381 21.07 21.07 38.65 4.06
12 13 1.207811 TCTCACGTCATGGTCATGCAT 59.792 47.619 6.10 0.00 38.65 3.96
13 14 0.607620 TCTCACGTCATGGTCATGCA 59.392 50.000 6.10 0.00 38.65 3.96
17 18 1.899142 TGGAATCTCACGTCATGGTCA 59.101 47.619 0.00 0.00 0.00 4.02
28 29 3.678289 CCATCACTTGTGTGGAATCTCA 58.322 45.455 13.33 0.00 43.94 3.27
49 50 3.203546 CTGCTTATGCGGGCATGGC 62.204 63.158 16.03 11.56 43.34 4.40
67 68 2.855728 CTTGTCGCGCCTTGATTGCC 62.856 60.000 0.00 0.00 0.00 4.52
74 75 2.740055 CAGCTCTTGTCGCGCCTT 60.740 61.111 0.00 0.00 0.00 4.35
89 90 3.365265 GGTTTGAGTGGCGGGCAG 61.365 66.667 3.75 0.00 0.00 4.85
96 97 1.790755 TCATTCGACGGTTTGAGTGG 58.209 50.000 0.00 0.00 0.00 4.00
105 106 6.202762 TCAAAGGATATTTCATCATTCGACGG 59.797 38.462 0.00 0.00 0.00 4.79
122 123 4.010349 GACATTTTCCCTCGTCAAAGGAT 58.990 43.478 0.00 0.00 38.87 3.24
134 135 3.429410 GGCAATGCTAGTGACATTTTCCC 60.429 47.826 4.82 0.00 35.58 3.97
141 142 2.401583 AATCGGCAATGCTAGTGACA 57.598 45.000 4.82 0.00 0.00 3.58
147 148 7.744087 AGAATTACATAAATCGGCAATGCTA 57.256 32.000 4.82 0.00 0.00 3.49
149 150 7.746475 GTCTAGAATTACATAAATCGGCAATGC 59.254 37.037 0.00 0.00 0.00 3.56
155 156 8.141909 TGGAGTGTCTAGAATTACATAAATCGG 58.858 37.037 0.00 0.00 0.00 4.18
160 161 8.375493 AGGTTGGAGTGTCTAGAATTACATAA 57.625 34.615 0.00 0.00 0.00 1.90
165 166 7.786046 TTGTAGGTTGGAGTGTCTAGAATTA 57.214 36.000 0.00 0.00 0.00 1.40
170 171 5.046591 TCCATTTGTAGGTTGGAGTGTCTAG 60.047 44.000 0.00 0.00 34.65 2.43
171 172 4.841813 TCCATTTGTAGGTTGGAGTGTCTA 59.158 41.667 0.00 0.00 34.65 2.59
172 173 3.650942 TCCATTTGTAGGTTGGAGTGTCT 59.349 43.478 0.00 0.00 34.65 3.41
205 206 8.246180 AGTGCTTTGGTTGATGTATATTTTGAG 58.754 33.333 0.00 0.00 0.00 3.02
228 229 5.823209 TTGATGTTTCTATGGCATCAGTG 57.177 39.130 1.65 0.00 46.20 3.66
229 230 5.711506 TGTTTGATGTTTCTATGGCATCAGT 59.288 36.000 1.65 0.00 46.20 3.41
230 231 6.198650 TGTTTGATGTTTCTATGGCATCAG 57.801 37.500 1.65 0.24 46.20 2.90
233 234 6.153170 TCACATGTTTGATGTTTCTATGGCAT 59.847 34.615 4.88 4.88 0.00 4.40
234 235 5.476254 TCACATGTTTGATGTTTCTATGGCA 59.524 36.000 0.00 0.00 0.00 4.92
235 236 5.953183 TCACATGTTTGATGTTTCTATGGC 58.047 37.500 0.00 0.00 0.00 4.40
246 247 8.836268 ACTTTTAATTGCATCACATGTTTGAT 57.164 26.923 9.26 1.79 36.62 2.57
247 248 9.755804 TTACTTTTAATTGCATCACATGTTTGA 57.244 25.926 9.26 0.00 0.00 2.69
270 271 4.024725 TGTGCCACGTTTGAACTACATTAC 60.025 41.667 0.00 0.00 0.00 1.89
287 288 3.838244 ACTACACTTTCTTCTGTGCCA 57.162 42.857 0.00 0.00 37.68 4.92
288 289 5.054477 TGTTACTACACTTTCTTCTGTGCC 58.946 41.667 0.00 0.00 37.68 5.01
289 290 6.202954 ACATGTTACTACACTTTCTTCTGTGC 59.797 38.462 0.00 0.00 37.03 4.57
318 319 1.268488 TGCATCGTGTGTTTCAACTGC 60.268 47.619 0.00 0.00 0.00 4.40
366 382 6.708949 TCAACTCCCTCACATGTTTTAACTAC 59.291 38.462 0.00 0.00 0.00 2.73
367 383 6.833041 TCAACTCCCTCACATGTTTTAACTA 58.167 36.000 0.00 0.00 0.00 2.24
380 396 7.610305 GGTAACTTCATTTTATCAACTCCCTCA 59.390 37.037 0.00 0.00 0.00 3.86
384 400 6.255950 GCGGTAACTTCATTTTATCAACTCC 58.744 40.000 0.00 0.00 0.00 3.85
385 401 6.255950 GGCGGTAACTTCATTTTATCAACTC 58.744 40.000 0.00 0.00 0.00 3.01
410 426 1.158434 CGCCTCTATACCTCCGTCTC 58.842 60.000 0.00 0.00 0.00 3.36
414 430 1.461091 TTGCCGCCTCTATACCTCCG 61.461 60.000 0.00 0.00 0.00 4.63
421 437 2.200373 AAACTTGTTGCCGCCTCTAT 57.800 45.000 0.00 0.00 0.00 1.98
422 438 1.606668 CAAAACTTGTTGCCGCCTCTA 59.393 47.619 0.00 0.00 0.00 2.43
453 469 2.227089 CTCCTATATCCACCGGCGGC 62.227 65.000 28.71 0.00 0.00 6.53
466 482 2.696187 GCCGAAGTCTTCTTCCTCCTAT 59.304 50.000 10.81 0.00 45.02 2.57
514 530 3.512033 AAAACACGCTTGCCAAAACTA 57.488 38.095 0.00 0.00 0.00 2.24
540 556 9.788889 AAGGCCATATATTAAGTAGTACAAACC 57.211 33.333 5.01 0.00 0.00 3.27
594 610 4.410492 TTCTCTTCTTCAATCGCTTTGC 57.590 40.909 0.00 0.00 35.16 3.68
595 611 8.955061 TTTATTTCTCTTCTTCAATCGCTTTG 57.045 30.769 0.00 0.00 36.61 2.77
598 614 9.565213 CAATTTTATTTCTCTTCTTCAATCGCT 57.435 29.630 0.00 0.00 0.00 4.93
613 635 9.345517 GGGAGTACCGTTTTACAATTTTATTTC 57.654 33.333 0.00 0.00 36.97 2.17
657 679 5.244178 GGTGTTAGACATCTATTCGAGGGAT 59.756 44.000 0.00 0.00 0.00 3.85
659 681 4.341235 TGGTGTTAGACATCTATTCGAGGG 59.659 45.833 0.00 0.00 28.61 4.30
664 686 7.752695 CCAAACTTGGTGTTAGACATCTATTC 58.247 38.462 0.00 0.00 43.43 1.75
684 708 2.650322 TGTCTCAAGGTTGTCCCAAAC 58.350 47.619 0.00 0.00 34.66 2.93
706 730 1.485066 ACTCACTCGGTCCAAAACAGT 59.515 47.619 0.00 0.00 0.00 3.55
708 732 3.823281 TTACTCACTCGGTCCAAAACA 57.177 42.857 0.00 0.00 0.00 2.83
709 733 6.592607 TCAATATTACTCACTCGGTCCAAAAC 59.407 38.462 0.00 0.00 0.00 2.43
718 742 5.570344 ACGTCACTCAATATTACTCACTCG 58.430 41.667 0.00 0.00 0.00 4.18
740 764 9.884465 CAAATAAATTAGGGATGATTCGAAGAC 57.116 33.333 3.35 0.93 34.32 3.01
741 765 8.567948 GCAAATAAATTAGGGATGATTCGAAGA 58.432 33.333 3.35 0.00 0.00 2.87
858 907 2.224499 TGCTCAGATGTGTGGCAGTTAA 60.224 45.455 8.56 0.00 32.67 2.01
1186 1237 6.259608 CAGAATGCTTAGGAATGGAGTGTAAG 59.740 42.308 0.00 0.00 0.00 2.34
1310 1373 3.055094 TCTTGGGATACTTCTTGACTGCC 60.055 47.826 0.00 0.00 0.00 4.85
1382 1445 7.274447 ACCATTTTGCCCATTATACTGAATTG 58.726 34.615 0.00 0.00 0.00 2.32
1477 1544 3.568007 ACACTTGTTCATACGTTTGCCAT 59.432 39.130 0.00 0.00 0.00 4.40
1543 1610 1.001633 TCTTGACTCACCGGCTTAACC 59.998 52.381 0.00 0.00 0.00 2.85
1589 1656 9.292195 AGATTTTGCATGATCAAAAGGAATTTT 57.708 25.926 14.06 0.14 45.55 1.82
1590 1657 8.857694 AGATTTTGCATGATCAAAAGGAATTT 57.142 26.923 14.06 0.69 45.55 1.82
1595 1662 8.139350 TGCTATAGATTTTGCATGATCAAAAGG 58.861 33.333 14.06 0.00 45.55 3.11
1600 1667 8.512138 CATTCTGCTATAGATTTTGCATGATCA 58.488 33.333 3.21 0.00 34.80 2.92
1605 1672 8.472413 ACAAACATTCTGCTATAGATTTTGCAT 58.528 29.630 3.21 0.00 35.49 3.96
1615 1682 9.448438 ACAATGTCTAACAAACATTCTGCTATA 57.552 29.630 0.00 0.00 43.62 1.31
1736 1804 5.841810 TGTTCCTGAAGCCTTGTTAAAATG 58.158 37.500 0.00 0.00 0.00 2.32
1737 1805 6.670695 ATGTTCCTGAAGCCTTGTTAAAAT 57.329 33.333 0.00 0.00 0.00 1.82
1742 1810 3.571401 CAGAATGTTCCTGAAGCCTTGTT 59.429 43.478 0.00 0.00 33.65 2.83
1744 1812 3.844577 CAGAATGTTCCTGAAGCCTTG 57.155 47.619 0.00 0.00 33.65 3.61
1762 1840 9.903682 AAAATGAAATCTCACATCAGTTTACAG 57.096 29.630 0.00 0.00 38.94 2.74
1766 1844 9.991906 AATCAAAATGAAATCTCACATCAGTTT 57.008 25.926 0.00 0.00 40.67 2.66
1785 1864 7.652909 CCTGCAGAAGAAACAATACAATCAAAA 59.347 33.333 17.39 0.00 0.00 2.44
1873 1952 3.132111 TGTCTTAGTGTGTGTGAGCAAGA 59.868 43.478 0.00 0.00 0.00 3.02
1925 2004 6.645790 AAAAAGTGCTCTTCATGAAGACAT 57.354 33.333 30.05 14.32 42.06 3.06
1926 2005 7.750229 ATAAAAAGTGCTCTTCATGAAGACA 57.250 32.000 30.05 26.82 42.06 3.41
1927 2006 8.909671 CAAATAAAAAGTGCTCTTCATGAAGAC 58.090 33.333 30.05 25.01 42.06 3.01
1928 2007 8.084073 CCAAATAAAAAGTGCTCTTCATGAAGA 58.916 33.333 31.10 31.10 44.47 2.87
1929 2008 7.330208 CCCAAATAAAAAGTGCTCTTCATGAAG 59.670 37.037 26.56 26.56 39.71 3.02
2073 2174 4.154015 CGTTGCAACTTATCCAGTCAATGA 59.846 41.667 26.09 0.00 32.94 2.57
2074 2175 4.406069 CGTTGCAACTTATCCAGTCAATG 58.594 43.478 26.09 2.68 32.94 2.82
2237 2463 1.664016 GCCACGCAGAAGACAACAATG 60.664 52.381 0.00 0.00 0.00 2.82
2273 2499 7.245466 TGCACAGTAGCATTTAATGGAGACAA 61.245 38.462 7.08 0.00 41.75 3.18
2293 2519 9.836864 AATCAACTCTATAGAAACATATGCACA 57.163 29.630 3.57 0.00 0.00 4.57
2356 2582 5.741040 GCTTAGTAACATTGATTTCTGCAGC 59.259 40.000 9.47 0.00 0.00 5.25
2360 2586 8.939929 TCTCAAGCTTAGTAACATTGATTTCTG 58.060 33.333 0.00 0.00 30.13 3.02
2389 2615 3.064207 TGTAACTGTGATCTTCGCAACC 58.936 45.455 0.00 0.00 36.34 3.77
2565 2791 0.661187 CAATGGCTGACGTTGCACAC 60.661 55.000 14.70 0.00 39.08 3.82
2574 2800 4.518970 TCTCCAAAACTAACAATGGCTGAC 59.481 41.667 0.00 0.00 32.87 3.51
2613 2839 8.002459 ACTCCTAATTGTTCAACTTCCCTTTTA 58.998 33.333 0.00 0.00 0.00 1.52
2760 2986 9.952188 CCTTTTGTTTCTTAGGAAGTTCTTTAG 57.048 33.333 2.25 0.00 32.61 1.85
2762 2988 8.467598 GTCCTTTTGTTTCTTAGGAAGTTCTTT 58.532 33.333 2.25 0.00 38.46 2.52
2795 3021 7.093068 TGTTCCACTGGTATACATGATTGTACT 60.093 37.037 5.01 0.00 41.02 2.73
2809 3035 0.768622 CCCCTGTTGTTCCACTGGTA 59.231 55.000 0.00 0.00 34.66 3.25
2878 3104 1.294780 GAGGAGGTGCTCTGTGGTG 59.705 63.158 0.00 0.00 0.00 4.17
2930 3156 7.360861 CCACTGAAATTCTAGTTTTGACGCATA 60.361 37.037 0.00 0.00 0.00 3.14
2993 3219 7.980062 TGCCATTCTTTTGTTTAAACCTTTTC 58.020 30.769 15.59 0.00 0.00 2.29
3014 3240 0.673333 ACATTCACGCTCGATTGCCA 60.673 50.000 0.00 0.00 0.00 4.92
3015 3241 0.247814 CACATTCACGCTCGATTGCC 60.248 55.000 0.00 0.00 0.00 4.52
3105 3331 2.811431 TCGATGAACAAACCATGACCAC 59.189 45.455 0.00 0.00 0.00 4.16
3126 3352 7.231317 TGACAGGAAAACAAAGCTCTAAATCAT 59.769 33.333 0.00 0.00 0.00 2.45
3275 3501 4.026052 CCCCTTTGGAGATGCAGTAATTT 58.974 43.478 0.00 0.00 35.39 1.82
3350 3576 4.632153 AGTCACAGAAAAGCGACATAAGT 58.368 39.130 0.00 0.00 0.00 2.24
3351 3577 5.389935 GGAAGTCACAGAAAAGCGACATAAG 60.390 44.000 0.00 0.00 0.00 1.73
3359 3585 4.322567 AGATGAGGAAGTCACAGAAAAGC 58.677 43.478 0.00 0.00 38.28 3.51
3363 3589 6.522625 CTCTTAGATGAGGAAGTCACAGAA 57.477 41.667 0.00 0.00 38.28 3.02
3435 3661 7.031372 CCACAGAATATTGTTGGTTTCATCAG 58.969 38.462 0.00 0.00 0.00 2.90
3497 3723 7.821846 GGAAAAACAATAATGGAGGTTTGCATA 59.178 33.333 0.00 0.00 33.86 3.14
3512 3738 5.992217 CGGTGGGAATTTTGGAAAAACAATA 59.008 36.000 0.00 0.00 0.00 1.90
3519 3745 1.414158 TGCGGTGGGAATTTTGGAAA 58.586 45.000 0.00 0.00 0.00 3.13
3537 3763 6.700081 CCTCAATTATGATGGAGCACAAAATG 59.300 38.462 0.00 0.00 32.74 2.32
3541 3767 5.114764 TCCTCAATTATGATGGAGCACAA 57.885 39.130 0.00 0.00 32.74 3.33
3545 3771 8.675504 CATAAGATTCCTCAATTATGATGGAGC 58.324 37.037 0.00 0.00 37.67 4.70
3560 3786 8.324191 TGATACCTTCAGTTCATAAGATTCCT 57.676 34.615 0.00 0.00 0.00 3.36
3569 3795 7.595819 TTTTTGGTTGATACCTTCAGTTCAT 57.404 32.000 0.00 0.00 45.27 2.57
3611 3837 3.507622 ACTGAAAAAGGTGCTTGGCTATC 59.492 43.478 0.00 0.00 0.00 2.08
3739 3967 9.747898 TGAAAAGGGAGTAAAAATTAGATGCTA 57.252 29.630 0.00 0.00 0.00 3.49
3905 4133 7.902087 TGGAGTAAAAATAAAGAAACATGGGG 58.098 34.615 0.00 0.00 0.00 4.96
4002 4230 2.740055 GCGCCGGATAGCATGAGG 60.740 66.667 5.05 0.00 0.00 3.86
4023 4251 1.340889 TCAATGTGTCTTGGCAAAGGC 59.659 47.619 0.00 0.00 38.58 4.35
4077 4305 2.840038 AGTCTCACCATATCCTTGTGCA 59.160 45.455 0.00 0.00 0.00 4.57
4099 4327 8.798859 AGCACAGTTGTCATAAGAATTCTAAT 57.201 30.769 8.75 0.00 0.00 1.73
4138 4366 1.402787 ACCAAGGACAAACTTGCCAG 58.597 50.000 0.00 0.00 44.98 4.85
4140 4368 2.031870 AGAACCAAGGACAAACTTGCC 58.968 47.619 0.00 0.00 44.98 4.52
4173 4401 7.335924 GTCCATAACTAGTTAAATGCTGAACCA 59.664 37.037 18.88 0.00 0.00 3.67
4180 4408 8.813643 ATCGTAGTCCATAACTAGTTAAATGC 57.186 34.615 18.88 10.10 41.17 3.56
4181 4409 9.961265 TGATCGTAGTCCATAACTAGTTAAATG 57.039 33.333 18.88 14.13 41.17 2.32
4183 4411 9.961265 CATGATCGTAGTCCATAACTAGTTAAA 57.039 33.333 18.88 5.65 41.17 1.52
4190 4426 6.465439 TTCACATGATCGTAGTCCATAACT 57.535 37.500 0.00 0.00 42.33 2.24
4262 4512 5.168569 TCGGCATCAAAAGTAACTAGACTG 58.831 41.667 0.00 0.00 0.00 3.51
4276 4526 4.576053 CAGTTTATCATTCCTCGGCATCAA 59.424 41.667 0.00 0.00 0.00 2.57
4310 4568 1.133976 AGTGAGCCCTGCATACCAATC 60.134 52.381 0.00 0.00 0.00 2.67
4339 4597 0.527113 TCGACGTAAAGCATCCCGAA 59.473 50.000 0.00 0.00 0.00 4.30
4372 4630 1.290203 CAACCGTCCCAATCATCGAG 58.710 55.000 0.00 0.00 0.00 4.04
4408 4666 3.934391 CTCCAACCGTGCCTCGACC 62.934 68.421 0.02 0.00 42.86 4.79
4507 4765 2.202837 GGGCGCTTGTAGTACCCG 60.203 66.667 7.64 0.00 0.00 5.28
4545 4803 0.836400 ATGGAACCACCCGTCTGAGT 60.836 55.000 0.00 0.00 38.00 3.41
4552 4810 0.392461 CACCTGTATGGAACCACCCG 60.392 60.000 0.00 0.00 39.71 5.28
4555 4813 1.453155 CTGCACCTGTATGGAACCAC 58.547 55.000 0.00 0.00 39.71 4.16
4601 4859 7.380333 CCATATGTTCATTCATGTGTTGTATGC 59.620 37.037 1.24 0.00 35.94 3.14
4603 4861 8.523915 ACCATATGTTCATTCATGTGTTGTAT 57.476 30.769 1.24 0.00 35.94 2.29
4686 4946 3.661944 GATGATCTTCATCGTGCCATCT 58.338 45.455 3.80 0.00 43.11 2.90
4752 5012 1.779061 TTTCCAGGACCTCCACTGCC 61.779 60.000 0.00 0.00 38.89 4.85
4780 5040 1.215655 GCAACGAGTTGAGACTGCGT 61.216 55.000 18.93 0.00 42.93 5.24
4800 5060 4.386652 TCTGTTTTTGCTTATCGTACCGAC 59.613 41.667 0.00 0.00 39.18 4.79
4844 5104 1.002430 ACCATGAATCTGACGCACTGT 59.998 47.619 0.00 0.00 0.00 3.55
4899 5159 4.496840 CGTAGACCCAAACCTTGTTCAAAC 60.497 45.833 0.00 0.00 0.00 2.93
5038 5298 0.105039 GGATGTACCTCCTCGCCTTG 59.895 60.000 9.76 0.00 35.41 3.61
5044 5304 2.896685 CTCATCCTGGATGTACCTCCTC 59.103 54.545 30.36 0.00 40.55 3.71
5080 5340 1.730446 CGACGTACCCCGAGTTTCTTC 60.730 57.143 0.00 0.00 40.70 2.87
5136 5396 6.040842 GGAATACAAAATGGGCACAGATACAT 59.959 38.462 0.00 0.00 0.00 2.29
5139 5399 5.514169 TGGAATACAAAATGGGCACAGATA 58.486 37.500 0.00 0.00 0.00 1.98
5140 5400 4.352009 TGGAATACAAAATGGGCACAGAT 58.648 39.130 0.00 0.00 0.00 2.90
5141 5401 3.772387 TGGAATACAAAATGGGCACAGA 58.228 40.909 0.00 0.00 0.00 3.41
5142 5402 4.160065 TGATGGAATACAAAATGGGCACAG 59.840 41.667 0.00 0.00 0.00 3.66
5143 5403 4.092279 TGATGGAATACAAAATGGGCACA 58.908 39.130 0.00 0.00 0.00 4.57
5144 5404 4.734398 TGATGGAATACAAAATGGGCAC 57.266 40.909 0.00 0.00 0.00 5.01
5145 5405 6.462768 GCTTATGATGGAATACAAAATGGGCA 60.463 38.462 0.00 0.00 0.00 5.36
5146 5406 5.928264 GCTTATGATGGAATACAAAATGGGC 59.072 40.000 0.00 0.00 0.00 5.36
5155 5415 6.689241 CGAGATCGTAGCTTATGATGGAATAC 59.311 42.308 0.00 0.00 34.68 1.89
5157 5417 5.645624 CGAGATCGTAGCTTATGATGGAAT 58.354 41.667 0.00 0.00 34.68 3.01
5159 5419 4.686839 CGAGATCGTAGCTTATGATGGA 57.313 45.455 0.00 0.00 34.68 3.41
5180 5440 0.457853 CTCAACTGCATGCATGGCAC 60.458 55.000 27.34 11.97 43.04 5.01
5236 5496 0.321475 TGTCGATGCTGAATGGCACA 60.321 50.000 0.00 0.00 45.36 4.57
5346 5606 3.181491 TGTGAGCAAAAACCACTAACTGC 60.181 43.478 0.00 0.00 0.00 4.40
5361 5622 6.680810 CATAATTTTGTTCCTCTTGTGAGCA 58.319 36.000 0.00 0.00 38.93 4.26
5372 5633 2.165437 TCCTGCGGCATAATTTTGTTCC 59.835 45.455 1.75 0.00 0.00 3.62
5412 5673 1.143684 GCTCCCATCTTGGCATCCTTA 59.856 52.381 0.00 0.00 35.79 2.69
5431 5692 3.998341 ACCATCATTTTTCATTGTGCAGC 59.002 39.130 0.00 0.00 0.00 5.25
5468 5729 5.998454 AACATTCAGAAAGCTCATATCCG 57.002 39.130 0.00 0.00 0.00 4.18
5550 5829 3.415212 ACGCAGTAGTAGTGGTACAGAA 58.585 45.455 7.11 0.00 41.94 3.02
5552 5831 3.189910 TGAACGCAGTAGTAGTGGTACAG 59.810 47.826 7.11 0.00 45.00 2.74
5570 5849 0.744771 GCTGGATCCGGGTCTTGAAC 60.745 60.000 22.38 0.00 0.00 3.18
5665 5946 6.284459 GGCTCTAACTAGCACAATATGTTCT 58.716 40.000 0.00 0.00 44.64 3.01
5745 6026 6.964934 CGGCAACTTTGTAGTGGTTTAATATC 59.035 38.462 0.00 0.00 34.01 1.63
5746 6027 6.127842 CCGGCAACTTTGTAGTGGTTTAATAT 60.128 38.462 0.00 0.00 34.01 1.28
5747 6028 5.181622 CCGGCAACTTTGTAGTGGTTTAATA 59.818 40.000 0.00 0.00 34.01 0.98
5748 6029 4.022676 CCGGCAACTTTGTAGTGGTTTAAT 60.023 41.667 0.00 0.00 34.01 1.40
5749 6030 3.315749 CCGGCAACTTTGTAGTGGTTTAA 59.684 43.478 0.00 0.00 34.01 1.52
5767 6052 1.808411 TGTCATCTCTCAAAACCGGC 58.192 50.000 0.00 0.00 0.00 6.13
5780 6065 9.684448 TCGAAATCTGAGAATAGTAATGTCATC 57.316 33.333 0.00 0.00 0.00 2.92
5819 6104 9.971922 GGTACTTTTATACTACGTGACCATATT 57.028 33.333 0.00 0.00 0.00 1.28
5820 6105 8.292448 CGGTACTTTTATACTACGTGACCATAT 58.708 37.037 0.00 0.00 0.00 1.78
5821 6106 7.282224 ACGGTACTTTTATACTACGTGACCATA 59.718 37.037 0.00 0.00 31.60 2.74
5822 6107 6.095440 ACGGTACTTTTATACTACGTGACCAT 59.905 38.462 0.00 0.00 31.60 3.55
5823 6108 5.414454 ACGGTACTTTTATACTACGTGACCA 59.586 40.000 0.00 0.00 31.60 4.02
5824 6109 5.880341 ACGGTACTTTTATACTACGTGACC 58.120 41.667 0.00 0.00 31.60 4.02
5825 6110 7.007456 GTGAACGGTACTTTTATACTACGTGAC 59.993 40.741 0.00 0.00 33.27 3.67
5826 6111 7.021196 GTGAACGGTACTTTTATACTACGTGA 58.979 38.462 0.00 0.00 33.27 4.35
5827 6112 6.801377 TGTGAACGGTACTTTTATACTACGTG 59.199 38.462 0.00 0.00 33.27 4.49
5828 6113 6.908825 TGTGAACGGTACTTTTATACTACGT 58.091 36.000 0.00 0.00 34.52 3.57
5829 6114 7.795431 TTGTGAACGGTACTTTTATACTACG 57.205 36.000 0.00 0.00 0.00 3.51
5832 6117 9.059260 ACATTTTGTGAACGGTACTTTTATACT 57.941 29.630 0.00 0.00 0.00 2.12
5860 6145 4.332543 GCGAATATGTCTTCCAATGTCACA 59.667 41.667 0.00 0.00 0.00 3.58
5875 6160 8.601243 ACATTTTCTTTAAACTCGCGAATATG 57.399 30.769 11.33 5.47 32.79 1.78
5882 6167 7.008810 TGACACAAACATTTTCTTTAAACTCGC 59.991 33.333 0.00 0.00 0.00 5.03
5917 6202 8.217131 ACCCGGTTTTCTTTACATTGTATATC 57.783 34.615 0.00 0.00 0.00 1.63
5972 6265 7.476667 ACATTTTTCAGATACACGTTGAACAA 58.523 30.769 0.00 0.81 31.11 2.83
6117 6411 9.658799 TTTTCCATTTGTTCAACACATTTCTAA 57.341 25.926 0.00 0.00 34.43 2.10
6137 6435 8.299990 TCTTCTATGGTTTTCTTTGTTTTCCA 57.700 30.769 0.00 0.00 0.00 3.53
6144 6442 8.197439 ACCTGTTTTCTTCTATGGTTTTCTTTG 58.803 33.333 0.00 0.00 0.00 2.77
6148 6446 7.272037 TCACCTGTTTTCTTCTATGGTTTTC 57.728 36.000 0.00 0.00 0.00 2.29
6157 6455 8.980481 TCTTATTTCTTCACCTGTTTTCTTCT 57.020 30.769 0.00 0.00 0.00 2.85
6165 6463 8.712228 ATTTTTCCTCTTATTTCTTCACCTGT 57.288 30.769 0.00 0.00 0.00 4.00
6166 6464 9.987272 AAATTTTTCCTCTTATTTCTTCACCTG 57.013 29.630 0.00 0.00 0.00 4.00
6167 6465 9.987272 CAAATTTTTCCTCTTATTTCTTCACCT 57.013 29.630 0.00 0.00 0.00 4.00
6168 6466 9.981114 TCAAATTTTTCCTCTTATTTCTTCACC 57.019 29.630 0.00 0.00 0.00 4.02
6170 6468 9.696917 GCTCAAATTTTTCCTCTTATTTCTTCA 57.303 29.630 0.00 0.00 0.00 3.02
6185 6523 3.504375 AGCTCCTCTGGCTCAAATTTTT 58.496 40.909 0.00 0.00 34.70 1.94
6196 6542 2.366916 CCCAATACTGTAGCTCCTCTGG 59.633 54.545 0.00 0.00 0.00 3.86
6203 6549 2.399580 GGAGGTCCCAATACTGTAGCT 58.600 52.381 0.00 0.00 34.14 3.32
6220 6566 1.980784 CTGGCATGAGGGAGTGGGAG 61.981 65.000 0.00 0.00 0.00 4.30
6221 6567 1.997311 CTGGCATGAGGGAGTGGGA 60.997 63.158 0.00 0.00 0.00 4.37
6274 6620 4.813346 AAAAATGACGTCGGGCCT 57.187 50.000 11.62 0.00 0.00 5.19
6322 6668 3.695830 ACACACGGTTATCTTCCACAT 57.304 42.857 0.00 0.00 0.00 3.21
6336 6682 3.125698 AGTTTCACGGAAAAACACACG 57.874 42.857 10.75 0.00 38.73 4.49
6361 6707 7.067372 TCCTCTATTCGGAAATAACTGACGTTA 59.933 37.037 0.00 0.00 39.73 3.18
6412 6758 5.824904 AATCGGATGAATTCTTGAACAGG 57.175 39.130 7.05 0.00 0.00 4.00
6413 6759 7.148255 TGGTTAATCGGATGAATTCTTGAACAG 60.148 37.037 7.05 0.00 0.00 3.16
6414 6760 6.657117 TGGTTAATCGGATGAATTCTTGAACA 59.343 34.615 7.05 0.00 0.00 3.18
6415 6761 7.083875 TGGTTAATCGGATGAATTCTTGAAC 57.916 36.000 7.05 0.68 0.00 3.18
6416 6762 6.884295 ACTGGTTAATCGGATGAATTCTTGAA 59.116 34.615 7.05 0.00 0.00 2.69
6417 6763 6.414732 ACTGGTTAATCGGATGAATTCTTGA 58.585 36.000 7.05 0.00 0.00 3.02
6418 6764 6.683974 ACTGGTTAATCGGATGAATTCTTG 57.316 37.500 7.05 0.00 0.00 3.02


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

AutoCloner maintained by Alex Coulton.