Multiple sequence alignment - TraesCS5A01G163300

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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 TraesCS5A01G163300 chr5A 100.000 6986 0 0 1 6986 350071999 350065014 0.000000e+00 12901.0
1 TraesCS5A01G163300 chr5A 86.008 243 24 6 5411 5646 313309841 313310080 1.160000e-62 252.0
2 TraesCS5A01G163300 chr5B 94.848 2698 90 21 351 3032 295585598 295588262 0.000000e+00 4167.0
3 TraesCS5A01G163300 chr5B 96.824 1543 40 6 3106 4646 295588257 295589792 0.000000e+00 2569.0
4 TraesCS5A01G163300 chr5B 95.820 1531 35 10 4638 6161 295593964 295595472 0.000000e+00 2446.0
5 TraesCS5A01G163300 chr5B 88.988 672 48 11 6198 6867 295595460 295596107 0.000000e+00 808.0
6 TraesCS5A01G163300 chr5B 92.273 220 15 1 6751 6970 295596351 295596568 1.890000e-80 311.0
7 TraesCS5A01G163300 chr5B 93.939 198 8 4 66 262 295583593 295583787 5.300000e-76 296.0
8 TraesCS5A01G163300 chr5B 91.946 149 12 0 6719 6867 295596032 295596180 7.100000e-50 209.0
9 TraesCS5A01G163300 chr5B 92.727 110 8 0 6719 6828 295596105 295596214 7.250000e-35 159.0
10 TraesCS5A01G163300 chr5B 90.000 50 2 3 6414 6462 79465682 79465635 2.100000e-05 62.1
11 TraesCS5A01G163300 chr5D 93.322 1842 67 16 2 1838 263137801 263139591 0.000000e+00 2669.0
12 TraesCS5A01G163300 chr5D 94.891 1644 76 6 3475 5116 263141200 263142837 0.000000e+00 2564.0
13 TraesCS5A01G163300 chr5D 93.111 1292 66 11 1840 3126 263139560 263140833 0.000000e+00 1871.0
14 TraesCS5A01G163300 chr5D 87.921 1424 114 27 5115 6518 263142942 263144327 0.000000e+00 1624.0
15 TraesCS5A01G163300 chr5D 92.000 275 22 0 3124 3398 263140926 263141200 3.060000e-103 387.0
16 TraesCS5A01G163300 chr5D 88.115 244 23 3 5405 5643 4030145 4029903 1.150000e-72 285.0
17 TraesCS5A01G163300 chr4B 88.066 243 22 5 5411 5647 87400943 87400702 1.480000e-71 281.0
18 TraesCS5A01G163300 chr2B 86.722 241 24 5 5411 5644 273869770 273870009 1.930000e-65 261.0
19 TraesCS5A01G163300 chr2B 88.584 219 19 5 5428 5643 493711794 493711579 1.930000e-65 261.0
20 TraesCS5A01G163300 chr2B 87.558 217 21 5 5435 5648 449827055 449826842 5.410000e-61 246.0
21 TraesCS5A01G163300 chr2B 84.483 58 8 1 6405 6461 419618843 419618900 1.000000e-03 56.5
22 TraesCS5A01G163300 chr7B 85.833 240 28 3 5411 5644 384201303 384201064 4.180000e-62 250.0
23 TraesCS5A01G163300 chr7B 88.235 51 3 3 6413 6462 589138837 589138789 2.720000e-04 58.4
24 TraesCS5A01G163300 chr6A 95.000 40 2 0 6403 6442 51498000 51497961 5.850000e-06 63.9
25 TraesCS5A01G163300 chr2D 89.796 49 4 1 6414 6462 70291771 70291724 2.100000e-05 62.1
26 TraesCS5A01G163300 chr1A 92.857 42 0 3 6402 6443 29807345 29807307 2.720000e-04 58.4
27 TraesCS5A01G163300 chr3B 83.333 60 8 2 6413 6471 715254548 715254490 4.000000e-03 54.7


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 TraesCS5A01G163300 chr5A 350065014 350071999 6985 True 12901.0 12901 100.000000 1 6986 1 chr5A.!!$R1 6985
1 TraesCS5A01G163300 chr5B 295583593 295589792 6199 False 2344.0 4167 95.203667 66 4646 3 chr5B.!!$F1 4580
2 TraesCS5A01G163300 chr5B 295593964 295596568 2604 False 786.6 2446 92.350800 4638 6970 5 chr5B.!!$F2 2332
3 TraesCS5A01G163300 chr5D 263137801 263144327 6526 False 1823.0 2669 92.249000 2 6518 5 chr5D.!!$F1 6516

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
960 2706 0.035317 TTGCGACCACTCTTGCATCT 59.965 50.000 0.00 0.0 37.17 2.90 F
1398 3144 0.248458 AGTTTGCCGCAGTTTGTTCG 60.248 50.000 0.00 0.0 0.00 3.95 F
3152 5036 0.327000 ATACCAGCCCAGCTTCTCCT 60.327 55.000 0.00 0.0 36.40 3.69 F
4400 6285 1.000843 CCCTTGCTGTTTGGTTAAGCC 59.999 52.381 1.51 0.0 36.05 4.35 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2253 4036 1.933021 TCGTGTAGACCCATGTTCCT 58.067 50.000 0.0 0.0 0.00 3.36 R
3323 5207 2.093764 ACTGAGCCAGTAAGATGAGCAC 60.094 50.000 6.1 0.0 43.46 4.40 R
4812 6698 2.663196 GCCCGGTAGCTGTCTGTT 59.337 61.111 0.0 0.0 0.00 3.16 R
5998 8005 0.106335 TGCTCCGGTCGTGGTTAAAA 59.894 50.000 0.0 0.0 0.00 1.52 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 5.640732 GGTCTAGTGCAATTAAACACATGG 58.359 41.667 0.00 0.00 39.30 3.66
34 35 3.761218 TGCAATTAAACACATGGACCGAT 59.239 39.130 0.00 0.00 0.00 4.18
40 41 4.664150 AAACACATGGACCGATTTTTGT 57.336 36.364 0.00 0.00 0.00 2.83
56 57 4.944619 TTTTGTGGTGCCAATGTAATCA 57.055 36.364 0.00 0.00 0.00 2.57
59 60 1.750778 GTGGTGCCAATGTAATCAGGG 59.249 52.381 0.00 0.00 0.00 4.45
69 70 3.275617 TGTAATCAGGGAAACGGGATG 57.724 47.619 0.00 0.00 0.00 3.51
88 89 6.099341 GGGATGAAATTAGCGAAACAAACAT 58.901 36.000 0.00 0.00 0.00 2.71
201 205 4.516365 ACGGTAAGGAAGAGTGTAACAG 57.484 45.455 0.00 0.00 41.43 3.16
259 264 2.418976 GGAGGCAAATGAAGTTCGTACC 59.581 50.000 0.00 1.18 0.00 3.34
260 265 3.071479 GAGGCAAATGAAGTTCGTACCA 58.929 45.455 12.02 0.00 0.00 3.25
261 266 3.482436 AGGCAAATGAAGTTCGTACCAA 58.518 40.909 12.02 0.00 0.00 3.67
262 267 3.886505 AGGCAAATGAAGTTCGTACCAAA 59.113 39.130 12.02 0.00 0.00 3.28
263 268 3.978855 GGCAAATGAAGTTCGTACCAAAC 59.021 43.478 0.00 0.00 0.00 2.93
264 269 4.261447 GGCAAATGAAGTTCGTACCAAACT 60.261 41.667 0.00 3.12 38.59 2.66
265 270 5.278604 GCAAATGAAGTTCGTACCAAACTT 58.721 37.500 16.77 16.77 46.74 2.66
266 271 5.746721 GCAAATGAAGTTCGTACCAAACTTT 59.253 36.000 17.48 5.24 44.72 2.66
291 296 2.716217 ACAGCTGGGCAAATCTAGAAC 58.284 47.619 19.93 0.00 0.00 3.01
333 1815 4.320456 CCAGTGACGCTGCCACCT 62.320 66.667 10.65 0.00 43.71 4.00
334 1816 3.046087 CAGTGACGCTGCCACCTG 61.046 66.667 2.48 0.00 38.52 4.00
714 2460 8.416329 AGATTAGATTTGCTTGTCTTGTTGTTT 58.584 29.630 0.00 0.00 0.00 2.83
715 2461 8.947055 ATTAGATTTGCTTGTCTTGTTGTTTT 57.053 26.923 0.00 0.00 0.00 2.43
716 2462 8.770438 TTAGATTTGCTTGTCTTGTTGTTTTT 57.230 26.923 0.00 0.00 0.00 1.94
782 2528 2.554032 AGGTCTTCCTTGATTTGTTGCG 59.446 45.455 0.00 0.00 42.12 4.85
787 2533 4.277174 TCTTCCTTGATTTGTTGCGCTTTA 59.723 37.500 9.73 0.00 0.00 1.85
830 2576 1.149148 GGAATAGCCCGATTCGCTTC 58.851 55.000 0.00 0.00 36.80 3.86
834 2580 0.314302 TAGCCCGATTCGCTTCTAGC 59.686 55.000 0.00 0.00 37.79 3.42
857 2603 0.606604 GTCCCCTTGCTCACGAGTTA 59.393 55.000 0.00 0.00 0.00 2.24
936 2682 0.332972 AGGAGAAGGGGGATGCAAAC 59.667 55.000 0.00 0.00 0.00 2.93
937 2683 0.332972 GGAGAAGGGGGATGCAAACT 59.667 55.000 0.00 0.00 0.00 2.66
940 2686 2.232208 GAGAAGGGGGATGCAAACTTTG 59.768 50.000 0.00 0.00 0.00 2.77
941 2687 1.970640 GAAGGGGGATGCAAACTTTGT 59.029 47.619 3.48 0.00 0.00 2.83
943 2689 1.693606 AGGGGGATGCAAACTTTGTTG 59.306 47.619 3.48 0.00 0.00 3.33
956 2702 0.380378 TTTGTTGCGACCACTCTTGC 59.620 50.000 0.45 0.00 0.00 4.01
960 2706 0.035317 TTGCGACCACTCTTGCATCT 59.965 50.000 0.00 0.00 37.17 2.90
974 2720 7.965107 CACTCTTGCATCTCCATTTTTAAGTAC 59.035 37.037 0.00 0.00 0.00 2.73
975 2721 7.885399 ACTCTTGCATCTCCATTTTTAAGTACT 59.115 33.333 0.00 0.00 0.00 2.73
976 2722 9.383519 CTCTTGCATCTCCATTTTTAAGTACTA 57.616 33.333 0.00 0.00 0.00 1.82
994 2740 7.164230 AGTACTATATATGCTTGTCTCAGGC 57.836 40.000 0.00 0.00 36.98 4.85
1033 2779 0.598158 TACGGTCCAGTTCGTTGTGC 60.598 55.000 0.00 0.00 40.31 4.57
1049 2795 1.305297 TGCCGATGTCTCCTCTGGT 60.305 57.895 0.00 0.00 0.00 4.00
1050 2796 1.323271 TGCCGATGTCTCCTCTGGTC 61.323 60.000 0.00 0.00 0.00 4.02
1052 2798 0.684479 CCGATGTCTCCTCTGGTCCA 60.684 60.000 0.00 0.00 0.00 4.02
1053 2799 1.407936 CGATGTCTCCTCTGGTCCAT 58.592 55.000 0.00 0.00 0.00 3.41
1145 2891 0.807496 GCCTGTGGAGATGAACAAGC 59.193 55.000 0.00 0.00 0.00 4.01
1284 3030 1.589993 CGATGAGCGGTCGCAATCT 60.590 57.895 17.71 0.00 44.88 2.40
1291 3037 1.218047 CGGTCGCAATCTTGGAGGA 59.782 57.895 0.00 0.00 0.00 3.71
1312 3058 3.388134 CGTGGATGCGCTACTGTG 58.612 61.111 9.73 0.00 0.00 3.66
1332 3078 1.143305 GCGATGATGGGAGTCAATCG 58.857 55.000 0.00 0.00 34.88 3.34
1383 3129 0.463654 TTCAGCTGTGTCCGCAGTTT 60.464 50.000 14.67 0.00 38.65 2.66
1384 3130 1.159713 TCAGCTGTGTCCGCAGTTTG 61.160 55.000 14.67 8.40 38.65 2.93
1385 3131 2.050985 GCTGTGTCCGCAGTTTGC 60.051 61.111 9.39 0.00 40.69 3.68
1386 3132 2.639286 CTGTGTCCGCAGTTTGCC 59.361 61.111 0.00 0.00 41.12 4.52
1387 3133 3.240606 CTGTGTCCGCAGTTTGCCG 62.241 63.158 0.00 0.00 41.12 5.69
1388 3134 4.683334 GTGTCCGCAGTTTGCCGC 62.683 66.667 0.00 0.00 41.12 6.53
1390 3136 4.389576 GTCCGCAGTTTGCCGCAG 62.390 66.667 0.00 0.00 41.12 5.18
1391 3137 4.927782 TCCGCAGTTTGCCGCAGT 62.928 61.111 0.00 0.00 41.12 4.40
1392 3138 3.964875 CCGCAGTTTGCCGCAGTT 61.965 61.111 0.00 0.00 41.12 3.16
1398 3144 0.248458 AGTTTGCCGCAGTTTGTTCG 60.248 50.000 0.00 0.00 0.00 3.95
1434 3180 6.832520 TTGTATAAGAGCTTGAATTGGCAA 57.167 33.333 0.68 0.68 0.00 4.52
1448 3194 9.903682 CTTGAATTGGCAAAGTATATATGGAAG 57.096 33.333 3.01 0.00 0.00 3.46
1636 3382 0.803117 CTGGATTGTGCTGTGCTGAG 59.197 55.000 0.00 0.00 0.00 3.35
1689 3435 1.035139 GATTGGCACAGCAATAGGGG 58.965 55.000 0.00 0.00 42.39 4.79
1827 3609 6.747280 GGTATGATTCTGTTTACAACACATGC 59.253 38.462 0.00 0.00 36.25 4.06
1828 3610 5.764487 TGATTCTGTTTACAACACATGCA 57.236 34.783 0.00 0.00 36.25 3.96
1829 3611 6.330004 TGATTCTGTTTACAACACATGCAT 57.670 33.333 0.00 0.00 36.25 3.96
1830 3612 6.747125 TGATTCTGTTTACAACACATGCATT 58.253 32.000 0.00 0.00 36.25 3.56
1831 3613 6.641723 TGATTCTGTTTACAACACATGCATTG 59.358 34.615 0.00 7.76 36.25 2.82
1832 3614 5.512753 TCTGTTTACAACACATGCATTGT 57.487 34.783 16.76 16.76 41.77 2.71
1833 3615 6.625873 TCTGTTTACAACACATGCATTGTA 57.374 33.333 15.10 15.10 39.67 2.41
1834 3616 6.434596 TCTGTTTACAACACATGCATTGTAC 58.565 36.000 17.60 12.54 40.19 2.90
1835 3617 6.262049 TCTGTTTACAACACATGCATTGTACT 59.738 34.615 17.60 4.30 40.19 2.73
1836 3618 6.205071 TGTTTACAACACATGCATTGTACTG 58.795 36.000 17.60 9.78 40.19 2.74
1837 3619 6.038714 TGTTTACAACACATGCATTGTACTGA 59.961 34.615 17.60 5.56 40.19 3.41
1838 3620 4.488126 ACAACACATGCATTGTACTGAC 57.512 40.909 12.28 0.00 37.27 3.51
1839 3621 4.136796 ACAACACATGCATTGTACTGACT 58.863 39.130 12.28 0.00 37.27 3.41
1840 3622 4.023792 ACAACACATGCATTGTACTGACTG 60.024 41.667 12.28 9.67 37.27 3.51
1841 3623 4.006780 ACACATGCATTGTACTGACTGA 57.993 40.909 11.30 0.00 36.57 3.41
1842 3624 4.582869 ACACATGCATTGTACTGACTGAT 58.417 39.130 11.30 0.00 36.57 2.90
1843 3625 5.005740 ACACATGCATTGTACTGACTGATT 58.994 37.500 11.30 0.00 36.57 2.57
1844 3626 5.122869 ACACATGCATTGTACTGACTGATTC 59.877 40.000 11.30 0.00 36.57 2.52
1845 3627 4.330894 ACATGCATTGTACTGACTGATTCG 59.669 41.667 0.00 0.00 36.57 3.34
1846 3628 3.261580 TGCATTGTACTGACTGATTCGG 58.738 45.455 0.00 0.00 36.55 4.30
1847 3629 3.262420 GCATTGTACTGACTGATTCGGT 58.738 45.455 0.00 0.00 46.38 4.69
1848 3630 3.684788 GCATTGTACTGACTGATTCGGTT 59.315 43.478 0.00 0.00 41.51 4.44
1849 3631 4.154195 GCATTGTACTGACTGATTCGGTTT 59.846 41.667 0.00 0.00 41.51 3.27
1850 3632 5.350365 GCATTGTACTGACTGATTCGGTTTA 59.650 40.000 0.00 0.00 41.51 2.01
1851 3633 6.672357 GCATTGTACTGACTGATTCGGTTTAC 60.672 42.308 0.00 3.46 41.51 2.01
1852 3634 5.456548 TGTACTGACTGATTCGGTTTACA 57.543 39.130 0.00 5.77 41.51 2.41
1853 3635 5.845103 TGTACTGACTGATTCGGTTTACAA 58.155 37.500 0.00 0.00 41.51 2.41
1854 3636 5.693104 TGTACTGACTGATTCGGTTTACAAC 59.307 40.000 0.00 0.00 41.51 3.32
1855 3637 4.699637 ACTGACTGATTCGGTTTACAACA 58.300 39.130 0.00 0.00 41.51 3.33
1856 3638 4.510340 ACTGACTGATTCGGTTTACAACAC 59.490 41.667 0.00 0.00 41.51 3.32
1857 3639 4.443621 TGACTGATTCGGTTTACAACACA 58.556 39.130 0.00 0.00 0.00 3.72
1858 3640 5.060506 TGACTGATTCGGTTTACAACACAT 58.939 37.500 0.00 0.00 0.00 3.21
1859 3641 5.049749 TGACTGATTCGGTTTACAACACATG 60.050 40.000 0.00 0.00 0.00 3.21
1872 3654 9.677567 GTTTACAACACATGAATTGTACTGATT 57.322 29.630 19.40 0.00 40.19 2.57
1949 3731 7.797038 ATTCTTTAGTTTTGGTGTAGACGTT 57.203 32.000 0.00 0.00 0.00 3.99
1986 3768 6.186420 TGCCACTTCTATTCTATGCCATAA 57.814 37.500 0.00 0.00 0.00 1.90
2253 4036 4.574674 AAAGCTGAAGATGACCCATGTA 57.425 40.909 0.00 0.00 0.00 2.29
2471 4255 8.550376 CATGTGTTATTGTCCTTTTTCCTTTTG 58.450 33.333 0.00 0.00 0.00 2.44
2495 4279 5.915758 GCAACAAATGTGTTATTGTCCGTTA 59.084 36.000 0.00 0.00 46.47 3.18
2616 4400 9.059260 GTAGGCTAATTTGGGATAATCGTTTTA 57.941 33.333 0.00 0.00 0.00 1.52
2789 4573 4.919206 TGTGTGTTGCTACAAAAGTGATG 58.081 39.130 1.60 0.00 35.69 3.07
2881 4670 5.410355 AAGTGGCAATGCACAAATAGAAT 57.590 34.783 7.79 0.00 0.00 2.40
3046 4835 2.839486 TCTGCTGGAGTTAAGGTGTG 57.161 50.000 0.00 0.00 0.00 3.82
3047 4836 1.347707 TCTGCTGGAGTTAAGGTGTGG 59.652 52.381 0.00 0.00 0.00 4.17
3054 4843 5.475564 GCTGGAGTTAAGGTGTGGAAATTAA 59.524 40.000 0.00 0.00 0.00 1.40
3075 4864 9.442047 AATTAATGTTCAGCTATGATACTAGGC 57.558 33.333 0.00 0.00 34.73 3.93
3104 4893 6.917477 TCAAAAGTTGATTCACAGTTGTATGC 59.083 34.615 0.00 0.00 34.08 3.14
3152 5036 0.327000 ATACCAGCCCAGCTTCTCCT 60.327 55.000 0.00 0.00 36.40 3.69
3159 5043 1.831736 GCCCAGCTTCTCCTAACTACA 59.168 52.381 0.00 0.00 0.00 2.74
3236 5120 9.565213 GAACTTATGAGGAAATGATTTCTGTTG 57.435 33.333 16.58 5.05 39.59 3.33
3323 5207 8.976471 CAATATTATATAGCTCTTCTCATGCGG 58.024 37.037 0.00 0.00 0.00 5.69
3339 5223 1.432270 GCGGTGCTCATCTTACTGGC 61.432 60.000 0.00 0.00 0.00 4.85
3412 5296 1.250476 GCGCTGCATTTTTCACGTAG 58.750 50.000 0.00 0.00 0.00 3.51
3467 5351 8.849168 TCCGATATGAAAATCAATAAGCAATGT 58.151 29.630 0.00 0.00 0.00 2.71
3504 5388 5.952347 GGACTAAAATGTTCCCTGGAAGAAT 59.048 40.000 0.00 0.00 34.07 2.40
3977 5861 6.267928 AGTCAAGAGAGCTAAAAAGGTAGTGA 59.732 38.462 0.00 0.00 0.00 3.41
3996 5880 8.552034 GGTAGTGACATGCTATTGTTTCTTATC 58.448 37.037 0.00 0.00 0.00 1.75
4136 6021 2.550180 GCACTTCTTCAGGTGGAAACTC 59.450 50.000 0.00 0.00 34.44 3.01
4220 6105 1.303317 GTTTGCGGGTCCCAGTGAT 60.303 57.895 9.12 0.00 0.00 3.06
4310 6195 7.095187 GGTTATACTGATAAAGGAAATGAGCGG 60.095 40.741 0.00 0.00 29.20 5.52
4400 6285 1.000843 CCCTTGCTGTTTGGTTAAGCC 59.999 52.381 1.51 0.00 36.05 4.35
4536 6421 9.365906 CTTATCTCCATCTATATGCAGGTAGAT 57.634 37.037 14.63 14.63 37.98 1.98
4569 6454 4.038282 GCTTGTTCCATGGATATTGATGCA 59.962 41.667 17.06 0.00 37.85 3.96
4803 6689 3.261580 TCGCGATGTGAAGTCATCAAAT 58.738 40.909 3.71 0.00 42.82 2.32
5185 7178 6.721208 AGAATGTCATTTTGGAATGTGTACCT 59.279 34.615 0.00 0.00 42.61 3.08
5189 7182 6.773200 TGTCATTTTGGAATGTGTACCTAACA 59.227 34.615 0.00 0.00 42.61 2.41
5350 7352 8.627403 TCGTGAAAGGTGTATTACTATTAGAGG 58.373 37.037 0.00 0.00 0.00 3.69
5351 7353 8.411683 CGTGAAAGGTGTATTACTATTAGAGGT 58.588 37.037 0.00 0.00 0.00 3.85
5433 7440 2.842645 ACCTCCGTCTGGGTATTAGT 57.157 50.000 0.00 0.00 37.00 2.24
5535 7542 8.884124 TGGAAACCTCTTTTGAATATGAATCT 57.116 30.769 0.00 0.00 0.00 2.40
5593 7600 5.693104 TGTGTTAGTCAAATCTACGGTCAAC 59.307 40.000 0.00 0.00 0.00 3.18
5835 7842 2.435059 GACCCGCTGCTGGAAGAC 60.435 66.667 17.38 2.02 34.07 3.01
5998 8005 2.005451 GAGCGTGAAATCATGTGCTCT 58.995 47.619 19.35 4.80 41.24 4.09
6012 8020 1.193874 GTGCTCTTTTAACCACGACCG 59.806 52.381 0.00 0.00 0.00 4.79
6065 8092 5.534278 TCTTGATGGTAATGTTTTGTGCTCA 59.466 36.000 0.00 0.00 0.00 4.26
6066 8093 5.119931 TGATGGTAATGTTTTGTGCTCAC 57.880 39.130 0.00 0.00 0.00 3.51
6067 8094 4.582240 TGATGGTAATGTTTTGTGCTCACA 59.418 37.500 0.00 0.00 39.98 3.58
6068 8095 4.566545 TGGTAATGTTTTGTGCTCACAG 57.433 40.909 2.77 0.00 42.94 3.66
6069 8096 4.203226 TGGTAATGTTTTGTGCTCACAGA 58.797 39.130 2.77 0.00 42.94 3.41
6070 8097 4.642437 TGGTAATGTTTTGTGCTCACAGAA 59.358 37.500 2.77 2.56 42.94 3.02
6071 8098 5.301551 TGGTAATGTTTTGTGCTCACAGAAT 59.698 36.000 8.83 0.00 42.94 2.40
6072 8099 5.630680 GGTAATGTTTTGTGCTCACAGAATG 59.369 40.000 8.83 0.00 42.94 2.67
6073 8100 3.713858 TGTTTTGTGCTCACAGAATGG 57.286 42.857 8.83 0.00 43.62 3.16
6074 8101 3.286353 TGTTTTGTGCTCACAGAATGGA 58.714 40.909 8.83 0.00 43.62 3.41
6075 8102 3.698539 TGTTTTGTGCTCACAGAATGGAA 59.301 39.130 8.83 0.00 43.62 3.53
6076 8103 4.341806 TGTTTTGTGCTCACAGAATGGAAT 59.658 37.500 8.83 0.00 43.62 3.01
6077 8104 4.508461 TTTGTGCTCACAGAATGGAATG 57.492 40.909 2.77 0.00 43.62 2.67
6078 8105 3.144657 TGTGCTCACAGAATGGAATGT 57.855 42.857 0.00 0.00 43.62 2.71
6079 8106 2.815503 TGTGCTCACAGAATGGAATGTG 59.184 45.455 0.00 0.00 46.52 3.21
6080 8107 1.814394 TGCTCACAGAATGGAATGTGC 59.186 47.619 0.52 0.00 45.12 4.57
6081 8108 2.089980 GCTCACAGAATGGAATGTGCT 58.910 47.619 0.52 0.00 45.12 4.40
6082 8109 2.097142 GCTCACAGAATGGAATGTGCTC 59.903 50.000 0.52 0.00 45.12 4.26
6160 8187 4.022242 CAGTCTTCTTTCTCCGTGGACTTA 60.022 45.833 0.00 0.00 31.40 2.24
6162 8189 5.246429 AGTCTTCTTTCTCCGTGGACTTATT 59.754 40.000 0.00 0.00 29.78 1.40
6164 8191 4.884668 TCTTTCTCCGTGGACTTATTGT 57.115 40.909 0.00 0.00 0.00 2.71
6177 8204 5.538067 GACTTATTGTCCTCTTTGCTGAC 57.462 43.478 0.00 0.00 39.69 3.51
6178 8205 5.234466 ACTTATTGTCCTCTTTGCTGACT 57.766 39.130 0.00 0.00 0.00 3.41
6179 8206 4.999950 ACTTATTGTCCTCTTTGCTGACTG 59.000 41.667 0.00 0.00 0.00 3.51
6180 8207 3.498774 ATTGTCCTCTTTGCTGACTGT 57.501 42.857 0.00 0.00 0.00 3.55
6181 8208 2.245159 TGTCCTCTTTGCTGACTGTG 57.755 50.000 0.00 0.00 0.00 3.66
6182 8209 0.871057 GTCCTCTTTGCTGACTGTGC 59.129 55.000 0.00 0.00 0.00 4.57
6204 8231 3.486263 GTGCCATACACTCCGTGC 58.514 61.111 0.00 0.00 46.41 5.34
6205 8232 1.375396 GTGCCATACACTCCGTGCA 60.375 57.895 0.00 0.00 46.41 4.57
6246 8273 6.640518 AGTTTGTTCTCAGTTTAGACAGACA 58.359 36.000 0.00 0.00 0.00 3.41
6280 8307 7.922505 TTGAAATTTGTCCGTATTGAAAGTG 57.077 32.000 0.00 0.00 0.00 3.16
6281 8308 7.265647 TGAAATTTGTCCGTATTGAAAGTGA 57.734 32.000 0.00 0.00 0.00 3.41
6283 8310 8.191446 TGAAATTTGTCCGTATTGAAAGTGAAA 58.809 29.630 0.00 0.00 0.00 2.69
6284 8311 8.934507 AAATTTGTCCGTATTGAAAGTGAAAA 57.065 26.923 0.00 0.00 0.00 2.29
6287 8314 7.504924 TTGTCCGTATTGAAAGTGAAAATCT 57.495 32.000 0.00 0.00 0.00 2.40
6288 8315 7.504924 TGTCCGTATTGAAAGTGAAAATCTT 57.495 32.000 0.00 0.00 0.00 2.40
6289 8316 7.936584 TGTCCGTATTGAAAGTGAAAATCTTT 58.063 30.769 0.00 0.00 37.75 2.52
6290 8317 8.073768 TGTCCGTATTGAAAGTGAAAATCTTTC 58.926 33.333 10.30 10.30 46.10 2.62
6291 8318 7.537649 GTCCGTATTGAAAGTGAAAATCTTTCC 59.462 37.037 13.39 1.21 45.64 3.13
6292 8319 6.806739 CCGTATTGAAAGTGAAAATCTTTCCC 59.193 38.462 13.39 2.25 45.64 3.97
6293 8320 7.309194 CCGTATTGAAAGTGAAAATCTTTCCCT 60.309 37.037 13.39 5.85 45.64 4.20
6294 8321 8.082242 CGTATTGAAAGTGAAAATCTTTCCCTT 58.918 33.333 13.39 0.00 45.64 3.95
6295 8322 9.764363 GTATTGAAAGTGAAAATCTTTCCCTTT 57.236 29.630 8.66 8.66 45.64 3.11
6322 8349 1.005450 TGGAACCAAGCAAGTATCCCC 59.995 52.381 0.00 0.00 0.00 4.81
6335 8362 5.755849 CAAGTATCCCCCTGTTGTTTCTAT 58.244 41.667 0.00 0.00 0.00 1.98
6337 8364 3.669939 ATCCCCCTGTTGTTTCTATGG 57.330 47.619 0.00 0.00 0.00 2.74
6363 8390 8.877864 AAGTGTTGAAATGGGAACTTCATATA 57.122 30.769 0.00 0.00 31.85 0.86
6399 8430 4.261447 GCAAAACTACGGACCATGTTTCTT 60.261 41.667 6.86 0.00 32.35 2.52
6401 8432 6.513720 GCAAAACTACGGACCATGTTTCTTAA 60.514 38.462 6.86 0.00 32.35 1.85
6549 8580 7.328277 TGTGCTTGTTACAGTAATTGAGTTT 57.672 32.000 0.00 0.00 0.00 2.66
6574 8605 5.047847 TCAGTCCAACTAAACGAGTTCTTG 58.952 41.667 0.00 0.00 45.81 3.02
6578 8609 7.170998 CAGTCCAACTAAACGAGTTCTTGTTAT 59.829 37.037 5.95 1.18 45.81 1.89
6605 8636 8.960591 AGTAATGAAAATTAGCTAGCACATTGT 58.039 29.630 18.83 9.32 0.00 2.71
6642 8673 8.474006 AACAAAAACAATGTTTACAAGAGACC 57.526 30.769 12.11 0.00 37.74 3.85
6646 8677 7.881775 AAACAATGTTTACAAGAGACCTTCT 57.118 32.000 9.92 0.00 37.93 2.85
6686 8717 4.617223 GTCTAAACTTTTGCAAAGATCGCC 59.383 41.667 12.41 0.00 0.00 5.54
6728 8759 1.106285 GTCCCACCATCTTGATTGGC 58.894 55.000 0.00 0.00 37.81 4.52
6753 8857 7.484975 CCAATACAAAAGTTGTTCACCTGTAA 58.515 34.615 0.00 0.00 42.22 2.41
6773 8877 6.837312 TGTAAGGAGTCTGATTCCAAAGAAA 58.163 36.000 19.76 0.00 37.18 2.52
6788 8892 5.415701 TCCAAAGAAATGATCACTTGTAGGC 59.584 40.000 0.00 0.00 0.00 3.93
6825 9214 6.072175 GCCAATACAAAAGTTGATCACCTGTA 60.072 38.462 0.00 0.00 0.00 2.74
6842 9231 2.099921 CTGTAGGGAGTCTGATTCCACG 59.900 54.545 19.30 4.92 36.40 4.94
6845 9234 0.461961 GGGAGTCTGATTCCACGGAG 59.538 60.000 19.30 0.00 36.40 4.63
6864 9253 3.100671 GAGGTGATCACTTGTAGGGAGT 58.899 50.000 24.50 0.00 26.79 3.85
6868 9257 3.099905 TGATCACTTGTAGGGAGTCTGG 58.900 50.000 0.00 0.00 26.79 3.86
6938 9327 1.777941 TATGCATTGCCATTGCCTCA 58.222 45.000 3.54 0.00 39.39 3.86
6954 9343 5.219343 TGCCTCAGTGGTAATATCATCAG 57.781 43.478 0.00 0.00 38.35 2.90
6957 9346 5.236282 CCTCAGTGGTAATATCATCAGCAG 58.764 45.833 0.00 0.00 0.00 4.24
6965 9354 8.019669 GTGGTAATATCATCAGCAGCAAAATAG 58.980 37.037 0.00 0.00 0.00 1.73
6974 9363 8.876790 TCATCAGCAGCAAAATAGATATAATCG 58.123 33.333 0.00 0.00 0.00 3.34
6975 9364 7.065216 TCAGCAGCAAAATAGATATAATCGC 57.935 36.000 0.00 0.00 0.00 4.58
6976 9365 6.650390 TCAGCAGCAAAATAGATATAATCGCA 59.350 34.615 0.00 0.00 0.00 5.10
6977 9366 6.740002 CAGCAGCAAAATAGATATAATCGCAC 59.260 38.462 0.00 0.00 0.00 5.34
6978 9367 6.652481 AGCAGCAAAATAGATATAATCGCACT 59.348 34.615 0.00 0.00 0.00 4.40
6979 9368 6.740002 GCAGCAAAATAGATATAATCGCACTG 59.260 38.462 0.00 0.00 0.00 3.66
6980 9369 7.571983 GCAGCAAAATAGATATAATCGCACTGT 60.572 37.037 0.00 0.00 0.00 3.55
6981 9370 8.925700 CAGCAAAATAGATATAATCGCACTGTA 58.074 33.333 0.00 0.00 0.00 2.74
6982 9371 9.658799 AGCAAAATAGATATAATCGCACTGTAT 57.341 29.630 0.00 0.00 0.00 2.29
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 6.651643 TGTGTTTAATTGCACTAGACCGTAAT 59.348 34.615 0.00 0.00 36.63 1.89
18 19 5.508153 CCACAAAAATCGGTCCATGTGTTTA 60.508 40.000 6.85 0.00 37.14 2.01
28 29 0.671251 TGGCACCACAAAAATCGGTC 59.329 50.000 0.00 0.00 0.00 4.79
34 35 5.282055 TGATTACATTGGCACCACAAAAA 57.718 34.783 0.00 0.00 33.48 1.94
40 41 1.638070 TCCCTGATTACATTGGCACCA 59.362 47.619 0.00 0.00 0.00 4.17
56 57 3.288092 GCTAATTTCATCCCGTTTCCCT 58.712 45.455 0.00 0.00 0.00 4.20
59 60 4.609691 TTCGCTAATTTCATCCCGTTTC 57.390 40.909 0.00 0.00 0.00 2.78
69 70 8.420189 CAAGAAGATGTTTGTTTCGCTAATTTC 58.580 33.333 0.00 0.00 0.00 2.17
88 89 9.788889 AATAACATATGATCATCAGCAAGAAGA 57.211 29.630 12.53 0.00 0.00 2.87
201 205 4.962155 TCCTCTCCACTTTGACTCTTTTC 58.038 43.478 0.00 0.00 0.00 2.29
259 264 3.005684 TGCCCAGCTGTATTGAAAGTTTG 59.994 43.478 13.81 0.00 0.00 2.93
260 265 3.230134 TGCCCAGCTGTATTGAAAGTTT 58.770 40.909 13.81 0.00 0.00 2.66
261 266 2.875296 TGCCCAGCTGTATTGAAAGTT 58.125 42.857 13.81 0.00 0.00 2.66
262 267 2.584835 TGCCCAGCTGTATTGAAAGT 57.415 45.000 13.81 0.00 0.00 2.66
263 268 3.940209 TTTGCCCAGCTGTATTGAAAG 57.060 42.857 13.81 0.00 0.00 2.62
264 269 4.088634 AGATTTGCCCAGCTGTATTGAAA 58.911 39.130 13.81 4.70 0.00 2.69
265 270 3.700538 AGATTTGCCCAGCTGTATTGAA 58.299 40.909 13.81 1.22 0.00 2.69
266 271 3.370840 AGATTTGCCCAGCTGTATTGA 57.629 42.857 13.81 0.00 0.00 2.57
291 296 1.580845 CCGGGTTGCTCAGCTTTCTG 61.581 60.000 0.00 0.00 41.67 3.02
332 1814 2.481952 GGTGTGAAACTTCTAGCAGCAG 59.518 50.000 0.00 0.00 38.04 4.24
333 1815 2.494059 GGTGTGAAACTTCTAGCAGCA 58.506 47.619 0.00 0.00 38.04 4.41
334 1816 1.807142 GGGTGTGAAACTTCTAGCAGC 59.193 52.381 0.00 0.00 38.04 5.25
714 2460 4.681643 CGAGCGCCGCAGCAAAAA 62.682 61.111 13.36 0.00 39.83 1.94
723 2469 3.929948 GAATTGGAGCGAGCGCCG 61.930 66.667 11.66 9.10 43.17 6.46
782 2528 1.810151 TGAACTGGACGCCAATAAAGC 59.190 47.619 0.35 0.00 30.80 3.51
787 2533 0.744414 CGGATGAACTGGACGCCAAT 60.744 55.000 0.35 0.00 30.80 3.16
814 2560 1.067495 GCTAGAAGCGAATCGGGCTAT 60.067 52.381 4.35 0.00 40.53 2.97
826 2572 0.615850 AAGGGGACACAGCTAGAAGC 59.384 55.000 0.00 0.00 42.84 3.86
830 2576 0.107945 GAGCAAGGGGACACAGCTAG 60.108 60.000 0.00 0.00 34.74 3.42
834 2580 1.669115 CGTGAGCAAGGGGACACAG 60.669 63.158 0.00 0.00 33.56 3.66
857 2603 7.449704 AGAAGACAAAATGAAGTCAAGGCTATT 59.550 33.333 0.00 0.00 37.23 1.73
898 2644 2.285083 CTCCAACACAACGAGGACAAA 58.715 47.619 0.00 0.00 0.00 2.83
911 2657 0.121197 ATCCCCCTTCTCCTCCAACA 59.879 55.000 0.00 0.00 0.00 3.33
936 2682 1.597937 GCAAGAGTGGTCGCAACAAAG 60.598 52.381 0.00 0.00 0.00 2.77
937 2683 0.380378 GCAAGAGTGGTCGCAACAAA 59.620 50.000 0.00 0.00 0.00 2.83
940 2686 0.166814 GATGCAAGAGTGGTCGCAAC 59.833 55.000 0.00 0.00 38.01 4.17
941 2687 0.035317 AGATGCAAGAGTGGTCGCAA 59.965 50.000 0.00 0.00 38.01 4.85
943 2689 1.086634 GGAGATGCAAGAGTGGTCGC 61.087 60.000 0.00 0.00 0.00 5.19
944 2690 0.247460 TGGAGATGCAAGAGTGGTCG 59.753 55.000 0.00 0.00 0.00 4.79
974 2720 6.637657 TCATGCCTGAGACAAGCATATATAG 58.362 40.000 7.37 0.00 45.16 1.31
975 2721 6.610075 TCATGCCTGAGACAAGCATATATA 57.390 37.500 7.37 0.00 45.16 0.86
976 2722 5.494390 TCATGCCTGAGACAAGCATATAT 57.506 39.130 7.37 0.00 45.16 0.86
994 2740 5.740569 CCGTAAAATTCACAAGCATCTCATG 59.259 40.000 0.00 0.00 0.00 3.07
1002 2748 3.252458 ACTGGACCGTAAAATTCACAAGC 59.748 43.478 0.00 0.00 0.00 4.01
1033 2779 0.684479 TGGACCAGAGGAGACATCGG 60.684 60.000 0.00 0.00 0.00 4.18
1049 2795 2.014064 GAGCAGAGCGAGCAGATGGA 62.014 60.000 0.00 0.00 0.00 3.41
1050 2796 1.592131 GAGCAGAGCGAGCAGATGG 60.592 63.158 0.00 0.00 0.00 3.51
1052 2798 0.102844 GAAGAGCAGAGCGAGCAGAT 59.897 55.000 0.00 0.00 0.00 2.90
1053 2799 1.510383 GAAGAGCAGAGCGAGCAGA 59.490 57.895 0.00 0.00 0.00 4.26
1126 2872 0.807496 GCTTGTTCATCTCCACAGGC 59.193 55.000 0.00 0.00 38.63 4.85
1284 3030 1.296392 CATCCACGCACTCCTCCAA 59.704 57.895 0.00 0.00 0.00 3.53
1311 3057 0.839277 ATTGACTCCCATCATCGCCA 59.161 50.000 0.00 0.00 0.00 5.69
1312 3058 1.517242 GATTGACTCCCATCATCGCC 58.483 55.000 0.00 0.00 0.00 5.54
1332 3078 1.484240 AGAAGCCACTCACCATAGCTC 59.516 52.381 0.00 0.00 32.19 4.09
1383 3129 1.396648 CATATCGAACAAACTGCGGCA 59.603 47.619 1.29 1.29 0.00 5.69
1384 3130 1.396996 ACATATCGAACAAACTGCGGC 59.603 47.619 0.00 0.00 0.00 6.53
1385 3131 3.740044 AACATATCGAACAAACTGCGG 57.260 42.857 0.00 0.00 0.00 5.69
1386 3132 6.247903 ACATAAACATATCGAACAAACTGCG 58.752 36.000 0.00 0.00 0.00 5.18
1387 3133 8.365210 CAAACATAAACATATCGAACAAACTGC 58.635 33.333 0.00 0.00 0.00 4.40
1388 3134 9.393249 ACAAACATAAACATATCGAACAAACTG 57.607 29.630 0.00 0.00 0.00 3.16
1654 3400 6.038356 GTGCCAATCTTTTCATACTTGATGG 58.962 40.000 0.00 0.00 36.08 3.51
1655 3401 6.623486 TGTGCCAATCTTTTCATACTTGATG 58.377 36.000 0.00 0.00 36.82 3.07
1673 3419 0.407528 TTTCCCCTATTGCTGTGCCA 59.592 50.000 0.00 0.00 0.00 4.92
1827 3609 5.862924 AAACCGAATCAGTCAGTACAATG 57.137 39.130 0.00 0.00 0.00 2.82
1828 3610 6.460781 TGTAAACCGAATCAGTCAGTACAAT 58.539 36.000 0.00 0.00 0.00 2.71
1829 3611 5.845103 TGTAAACCGAATCAGTCAGTACAA 58.155 37.500 0.00 0.00 0.00 2.41
1830 3612 5.456548 TGTAAACCGAATCAGTCAGTACA 57.543 39.130 0.00 0.00 0.00 2.90
1831 3613 6.149504 GTTGTAAACCGAATCAGTCAGTAC 57.850 41.667 0.00 0.00 42.21 2.73
1847 3629 9.676195 CAATCAGTACAATTCATGTGTTGTAAA 57.324 29.630 19.68 12.62 43.77 2.01
1848 3630 9.061435 TCAATCAGTACAATTCATGTGTTGTAA 57.939 29.630 19.68 10.52 43.77 2.41
1849 3631 8.614469 TCAATCAGTACAATTCATGTGTTGTA 57.386 30.769 16.32 16.32 43.77 2.41
1850 3632 7.509141 TCAATCAGTACAATTCATGTGTTGT 57.491 32.000 17.81 17.81 43.77 3.32
1851 3633 7.061441 GCTTCAATCAGTACAATTCATGTGTTG 59.939 37.037 10.03 10.03 43.77 3.33
1852 3634 7.040201 AGCTTCAATCAGTACAATTCATGTGTT 60.040 33.333 0.00 0.00 43.77 3.32
1853 3635 6.432162 AGCTTCAATCAGTACAATTCATGTGT 59.568 34.615 0.00 0.00 43.77 3.72
1854 3636 6.745907 CAGCTTCAATCAGTACAATTCATGTG 59.254 38.462 0.00 0.00 43.77 3.21
1855 3637 6.432162 ACAGCTTCAATCAGTACAATTCATGT 59.568 34.615 0.00 0.00 46.36 3.21
1856 3638 6.849502 ACAGCTTCAATCAGTACAATTCATG 58.150 36.000 0.00 0.00 0.00 3.07
1857 3639 7.040201 ACAACAGCTTCAATCAGTACAATTCAT 60.040 33.333 0.00 0.00 0.00 2.57
1858 3640 6.262944 ACAACAGCTTCAATCAGTACAATTCA 59.737 34.615 0.00 0.00 0.00 2.57
1859 3641 6.672147 ACAACAGCTTCAATCAGTACAATTC 58.328 36.000 0.00 0.00 0.00 2.17
1872 3654 2.869801 CGAAGTACCAACAACAGCTTCA 59.130 45.455 0.00 0.00 33.91 3.02
1986 3768 6.924060 GCTCACATTAACGGATATAGTCAGTT 59.076 38.462 0.00 0.00 45.32 3.16
2129 3911 7.913297 GCATGTGTGTAAACAGAACTTAGAAAA 59.087 33.333 0.00 0.00 32.52 2.29
2253 4036 1.933021 TCGTGTAGACCCATGTTCCT 58.067 50.000 0.00 0.00 0.00 3.36
2260 4043 6.231951 TCATGTTTATTTTCGTGTAGACCCA 58.768 36.000 0.00 0.00 0.00 4.51
2375 4158 2.806244 TCTTCCTTCTTTTCTTTCGGCG 59.194 45.455 0.00 0.00 0.00 6.46
2471 4255 4.295051 ACGGACAATAACACATTTGTTGC 58.705 39.130 7.50 0.00 45.91 4.17
2563 4347 6.591834 CCAATTTGAGTCCAGACAACTACTAG 59.408 42.308 0.00 0.00 0.00 2.57
2881 4670 4.362279 GCGTTATGATCAGGTTTACGGTA 58.638 43.478 0.09 0.00 0.00 4.02
3054 4843 6.678568 AAGCCTAGTATCATAGCTGAACAT 57.321 37.500 0.00 0.00 34.37 2.71
3104 4893 8.816640 ACAGGTAGATAAAAAGTTTGCAAATG 57.183 30.769 16.21 6.63 0.00 2.32
3152 5036 4.877378 ACGGAAATGGACACTGTAGTTA 57.123 40.909 0.00 0.00 0.00 2.24
3159 5043 3.438183 ACCTACTACGGAAATGGACACT 58.562 45.455 0.00 0.00 0.00 3.55
3278 5162 3.567576 TGAACCAACATTACGCAATGG 57.432 42.857 12.84 0.00 44.97 3.16
3323 5207 2.093764 ACTGAGCCAGTAAGATGAGCAC 60.094 50.000 6.10 0.00 43.46 4.40
3441 5325 8.849168 ACATTGCTTATTGATTTTCATATCGGA 58.151 29.630 0.00 0.00 0.00 4.55
3472 5356 8.371699 CCAGGGAACATTTTAGTCCAAATAAAA 58.628 33.333 0.00 0.00 36.75 1.52
3977 5861 8.526147 AGCAAAAGATAAGAAACAATAGCATGT 58.474 29.630 0.00 0.00 34.24 3.21
4136 6021 7.040823 AGCAGAGAACCAAAGAACTAAAATCAG 60.041 37.037 0.00 0.00 0.00 2.90
4220 6105 5.698089 CAGTTCTACTTCATTGCTGAACTCA 59.302 40.000 0.00 0.00 41.11 3.41
4569 6454 8.542497 TGAATCTAACGTATTTAAGTTGCAGT 57.458 30.769 0.00 0.00 0.00 4.40
4732 6618 5.930837 ATAGAAGTTCTCAGTCCCTCAAG 57.069 43.478 9.12 0.00 0.00 3.02
4803 6689 5.530171 CCGGTAGCTGTCTGTTAGAAGTATA 59.470 44.000 0.00 0.00 0.00 1.47
4812 6698 2.663196 GCCCGGTAGCTGTCTGTT 59.337 61.111 0.00 0.00 0.00 3.16
5138 7131 7.353414 TCTGAAGGGAATGATAAGAGTACTG 57.647 40.000 0.00 0.00 0.00 2.74
5347 7349 5.615289 AGGTCAATAACAGCATGATACCTC 58.385 41.667 0.00 0.00 39.69 3.85
5350 7352 8.839310 AGATTAGGTCAATAACAGCATGATAC 57.161 34.615 0.00 0.00 39.69 2.24
5381 7385 5.643379 AAACTGAGCACAAAGTTCTGAAA 57.357 34.783 0.00 0.00 35.60 2.69
5433 7440 8.198778 GGTCAAACTTTAACCCAAAATACAAGA 58.801 33.333 0.00 0.00 0.00 3.02
5593 7600 4.380444 CCCCTTCGTATTTTGTGTCCAATG 60.380 45.833 0.00 0.00 0.00 2.82
5916 7923 1.826024 CTCCCCGACCTCCTTCATG 59.174 63.158 0.00 0.00 0.00 3.07
5998 8005 0.106335 TGCTCCGGTCGTGGTTAAAA 59.894 50.000 0.00 0.00 0.00 1.52
6012 8020 5.643379 TGGAAAGAATTTGTGTATGCTCC 57.357 39.130 0.00 0.00 39.27 4.70
6065 8092 4.025040 TCAAGAGCACATTCCATTCTGT 57.975 40.909 0.00 0.00 0.00 3.41
6066 8093 4.216902 TGTTCAAGAGCACATTCCATTCTG 59.783 41.667 0.00 0.00 0.00 3.02
6067 8094 4.401022 TGTTCAAGAGCACATTCCATTCT 58.599 39.130 0.00 0.00 0.00 2.40
6068 8095 4.771590 TGTTCAAGAGCACATTCCATTC 57.228 40.909 0.00 0.00 0.00 2.67
6069 8096 5.011329 ACATTGTTCAAGAGCACATTCCATT 59.989 36.000 0.00 0.00 0.00 3.16
6070 8097 4.525487 ACATTGTTCAAGAGCACATTCCAT 59.475 37.500 0.00 0.00 0.00 3.41
6071 8098 3.890756 ACATTGTTCAAGAGCACATTCCA 59.109 39.130 0.00 0.00 0.00 3.53
6072 8099 4.510038 ACATTGTTCAAGAGCACATTCC 57.490 40.909 0.00 0.00 0.00 3.01
6073 8100 6.000891 TGTACATTGTTCAAGAGCACATTC 57.999 37.500 0.00 0.00 0.00 2.67
6074 8101 5.764686 TCTGTACATTGTTCAAGAGCACATT 59.235 36.000 0.00 0.00 0.00 2.71
6075 8102 5.180117 GTCTGTACATTGTTCAAGAGCACAT 59.820 40.000 0.00 0.00 0.00 3.21
6076 8103 4.511454 GTCTGTACATTGTTCAAGAGCACA 59.489 41.667 0.00 0.00 0.00 4.57
6077 8104 4.376413 CGTCTGTACATTGTTCAAGAGCAC 60.376 45.833 0.00 0.00 0.00 4.40
6078 8105 3.740832 CGTCTGTACATTGTTCAAGAGCA 59.259 43.478 0.00 0.00 0.00 4.26
6079 8106 3.987868 TCGTCTGTACATTGTTCAAGAGC 59.012 43.478 0.00 0.00 0.00 4.09
6080 8107 5.107453 GGTTCGTCTGTACATTGTTCAAGAG 60.107 44.000 0.00 0.00 0.00 2.85
6081 8108 4.748102 GGTTCGTCTGTACATTGTTCAAGA 59.252 41.667 0.00 0.00 0.00 3.02
6082 8109 4.509970 TGGTTCGTCTGTACATTGTTCAAG 59.490 41.667 0.00 0.00 0.00 3.02
6160 8187 3.144506 CACAGTCAGCAAAGAGGACAAT 58.855 45.455 0.00 0.00 34.04 2.71
6162 8189 1.811558 GCACAGTCAGCAAAGAGGACA 60.812 52.381 0.00 0.00 34.04 4.02
6164 8191 0.601046 CGCACAGTCAGCAAAGAGGA 60.601 55.000 0.00 0.00 0.00 3.71
6167 8194 2.597713 CGCGCACAGTCAGCAAAGA 61.598 57.895 8.75 0.00 0.00 2.52
6197 8224 3.937706 AGAGAGAAATTTCATGCACGGAG 59.062 43.478 19.99 0.00 0.00 4.63
6204 8231 7.211966 ACAAACTCCAGAGAGAAATTTCATG 57.788 36.000 19.99 11.99 43.39 3.07
6205 8232 7.723172 AGAACAAACTCCAGAGAGAAATTTCAT 59.277 33.333 19.99 8.20 43.39 2.57
6278 8305 7.386025 CCAGATCAAAAAGGGAAAGATTTTCAC 59.614 37.037 0.00 0.13 0.00 3.18
6280 8307 7.670364 TCCAGATCAAAAAGGGAAAGATTTTC 58.330 34.615 0.00 0.00 0.00 2.29
6281 8308 7.616528 TCCAGATCAAAAAGGGAAAGATTTT 57.383 32.000 0.00 0.00 0.00 1.82
6283 8310 6.014242 GGTTCCAGATCAAAAAGGGAAAGATT 60.014 38.462 0.00 0.00 39.18 2.40
6284 8311 5.481824 GGTTCCAGATCAAAAAGGGAAAGAT 59.518 40.000 0.00 0.00 39.18 2.40
6287 8314 4.551671 TGGTTCCAGATCAAAAAGGGAAA 58.448 39.130 0.00 0.00 39.18 3.13
6288 8315 4.191804 TGGTTCCAGATCAAAAAGGGAA 57.808 40.909 0.00 0.00 35.38 3.97
6289 8316 3.893753 TGGTTCCAGATCAAAAAGGGA 57.106 42.857 0.00 0.00 0.00 4.20
6290 8317 3.306294 GCTTGGTTCCAGATCAAAAAGGG 60.306 47.826 0.00 0.00 0.00 3.95
6291 8318 3.321682 TGCTTGGTTCCAGATCAAAAAGG 59.678 43.478 0.00 0.00 0.00 3.11
6292 8319 4.589216 TGCTTGGTTCCAGATCAAAAAG 57.411 40.909 0.00 0.00 0.00 2.27
6293 8320 4.405358 ACTTGCTTGGTTCCAGATCAAAAA 59.595 37.500 0.00 0.00 0.00 1.94
6294 8321 3.960102 ACTTGCTTGGTTCCAGATCAAAA 59.040 39.130 0.00 0.00 0.00 2.44
6295 8322 3.565307 ACTTGCTTGGTTCCAGATCAAA 58.435 40.909 0.00 0.00 0.00 2.69
6322 8349 5.530915 TCAACACTTCCATAGAAACAACAGG 59.469 40.000 0.00 0.00 0.00 4.00
6335 8362 3.909732 AGTTCCCATTTCAACACTTCCA 58.090 40.909 0.00 0.00 0.00 3.53
6337 8364 5.514274 TGAAGTTCCCATTTCAACACTTC 57.486 39.130 0.00 0.00 40.29 3.01
6363 8390 9.783256 GTCCGTAGTTTTGCAATCTAAAAATAT 57.217 29.630 0.00 0.00 32.48 1.28
6365 8392 7.088272 GGTCCGTAGTTTTGCAATCTAAAAAT 58.912 34.615 0.00 0.00 0.00 1.82
6373 8400 3.153919 ACATGGTCCGTAGTTTTGCAAT 58.846 40.909 0.00 0.00 0.00 3.56
6410 8441 1.637553 AGCCATGATGACCTTTCCTGT 59.362 47.619 0.00 0.00 0.00 4.00
6411 8442 2.431954 AGCCATGATGACCTTTCCTG 57.568 50.000 0.00 0.00 0.00 3.86
6426 8457 9.845740 TTGTTCTGATATTAATAAAGCTAGCCA 57.154 29.630 12.13 0.00 0.00 4.75
6543 8574 4.569162 CGTTTAGTTGGACTGACAAACTCA 59.431 41.667 3.20 0.00 31.17 3.41
6549 8580 4.395959 AACTCGTTTAGTTGGACTGACA 57.604 40.909 0.00 0.00 46.90 3.58
6585 8616 8.693542 ATCAAACAATGTGCTAGCTAATTTTC 57.306 30.769 17.23 0.00 0.00 2.29
6605 8636 8.715191 ACATTGTTTTTGTTCAGCTAATCAAA 57.285 26.923 0.00 0.00 0.00 2.69
6642 8673 7.846644 AGACTTAGCTTCAATGATTGAGAAG 57.153 36.000 8.01 12.03 41.38 2.85
6646 8677 9.507329 AAGTTTAGACTTAGCTTCAATGATTGA 57.493 29.630 3.29 3.29 44.13 2.57
6673 8704 2.869646 CTGCGGCGATCTTTGCAA 59.130 55.556 12.98 0.00 36.82 4.08
6700 8731 2.673200 ATGGTGGGACGCAGCATCT 61.673 57.895 26.13 10.97 43.02 2.90
6701 8732 2.124570 ATGGTGGGACGCAGCATC 60.125 61.111 26.13 0.70 43.02 3.91
6702 8733 2.124570 GATGGTGGGACGCAGCAT 60.125 61.111 30.24 30.24 43.02 3.79
6703 8734 2.894257 AAGATGGTGGGACGCAGCA 61.894 57.895 24.15 24.15 43.02 4.41
6704 8735 2.045926 AAGATGGTGGGACGCAGC 60.046 61.111 14.24 14.24 43.02 5.25
6705 8736 0.107508 ATCAAGATGGTGGGACGCAG 60.108 55.000 0.00 0.00 43.02 5.18
6706 8737 0.327924 AATCAAGATGGTGGGACGCA 59.672 50.000 0.00 0.00 43.02 5.24
6707 8738 0.734889 CAATCAAGATGGTGGGACGC 59.265 55.000 0.00 0.00 38.67 5.19
6728 8759 5.901552 ACAGGTGAACAACTTTTGTATTGG 58.098 37.500 0.00 0.00 44.59 3.16
6743 8774 4.223032 GGAATCAGACTCCTTACAGGTGAA 59.777 45.833 0.00 0.00 36.53 3.18
6753 8857 6.131972 TCATTTCTTTGGAATCAGACTCCT 57.868 37.500 0.00 0.00 33.77 3.69
6762 8866 7.363268 GCCTACAAGTGATCATTTCTTTGGAAT 60.363 37.037 0.00 0.00 0.00 3.01
6768 8872 5.564550 ACTGCCTACAAGTGATCATTTCTT 58.435 37.500 0.00 0.00 0.00 2.52
6773 8877 4.223700 TCAAGACTGCCTACAAGTGATCAT 59.776 41.667 0.00 0.00 0.00 2.45
6788 8892 5.389859 TTTGTATTGGCCAATCAAGACTG 57.610 39.130 33.89 0.00 39.00 3.51
6825 9214 0.041238 TCCGTGGAATCAGACTCCCT 59.959 55.000 0.00 0.00 31.32 4.20
6842 9231 2.432510 CTCCCTACAAGTGATCACCTCC 59.567 54.545 22.21 0.00 0.00 4.30
6845 9234 3.100671 AGACTCCCTACAAGTGATCACC 58.899 50.000 22.21 4.75 0.00 4.02
6864 9253 3.706373 GGCAGAGGCGGAACCAGA 61.706 66.667 0.00 0.00 43.14 3.86
6868 9257 4.162690 ATCGGGCAGAGGCGGAAC 62.163 66.667 5.04 0.00 40.31 3.62
6938 9327 4.694760 TGCTGCTGATGATATTACCACT 57.305 40.909 0.00 0.00 0.00 4.00
6948 9337 8.876790 CGATTATATCTATTTTGCTGCTGATGA 58.123 33.333 0.00 0.00 0.00 2.92
6954 9343 6.740002 CAGTGCGATTATATCTATTTTGCTGC 59.260 38.462 0.00 0.00 0.00 5.25


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

AutoCloner maintained by Alex Coulton.