Multiple sequence alignment - TraesCS6B01G137500

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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 TraesCS6B01G137500 chr6B 100.000 5819 0 0 1 5819 135111327 135117145 0.000000e+00 10746.0
1 TraesCS6B01G137500 chr6B 84.698 1490 164 26 3373 4837 130828474 130829924 0.000000e+00 1430.0
2 TraesCS6B01G137500 chr6B 78.783 641 96 26 2060 2679 130823650 130824271 1.520000e-105 394.0
3 TraesCS6B01G137500 chr6B 78.600 500 67 21 5338 5819 519134944 519135421 1.590000e-75 294.0
4 TraesCS6B01G137500 chr6B 80.870 230 32 7 1054 1283 130822740 130822957 2.790000e-38 171.0
5 TraesCS6B01G137500 chr6B 89.000 100 11 0 1758 1857 130823365 130823464 2.200000e-24 124.0
6 TraesCS6B01G137500 chr6B 77.215 158 36 0 5602 5759 52438492 52438335 6.210000e-15 93.5
7 TraesCS6B01G137500 chr6A 88.044 2894 253 58 1 2856 77779277 77782115 0.000000e+00 3341.0
8 TraesCS6B01G137500 chr6A 92.449 1907 116 11 3127 5022 77782294 77784183 0.000000e+00 2699.0
9 TraesCS6B01G137500 chr6A 83.046 1510 170 37 3373 4837 73555907 73557375 0.000000e+00 1291.0
10 TraesCS6B01G137500 chr6A 79.968 619 89 22 2082 2684 73543318 73543917 1.940000e-114 424.0
11 TraesCS6B01G137500 chr6A 83.568 213 26 5 1434 1640 73542748 73542957 2.140000e-44 191.0
12 TraesCS6B01G137500 chr6A 88.119 101 12 0 1757 1857 73543029 73543129 2.850000e-23 121.0
13 TraesCS6B01G137500 chr6A 85.567 97 5 5 3008 3104 77782211 77782298 6.210000e-15 93.5
14 TraesCS6B01G137500 chr6D 89.579 2303 154 37 678 2943 61134325 61136578 0.000000e+00 2844.0
15 TraesCS6B01G137500 chr6D 91.885 1183 68 11 3901 5079 61137517 61138675 0.000000e+00 1628.0
16 TraesCS6B01G137500 chr6D 83.847 1492 175 22 3373 4837 58239086 58240538 0.000000e+00 1360.0
17 TraesCS6B01G137500 chr6D 91.046 927 61 16 2939 3860 61136605 61137514 0.000000e+00 1232.0
18 TraesCS6B01G137500 chr6D 79.967 609 80 27 2086 2675 58235129 58235714 1.510000e-110 411.0
19 TraesCS6B01G137500 chr6D 80.880 523 84 10 5300 5808 343944592 343945112 1.170000e-106 398.0
20 TraesCS6B01G137500 chr6D 93.750 256 12 2 205 456 61132837 61133092 1.180000e-101 381.0
21 TraesCS6B01G137500 chr6D 91.327 196 12 2 276 466 61133089 61133284 4.470000e-66 263.0
22 TraesCS6B01G137500 chr6D 88.584 219 15 1 1 209 61106427 61106645 2.080000e-64 257.0
23 TraesCS6B01G137500 chr6D 83.444 151 21 3 1708 1857 58234760 58234907 2.830000e-28 137.0
24 TraesCS6B01G137500 chr6D 94.737 38 1 1 5248 5284 61138731 61138768 2.260000e-04 58.4
25 TraesCS6B01G137500 chr5D 87.996 1841 187 20 3187 5020 218053959 218055772 0.000000e+00 2145.0
26 TraesCS6B01G137500 chr5D 83.560 1101 105 41 1458 2541 218052272 218053313 0.000000e+00 961.0
27 TraesCS6B01G137500 chr5D 83.161 386 43 12 1047 1430 218051801 218052166 3.360000e-87 333.0
28 TraesCS6B01G137500 chr5D 77.670 515 78 25 5335 5819 435521479 435521986 4.440000e-71 279.0
29 TraesCS6B01G137500 chr5D 92.737 179 12 1 5065 5243 296949343 296949520 2.080000e-64 257.0
30 TraesCS6B01G137500 chr5D 83.219 292 36 4 5537 5816 8807098 8807388 7.480000e-64 255.0
31 TraesCS6B01G137500 chr5A 88.483 1754 184 13 3187 4933 290928393 290930135 0.000000e+00 2104.0
32 TraesCS6B01G137500 chr5A 82.343 1212 124 45 1462 2654 290925490 290926630 0.000000e+00 970.0
33 TraesCS6B01G137500 chr5A 84.960 379 31 16 1054 1430 290925027 290925381 1.540000e-95 361.0
34 TraesCS6B01G137500 chr5B 87.711 1245 119 11 3778 5015 234303457 234304674 0.000000e+00 1421.0
35 TraesCS6B01G137500 chr5B 83.524 1050 102 38 1508 2541 234296023 234297017 0.000000e+00 915.0
36 TraesCS6B01G137500 chr5B 89.632 598 58 4 3187 3781 234302748 234303344 0.000000e+00 758.0
37 TraesCS6B01G137500 chr5B 83.636 385 38 12 1048 1430 234295498 234295859 7.220000e-89 339.0
38 TraesCS6B01G137500 chr3D 85.645 411 44 10 5416 5816 602278982 602278577 9.020000e-113 418.0
39 TraesCS6B01G137500 chr3D 95.092 163 8 0 5081 5243 486739850 486739688 2.080000e-64 257.0
40 TraesCS6B01G137500 chr3D 84.834 211 27 1 5354 5559 27935771 27935981 2.130000e-49 207.0
41 TraesCS6B01G137500 chr2B 81.343 536 52 20 5298 5819 58315253 58315754 5.470000e-105 392.0
42 TraesCS6B01G137500 chr2B 94.767 172 8 1 5071 5242 237581401 237581571 3.460000e-67 267.0
43 TraesCS6B01G137500 chr7B 87.246 345 29 12 5298 5633 93432357 93432695 4.260000e-101 379.0
44 TraesCS6B01G137500 chr3B 86.466 266 30 2 5298 5558 46783849 46784113 2.650000e-73 287.0
45 TraesCS6B01G137500 chr3B 95.556 45 1 1 243 286 671135408 671135364 2.910000e-08 71.3
46 TraesCS6B01G137500 chr1A 83.648 318 36 8 5479 5780 22737195 22737512 9.540000e-73 285.0
47 TraesCS6B01G137500 chr1B 97.546 163 4 0 5080 5242 662157362 662157524 4.440000e-71 279.0
48 TraesCS6B01G137500 chr1B 96.933 163 5 0 5080 5242 662159916 662160078 2.070000e-69 274.0
49 TraesCS6B01G137500 chr1B 95.210 167 8 0 5076 5242 450130947 450130781 1.240000e-66 265.0
50 TraesCS6B01G137500 chr1B 95.679 162 7 0 5081 5242 334945845 334946006 1.610000e-65 261.0
51 TraesCS6B01G137500 chr7A 93.642 173 10 1 5070 5242 727851114 727851285 2.080000e-64 257.0
52 TraesCS6B01G137500 chr4A 92.045 176 13 1 5067 5242 696729846 696730020 4.500000e-61 246.0
53 TraesCS6B01G137500 chr4A 79.263 217 23 11 5581 5797 597867215 597867021 1.320000e-26 132.0
54 TraesCS6B01G137500 chr3A 87.755 98 12 0 5377 5474 37813619 37813716 1.330000e-21 115.0
55 TraesCS6B01G137500 chrUn 78.065 155 34 0 5602 5756 312334789 312334943 1.330000e-16 99.0
56 TraesCS6B01G137500 chr4D 96.364 55 2 0 2429 2483 34592255 34592201 2.230000e-14 91.6


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 TraesCS6B01G137500 chr6B 135111327 135117145 5818 False 10746.000000 10746 100.000000 1 5819 1 chr6B.!!$F2 5818
1 TraesCS6B01G137500 chr6B 130828474 130829924 1450 False 1430.000000 1430 84.698000 3373 4837 1 chr6B.!!$F1 1464
2 TraesCS6B01G137500 chr6B 130822740 130824271 1531 False 229.666667 394 82.884333 1054 2679 3 chr6B.!!$F4 1625
3 TraesCS6B01G137500 chr6A 77779277 77784183 4906 False 2044.500000 3341 88.686667 1 5022 3 chr6A.!!$F3 5021
4 TraesCS6B01G137500 chr6A 73555907 73557375 1468 False 1291.000000 1291 83.046000 3373 4837 1 chr6A.!!$F1 1464
5 TraesCS6B01G137500 chr6A 73542748 73543917 1169 False 245.333333 424 83.885000 1434 2684 3 chr6A.!!$F2 1250
6 TraesCS6B01G137500 chr6D 61132837 61138768 5931 False 1067.733333 2844 92.054000 205 5284 6 chr6D.!!$F4 5079
7 TraesCS6B01G137500 chr6D 58234760 58240538 5778 False 636.000000 1360 82.419333 1708 4837 3 chr6D.!!$F3 3129
8 TraesCS6B01G137500 chr6D 343944592 343945112 520 False 398.000000 398 80.880000 5300 5808 1 chr6D.!!$F2 508
9 TraesCS6B01G137500 chr5D 218051801 218055772 3971 False 1146.333333 2145 84.905667 1047 5020 3 chr5D.!!$F4 3973
10 TraesCS6B01G137500 chr5D 435521479 435521986 507 False 279.000000 279 77.670000 5335 5819 1 chr5D.!!$F3 484
11 TraesCS6B01G137500 chr5A 290925027 290930135 5108 False 1145.000000 2104 85.262000 1054 4933 3 chr5A.!!$F1 3879
12 TraesCS6B01G137500 chr5B 234302748 234304674 1926 False 1089.500000 1421 88.671500 3187 5015 2 chr5B.!!$F2 1828
13 TraesCS6B01G137500 chr5B 234295498 234297017 1519 False 627.000000 915 83.580000 1048 2541 2 chr5B.!!$F1 1493
14 TraesCS6B01G137500 chr2B 58315253 58315754 501 False 392.000000 392 81.343000 5298 5819 1 chr2B.!!$F1 521
15 TraesCS6B01G137500 chr1B 662157362 662160078 2716 False 276.500000 279 97.239500 5080 5242 2 chr1B.!!$F2 162

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
818 1849 0.179094 AGACAAAACGCACAGTCCGA 60.179 50.000 0.0 0.0 0.00 4.55 F
1421 2491 0.039165 CGCTGCCCTTTTCTTGGTTC 60.039 55.000 0.0 0.0 0.00 3.62 F
2690 3979 0.389817 TGTCGAATCAAGGGACAGCG 60.390 55.000 0.0 0.0 35.89 5.18 F
3051 8221 1.884579 AGGCAAACACATGCTTCTCAG 59.115 47.619 0.0 0.0 45.68 3.35 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2034 3259 0.752658 GGGCAAGCTGTGGAACTTTT 59.247 50.000 0.00 0.0 38.04 2.27 R
3238 8515 0.995024 ATGCACAGGCTAGGGAGTTT 59.005 50.000 0.00 0.0 41.91 2.66 R
4364 9850 1.683011 GGCATCTCTAGGGCTTTGCAA 60.683 52.381 12.25 0.0 0.00 4.08 R
4842 10373 0.794229 GGCGCAATCACACATTGTCG 60.794 55.000 10.83 0.0 34.34 4.35 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
29 30 2.080286 ATTGTACACACGAGAGCACC 57.920 50.000 0.00 0.00 0.00 5.01
30 31 0.747852 TTGTACACACGAGAGCACCA 59.252 50.000 0.00 0.00 0.00 4.17
58 59 1.152440 CCCATCTCTACTCCGGCCT 60.152 63.158 0.00 0.00 0.00 5.19
63 74 2.361992 TCTACTCCGGCCTCGCAA 60.362 61.111 0.00 0.00 34.56 4.85
68 79 1.450312 CTCCGGCCTCGCAAAAGAT 60.450 57.895 0.00 0.00 34.56 2.40
71 82 1.745115 CGGCCTCGCAAAAGATCCA 60.745 57.895 0.00 0.00 0.00 3.41
76 87 1.012841 CTCGCAAAAGATCCAGGCTC 58.987 55.000 0.00 0.00 0.00 4.70
77 88 0.615331 TCGCAAAAGATCCAGGCTCT 59.385 50.000 0.00 0.00 0.00 4.09
78 89 1.831106 TCGCAAAAGATCCAGGCTCTA 59.169 47.619 0.00 0.00 0.00 2.43
90 101 3.597728 GCTCTAGTCGGCCCGAGG 61.598 72.222 5.82 0.00 36.23 4.63
93 104 0.824182 CTCTAGTCGGCCCGAGGAAT 60.824 60.000 5.82 0.00 36.23 3.01
101 112 0.183731 GGCCCGAGGAATTTGGAGAT 59.816 55.000 0.00 0.00 31.06 2.75
113 124 3.857549 TTTGGAGATGACGACTCTCAG 57.142 47.619 13.00 0.00 40.78 3.35
114 125 2.498644 TGGAGATGACGACTCTCAGT 57.501 50.000 13.00 0.00 40.78 3.41
129 140 2.295349 TCTCAGTGGTGGTAGTTTCGAC 59.705 50.000 0.00 0.00 0.00 4.20
137 148 3.128349 GTGGTAGTTTCGACAGAAAGCA 58.872 45.455 0.00 0.00 45.92 3.91
145 156 1.858458 TCGACAGAAAGCAACTCGTTG 59.142 47.619 5.45 5.45 43.14 4.10
184 195 1.595794 CACCCAAATCCATACGCGTAC 59.404 52.381 23.19 0.00 0.00 3.67
187 198 1.519758 CCAAATCCATACGCGTACGAC 59.480 52.381 23.19 9.57 43.93 4.34
188 199 2.456989 CAAATCCATACGCGTACGACT 58.543 47.619 23.19 7.24 43.93 4.18
197 208 1.469126 CGCGTACGACTCCGGAATTG 61.469 60.000 21.65 0.71 43.93 2.32
223 234 1.407618 GAAAAGCACCAACGGAACCTT 59.592 47.619 0.00 0.00 0.00 3.50
308 503 9.645059 CAAGAATTAGACTTACTGATGAGAACA 57.355 33.333 0.00 0.00 0.00 3.18
344 539 3.599730 TCTCATGATCTTCTTGCGTGT 57.400 42.857 0.00 0.00 0.00 4.49
377 572 2.119495 GGGCTCTAATCCTGGTTCTCA 58.881 52.381 0.00 0.00 0.00 3.27
423 620 2.858729 CTTGTGTTGTGCAAGTCGC 58.141 52.632 0.00 0.00 38.68 5.19
499 1103 3.142174 GACCTTATAATGCAGTGCCTCC 58.858 50.000 13.72 0.00 0.00 4.30
509 1113 0.605589 CAGTGCCTCCGGGATATCTC 59.394 60.000 0.00 0.00 33.58 2.75
516 1120 2.356741 CCTCCGGGATATCTCTCTCCTC 60.357 59.091 0.00 0.00 33.58 3.71
517 1121 1.279558 TCCGGGATATCTCTCTCCTCG 59.720 57.143 0.00 0.00 0.00 4.63
520 1124 1.470051 GGATATCTCTCTCCTCGGGC 58.530 60.000 2.05 0.00 0.00 6.13
557 1161 4.325972 TGCAAGACTTACATTGATGCTCA 58.674 39.130 0.00 0.00 33.66 4.26
617 1221 5.560722 TTGTTTAGTGGAAGGAGACATCA 57.439 39.130 0.00 0.00 0.00 3.07
625 1229 3.274288 GGAAGGAGACATCACATCAACC 58.726 50.000 0.00 0.00 0.00 3.77
645 1249 2.579787 CGAGATGTGACGTCGGCC 60.580 66.667 11.62 0.00 0.00 6.13
648 1252 2.509336 GATGTGACGTCGGCCCAG 60.509 66.667 11.62 0.00 0.00 4.45
663 1267 1.753141 GCCCAGTATCTCGGAGGTACA 60.753 57.143 25.81 0.00 0.00 2.90
709 1740 7.550551 CCCGTGCAATGATAAAGATGAGTATAT 59.449 37.037 0.00 0.00 0.00 0.86
711 1742 8.929746 CGTGCAATGATAAAGATGAGTATATGT 58.070 33.333 0.00 0.00 0.00 2.29
736 1767 6.169419 GGCACCTGCAATTAATTTTCTTTC 57.831 37.500 0.00 0.00 44.36 2.62
818 1849 0.179094 AGACAAAACGCACAGTCCGA 60.179 50.000 0.00 0.00 0.00 4.55
834 1865 1.298413 CGATAGACGACCCAGCGTG 60.298 63.158 0.00 0.00 45.72 5.34
836 1867 3.411418 ATAGACGACCCAGCGTGCG 62.411 63.158 0.00 0.00 45.72 5.34
838 1869 4.409218 GACGACCCAGCGTGCGTA 62.409 66.667 0.00 0.00 45.72 4.42
839 1870 4.712425 ACGACCCAGCGTGCGTAC 62.712 66.667 0.00 0.00 43.79 3.67
840 1871 4.415332 CGACCCAGCGTGCGTACT 62.415 66.667 1.24 0.00 0.00 2.73
983 2023 2.760385 CCCCTCACCCTCCTCGAC 60.760 72.222 0.00 0.00 0.00 4.20
1035 2076 1.084370 CGAGAAGGCCACGACCATTC 61.084 60.000 5.01 0.00 0.00 2.67
1036 2077 0.744771 GAGAAGGCCACGACCATTCC 60.745 60.000 5.01 0.00 0.00 3.01
1037 2078 1.201429 AGAAGGCCACGACCATTCCT 61.201 55.000 5.01 0.00 0.00 3.36
1038 2079 0.322546 GAAGGCCACGACCATTCCTT 60.323 55.000 5.01 0.00 39.63 3.36
1052 2100 3.555168 CCATTCCTTGGCGGTAGATAGTC 60.555 52.174 0.00 0.00 39.09 2.59
1369 2424 0.447801 CGGTCAAGAAAATCGCCCAG 59.552 55.000 0.00 0.00 0.00 4.45
1421 2491 0.039165 CGCTGCCCTTTTCTTGGTTC 60.039 55.000 0.00 0.00 0.00 3.62
1431 2501 3.312736 TTTCTTGGTTCTTGCCCTCTT 57.687 42.857 0.00 0.00 0.00 2.85
1432 2502 3.312736 TTCTTGGTTCTTGCCCTCTTT 57.687 42.857 0.00 0.00 0.00 2.52
1499 2667 1.335872 GGTGCTGAAAATTCACCGGTG 60.336 52.381 29.26 29.26 40.54 4.94
1514 2694 1.226746 CGGTGTTCTCTGGTTTGGAC 58.773 55.000 0.00 0.00 0.00 4.02
1643 2828 2.354704 CCTCAACGCATCCAAGGTCTTA 60.355 50.000 0.00 0.00 0.00 2.10
1644 2829 3.334691 CTCAACGCATCCAAGGTCTTAA 58.665 45.455 0.00 0.00 0.00 1.85
1654 2839 5.319043 TCCAAGGTCTTAAACACATTCCT 57.681 39.130 0.00 0.00 0.00 3.36
1764 2963 8.730680 TCCTTATTTTTAACTCTCAACTCATGC 58.269 33.333 0.00 0.00 0.00 4.06
1847 3046 2.580815 CAGCACTGGATCGAGGCA 59.419 61.111 16.38 0.00 0.00 4.75
1879 3079 7.857456 ACAAAATATCCTACACATCCACTACA 58.143 34.615 0.00 0.00 0.00 2.74
1881 3082 9.173021 CAAAATATCCTACACATCCACTACAAA 57.827 33.333 0.00 0.00 0.00 2.83
1918 3119 1.710013 CAGTAGTGTTGTACGGCAGG 58.290 55.000 0.00 0.00 0.00 4.85
1924 3125 2.094182 AGTGTTGTACGGCAGGAGTATG 60.094 50.000 0.00 0.00 0.00 2.39
1928 3129 2.026641 TGTACGGCAGGAGTATGGTAC 58.973 52.381 0.00 0.00 0.00 3.34
1999 3216 3.726607 CTTCCCAGTATCAGCTGATCAC 58.273 50.000 31.92 24.62 38.70 3.06
2030 3255 4.679197 GTCAGCTCTGAACATCGATGATAC 59.321 45.833 31.33 19.84 41.85 2.24
2031 3256 4.339247 TCAGCTCTGAACATCGATGATACA 59.661 41.667 31.33 22.74 36.53 2.29
2032 3257 4.680567 CAGCTCTGAACATCGATGATACAG 59.319 45.833 31.33 28.81 0.00 2.74
2033 3258 4.340666 AGCTCTGAACATCGATGATACAGT 59.659 41.667 31.33 16.08 32.60 3.55
2034 3259 5.532779 AGCTCTGAACATCGATGATACAGTA 59.467 40.000 31.33 20.07 32.60 2.74
2078 3335 4.073293 TCTTGACTTGGGACTTCTGTTC 57.927 45.455 0.00 0.00 0.00 3.18
2135 3398 8.727100 TGTAGATTGATCCAAGACATAGGTAT 57.273 34.615 0.00 0.00 0.00 2.73
2278 3542 7.362662 ACGGAATCATGCAAATCAATATGTAC 58.637 34.615 0.00 0.00 0.00 2.90
2292 3562 7.316393 TCAATATGTACTCCCCATTTCCTAG 57.684 40.000 0.00 0.00 0.00 3.02
2340 3613 6.866770 CACGGAAACTGATAGTCTTTTACTCA 59.133 38.462 0.00 0.00 39.80 3.41
2343 3616 8.596380 CGGAAACTGATAGTCTTTTACTCATTC 58.404 37.037 0.00 0.00 39.80 2.67
2465 3738 4.641541 TGGTCCAGTAAGATCATTTGCATG 59.358 41.667 0.00 0.00 0.00 4.06
2525 3812 3.002791 CCAATGAGAGCTGCGTTAGAAA 58.997 45.455 0.00 0.00 0.00 2.52
2551 3838 3.624861 AGAGTGCTAAATTCATTCAGCGG 59.375 43.478 0.00 0.00 36.81 5.52
2561 3848 2.844946 TCATTCAGCGGTCAAGTTTCA 58.155 42.857 0.00 0.00 0.00 2.69
2628 3917 6.706270 TGTTTCTCATGTTCACCTTCTAGAAC 59.294 38.462 0.00 0.00 43.31 3.01
2642 3931 6.072286 ACCTTCTAGAACATGTTTTGCTCATG 60.072 38.462 13.36 4.66 45.41 3.07
2664 3953 2.147958 TGAGAACGTGGGTTATGTTGC 58.852 47.619 0.00 0.00 38.60 4.17
2688 3977 1.676014 GGGTGTCGAATCAAGGGACAG 60.676 57.143 0.00 0.00 40.99 3.51
2690 3979 0.389817 TGTCGAATCAAGGGACAGCG 60.390 55.000 0.00 0.00 35.89 5.18
2858 7916 9.936759 ATATTTAGTTAGGCAAGAGATAGCTTC 57.063 33.333 0.00 0.00 0.00 3.86
2860 7918 8.534954 TTTAGTTAGGCAAGAGATAGCTTCTA 57.465 34.615 0.00 0.00 33.74 2.10
2936 7996 2.876581 TCGACAGCGATTAGACCCA 58.123 52.632 0.00 0.00 42.51 4.51
2953 8043 2.601666 AGCCTCGGTCTCTGCACA 60.602 61.111 0.00 0.00 0.00 4.57
2954 8044 2.433318 GCCTCGGTCTCTGCACAC 60.433 66.667 0.00 0.00 0.00 3.82
3036 8200 5.397899 CCCTCTGTCCAGAATTATAAGGCAA 60.398 44.000 0.00 0.00 36.94 4.52
3051 8221 1.884579 AGGCAAACACATGCTTCTCAG 59.115 47.619 0.00 0.00 45.68 3.35
3067 8257 7.795047 TGCTTCTCAGATTTATTGGTCTATGA 58.205 34.615 0.00 0.00 0.00 2.15
3068 8258 7.712639 TGCTTCTCAGATTTATTGGTCTATGAC 59.287 37.037 0.00 0.00 0.00 3.06
3076 8266 9.607333 AGATTTATTGGTCTATGACTATGAGGA 57.393 33.333 0.00 0.00 32.47 3.71
3081 8271 6.819397 TGGTCTATGACTATGAGGATTACG 57.181 41.667 0.00 0.00 32.47 3.18
3082 8272 6.304624 TGGTCTATGACTATGAGGATTACGT 58.695 40.000 0.00 0.00 32.47 3.57
3083 8273 6.430308 TGGTCTATGACTATGAGGATTACGTC 59.570 42.308 0.00 0.00 32.47 4.34
3084 8274 6.430308 GGTCTATGACTATGAGGATTACGTCA 59.570 42.308 0.00 0.00 37.69 4.35
3086 8276 9.163899 GTCTATGACTATGAGGATTACGTCATA 57.836 37.037 0.00 0.00 45.67 2.15
3087 8277 9.163899 TCTATGACTATGAGGATTACGTCATAC 57.836 37.037 0.00 0.00 45.67 2.39
3088 8278 7.761038 ATGACTATGAGGATTACGTCATACA 57.239 36.000 0.00 0.00 45.67 2.29
3089 8279 7.576861 TGACTATGAGGATTACGTCATACAA 57.423 36.000 0.00 0.00 45.67 2.41
3127 8317 6.035220 CGTTGGATTCATACTAAACGCACTTA 59.965 38.462 0.00 0.00 34.73 2.24
3267 8545 4.757149 CCTAGCCTGTGCATTAATACTTCC 59.243 45.833 0.00 0.00 41.13 3.46
3295 8573 6.209192 TCAATTGTTCATCTTAACCACAGCAT 59.791 34.615 5.13 0.00 0.00 3.79
3335 8614 4.419522 AGTCGTAACAAATTGCCACATC 57.580 40.909 0.00 0.00 0.00 3.06
3559 8870 4.192317 GGGCAGGTAGTTTGATAACTCAG 58.808 47.826 0.00 0.00 43.45 3.35
3576 8887 6.579666 AACTCAGAGAATTTTATTGCTGCA 57.420 33.333 3.79 0.00 0.00 4.41
3577 8888 6.770746 ACTCAGAGAATTTTATTGCTGCAT 57.229 33.333 1.84 0.00 0.00 3.96
3615 8929 3.634910 TGTTTTGGAAGGTTAGCTTCACC 59.365 43.478 22.96 10.15 32.84 4.02
3629 8944 8.182227 GGTTAGCTTCACCATATGTTTAACTTC 58.818 37.037 9.44 0.00 34.04 3.01
3630 8945 6.759497 AGCTTCACCATATGTTTAACTTCC 57.241 37.500 1.24 0.00 0.00 3.46
3804 9236 9.216117 ACTATTTACGCAAAGATTTTACACTCT 57.784 29.630 0.00 0.00 0.00 3.24
3973 9425 5.883673 GGCTTATAGTGGACATTACAAACCA 59.116 40.000 0.00 0.00 0.00 3.67
4086 9545 2.231215 ATCTGAACACGCTCCTATGC 57.769 50.000 0.00 0.00 0.00 3.14
4128 9587 7.687005 TTCACTTAACCAACTTATTTTTGCG 57.313 32.000 0.00 0.00 0.00 4.85
4175 9634 7.147655 CCAAGGAAGACTACTATGAAGATCCAA 60.148 40.741 0.00 0.00 0.00 3.53
4243 9711 2.242196 TCCTCCACAATTGATTCTCCCC 59.758 50.000 13.59 0.00 0.00 4.81
4296 9779 2.235898 GGCCATCTTCTCAGACTGAAGT 59.764 50.000 6.61 0.00 41.04 3.01
4299 9782 4.252073 CCATCTTCTCAGACTGAAGTTGG 58.748 47.826 15.27 15.27 46.17 3.77
4301 9784 2.700371 TCTTCTCAGACTGAAGTTGGCA 59.300 45.455 6.61 0.00 41.04 4.92
4306 9792 2.373169 TCAGACTGAAGTTGGCAAGGAT 59.627 45.455 1.64 0.00 0.00 3.24
4387 9873 0.983378 AAAGCCCTAGAGATGCCGGT 60.983 55.000 1.90 0.00 0.00 5.28
4552 10048 2.758089 GCAAGCGCTGGAGATGGTG 61.758 63.158 18.24 6.53 34.30 4.17
4675 10198 2.914289 CCCCAGCCAAGCTAGGAG 59.086 66.667 2.39 0.00 39.75 3.69
4677 10200 2.191641 CCAGCCAAGCTAGGAGCC 59.808 66.667 0.00 0.00 43.77 4.70
4680 10203 1.614824 AGCCAAGCTAGGAGCCTGT 60.615 57.895 0.00 0.00 43.77 4.00
4765 10296 4.893608 AGTTTGTGCTTGTTGTTTTTCCT 58.106 34.783 0.00 0.00 0.00 3.36
4837 10368 7.304735 TGTATGAGTTCGAATTTGGTTGAATG 58.695 34.615 0.00 0.00 0.00 2.67
4842 10373 4.513198 TCGAATTTGGTTGAATGGAACC 57.487 40.909 0.00 0.00 45.06 3.62
4869 10400 1.035923 TGTGATTGCGCCTTTTTCCA 58.964 45.000 4.18 0.00 0.00 3.53
4955 10486 6.812998 TGGTACTGTAGTATCATTGCTTACC 58.187 40.000 0.97 0.00 36.77 2.85
4997 10529 4.261867 GGGACAAAACCTACAAACCATGAC 60.262 45.833 0.00 0.00 0.00 3.06
4998 10530 4.583073 GGACAAAACCTACAAACCATGACT 59.417 41.667 0.00 0.00 0.00 3.41
5022 10554 9.312904 ACTGAATTTAAGGAAAATCAAGGATCA 57.687 29.630 0.00 0.00 36.76 2.92
5046 10578 3.123621 CGAGTCAAAATCGCTAGCAAACT 59.876 43.478 16.45 6.43 32.81 2.66
5049 10581 3.058224 GTCAAAATCGCTAGCAAACTGGT 60.058 43.478 16.45 0.00 0.00 4.00
5114 10646 9.331282 CTGTTCCTAAATATAAGTCTTTGGAGG 57.669 37.037 0.00 0.00 0.00 4.30
5185 10717 5.412594 GTGTAGATTCACTCATTTTGCTCCA 59.587 40.000 0.00 0.00 35.68 3.86
5237 10769 7.761038 AAGACTTACATTTAGGAACAAAGGG 57.239 36.000 0.00 0.00 0.00 3.95
5242 10774 8.101419 ACTTACATTTAGGAACAAAGGGAGTAG 58.899 37.037 0.00 0.00 0.00 2.57
5243 10775 5.816682 ACATTTAGGAACAAAGGGAGTAGG 58.183 41.667 0.00 0.00 0.00 3.18
5244 10776 5.550403 ACATTTAGGAACAAAGGGAGTAGGA 59.450 40.000 0.00 0.00 0.00 2.94
5245 10777 6.217693 ACATTTAGGAACAAAGGGAGTAGGAT 59.782 38.462 0.00 0.00 0.00 3.24
5246 10778 6.713731 TTTAGGAACAAAGGGAGTAGGATT 57.286 37.500 0.00 0.00 0.00 3.01
5247 10779 6.713731 TTAGGAACAAAGGGAGTAGGATTT 57.286 37.500 0.00 0.00 0.00 2.17
5249 10781 6.314899 AGGAACAAAGGGAGTAGGATTTAG 57.685 41.667 0.00 0.00 0.00 1.85
5285 10877 7.010091 AGCAAATACAAACGAGAAAAACTTTGG 59.990 33.333 0.00 0.00 0.00 3.28
5289 10881 3.334272 AACGAGAAAAACTTTGGAGCG 57.666 42.857 0.00 0.00 0.00 5.03
5290 10882 2.557317 ACGAGAAAAACTTTGGAGCGA 58.443 42.857 0.00 0.00 0.00 4.93
5291 10883 2.544267 ACGAGAAAAACTTTGGAGCGAG 59.456 45.455 0.00 0.00 0.00 5.03
5294 10886 1.609072 GAAAAACTTTGGAGCGAGGCT 59.391 47.619 0.00 0.00 43.88 4.58
5327 10919 3.762288 TCTCTAGCAGATGTGGTAAACGT 59.238 43.478 3.18 0.00 36.23 3.99
5379 10971 3.730662 CGGAAATGTTTATTGCAGGACGG 60.731 47.826 0.00 0.00 0.00 4.79
5398 10990 1.874019 CGGACGCTGAGACGGAATG 60.874 63.158 1.86 0.00 37.37 2.67
5403 10995 0.103026 CGCTGAGACGGAATGGATCA 59.897 55.000 0.00 0.00 0.00 2.92
5404 10996 1.863267 GCTGAGACGGAATGGATCAG 58.137 55.000 0.00 0.00 40.26 2.90
5583 12585 1.968704 AGATCTACTCATCGTCGCCA 58.031 50.000 0.00 0.00 0.00 5.69
5648 12691 2.094757 TTGGAGAGGACTTGCGCGAA 62.095 55.000 12.10 0.00 0.00 4.70
5667 12710 2.289592 ACTGGTACTCCTCGAACAGT 57.710 50.000 1.78 1.78 34.63 3.55
5704 12747 2.185350 CAGCTTCATCTCCGGCGT 59.815 61.111 6.01 0.00 0.00 5.68
5781 13295 2.367202 GGGGGAGAAGATGCGGTCA 61.367 63.158 0.00 0.00 0.00 4.02
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
11 12 0.747852 TGGTGCTCTCGTGTGTACAA 59.252 50.000 0.00 0.00 0.00 2.41
13 14 1.419374 CTTGGTGCTCTCGTGTGTAC 58.581 55.000 0.07 0.07 0.00 2.90
29 30 3.764160 GAGATGGGGGAGGCGCTTG 62.764 68.421 7.64 0.00 0.00 4.01
30 31 2.605535 TAGAGATGGGGGAGGCGCTT 62.606 60.000 7.64 0.00 0.00 4.68
58 59 0.615331 AGAGCCTGGATCTTTTGCGA 59.385 50.000 9.03 0.00 0.00 5.10
63 74 2.035632 CCGACTAGAGCCTGGATCTTT 58.964 52.381 20.90 7.65 28.73 2.52
68 79 2.442272 GGCCGACTAGAGCCTGGA 60.442 66.667 13.64 0.00 46.14 3.86
76 87 0.464452 AAATTCCTCGGGCCGACTAG 59.536 55.000 27.46 16.00 0.00 2.57
77 88 0.177141 CAAATTCCTCGGGCCGACTA 59.823 55.000 27.46 13.35 0.00 2.59
78 89 1.078426 CAAATTCCTCGGGCCGACT 60.078 57.895 27.46 7.16 0.00 4.18
85 96 2.159099 TCGTCATCTCCAAATTCCTCGG 60.159 50.000 0.00 0.00 0.00 4.63
90 101 4.748892 TGAGAGTCGTCATCTCCAAATTC 58.251 43.478 10.34 0.00 42.13 2.17
93 104 3.057245 CACTGAGAGTCGTCATCTCCAAA 60.057 47.826 10.34 0.00 42.13 3.28
101 112 0.467474 ACCACCACTGAGAGTCGTCA 60.467 55.000 0.00 0.00 0.00 4.35
113 124 2.806608 TCTGTCGAAACTACCACCAC 57.193 50.000 0.00 0.00 0.00 4.16
114 125 3.724374 CTTTCTGTCGAAACTACCACCA 58.276 45.455 0.00 0.00 35.41 4.17
129 140 2.354510 TGTTCCAACGAGTTGCTTTCTG 59.645 45.455 10.25 0.00 39.16 3.02
184 195 2.683968 TCACTTTCAATTCCGGAGTCG 58.316 47.619 3.34 0.00 0.00 4.18
187 198 4.229876 GCTTTTCACTTTCAATTCCGGAG 58.770 43.478 3.34 0.00 0.00 4.63
188 199 3.634448 TGCTTTTCACTTTCAATTCCGGA 59.366 39.130 0.00 0.00 0.00 5.14
197 208 2.098443 TCCGTTGGTGCTTTTCACTTTC 59.902 45.455 0.00 0.00 44.98 2.62
217 228 4.313282 AGCTTAGTTTGTCGGTAAGGTTC 58.687 43.478 0.00 0.00 31.99 3.62
223 234 2.642139 CCGAGCTTAGTTTGTCGGTA 57.358 50.000 1.43 0.00 45.62 4.02
308 503 4.449131 CATGAGAACCATGCTAGACACAT 58.551 43.478 0.00 0.00 45.25 3.21
332 527 0.320421 GGTAGCCACACGCAAGAAGA 60.320 55.000 0.00 0.00 41.38 2.87
340 535 1.671054 CCTGGTTGGTAGCCACACG 60.671 63.158 0.00 0.00 30.78 4.49
344 539 2.531685 AGCCCTGGTTGGTAGCCA 60.532 61.111 0.00 0.00 34.42 4.75
422 619 1.874915 TATACGCAGCGAACACGGC 60.875 57.895 24.65 0.00 0.00 5.68
423 620 0.524816 AGTATACGCAGCGAACACGG 60.525 55.000 24.65 0.00 0.00 4.94
499 1103 1.680555 CCCGAGGAGAGAGATATCCCG 60.681 61.905 0.00 0.00 36.14 5.14
590 1194 6.126409 TGTCTCCTTCCACTAAACAAACATT 58.874 36.000 0.00 0.00 0.00 2.71
605 1209 3.054802 AGGGTTGATGTGATGTCTCCTTC 60.055 47.826 0.00 0.00 0.00 3.46
625 1229 1.062685 CCGACGTCACATCTCGAGG 59.937 63.158 17.16 0.88 0.00 4.63
645 1249 3.210232 TCTGTACCTCCGAGATACTGG 57.790 52.381 6.90 0.00 0.00 4.00
648 1252 6.040209 TCTCTATCTGTACCTCCGAGATAC 57.960 45.833 0.00 0.00 0.00 2.24
663 1267 4.093011 GGGTGCACATCCTATCTCTATCT 58.907 47.826 20.43 0.00 0.00 1.98
709 1740 1.935799 ATTAATTGCAGGTGCCCACA 58.064 45.000 0.00 0.00 41.18 4.17
711 1742 3.582208 AGAAAATTAATTGCAGGTGCCCA 59.418 39.130 0.39 0.00 41.18 5.36
776 1807 4.276146 GGGTATCGTCCCGTCGCC 62.276 72.222 0.00 0.00 37.93 5.54
818 1849 2.494918 GCACGCTGGGTCGTCTAT 59.505 61.111 0.00 0.00 41.21 1.98
845 1876 2.685017 TGAGCTCATGGTCCGGCT 60.685 61.111 13.74 0.00 39.75 5.52
848 1879 2.898738 AGCTGAGCTCATGGTCCG 59.101 61.111 18.63 5.37 39.75 4.79
972 2012 1.228894 TGCTCTTGTCGAGGAGGGT 60.229 57.895 10.61 0.00 40.25 4.34
983 2023 2.825836 GGGATGGCCGTGCTCTTG 60.826 66.667 16.82 0.00 33.83 3.02
1004 2045 1.595993 CCTTCTCGACTTGAGGCGGA 61.596 60.000 6.39 0.02 45.32 5.54
1012 2053 3.773370 TCGTGGCCTTCTCGACTT 58.227 55.556 3.32 0.00 36.60 3.01
1036 2077 2.351835 CCATCGACTATCTACCGCCAAG 60.352 54.545 0.00 0.00 0.00 3.61
1037 2078 1.611977 CCATCGACTATCTACCGCCAA 59.388 52.381 0.00 0.00 0.00 4.52
1038 2079 1.202842 TCCATCGACTATCTACCGCCA 60.203 52.381 0.00 0.00 0.00 5.69
1048 2096 1.564818 AGTCTCCACCTCCATCGACTA 59.435 52.381 0.00 0.00 30.65 2.59
1052 2100 1.142748 GCAGTCTCCACCTCCATCG 59.857 63.158 0.00 0.00 0.00 3.84
1303 2353 4.155644 AGAAAAGAAGCAGAGCAGTAATGC 59.844 41.667 7.15 7.15 40.29 3.56
1396 2465 3.009723 CAAGAAAAGGGCAGCGATAAGA 58.990 45.455 0.00 0.00 0.00 2.10
1431 2501 0.033228 CATTGCCGGCACCAGAAAAA 59.967 50.000 32.95 13.05 0.00 1.94
1432 2502 1.664873 CATTGCCGGCACCAGAAAA 59.335 52.632 32.95 13.97 0.00 2.29
1499 2667 2.158813 TGACCAGTCCAAACCAGAGAAC 60.159 50.000 0.00 0.00 0.00 3.01
1514 2694 2.620112 CGCTTGCCACCTTGACCAG 61.620 63.158 0.00 0.00 0.00 4.00
1546 2731 2.281070 CGGTGCTGTGGTTGAGCT 60.281 61.111 0.00 0.00 37.35 4.09
1643 2828 1.970640 GCAGGGGAAAGGAATGTGTTT 59.029 47.619 0.00 0.00 0.00 2.83
1644 2829 1.133199 TGCAGGGGAAAGGAATGTGTT 60.133 47.619 0.00 0.00 0.00 3.32
1654 2839 1.377202 GCGACTGATGCAGGGGAAA 60.377 57.895 0.00 0.00 35.51 3.13
1741 2936 9.283768 TGAGCATGAGTTGAGAGTTAAAAATAA 57.716 29.630 0.00 0.00 0.00 1.40
1743 2938 7.750229 TGAGCATGAGTTGAGAGTTAAAAAT 57.250 32.000 0.00 0.00 0.00 1.82
1745 2940 6.936335 TCATGAGCATGAGTTGAGAGTTAAAA 59.064 34.615 8.99 0.00 42.42 1.52
1749 2944 4.548451 TCATGAGCATGAGTTGAGAGTT 57.452 40.909 8.99 0.00 42.42 3.01
1764 2963 1.132453 CACCTGCAACATGCTCATGAG 59.868 52.381 18.84 18.84 45.31 2.90
1847 3046 8.204836 GGATGTGTAGGATATTTTGTACTCACT 58.795 37.037 0.00 0.00 0.00 3.41
1906 3107 1.206371 ACCATACTCCTGCCGTACAAC 59.794 52.381 0.00 0.00 0.00 3.32
1918 3119 4.657436 AGCAGCAAGTAGTACCATACTC 57.343 45.455 0.00 0.00 40.14 2.59
1924 3125 5.220681 GCATAGAAAAGCAGCAAGTAGTACC 60.221 44.000 0.00 0.00 0.00 3.34
1928 3129 4.874966 AGAGCATAGAAAAGCAGCAAGTAG 59.125 41.667 0.00 0.00 0.00 2.57
2030 3255 3.550842 GGCAAGCTGTGGAACTTTTACTG 60.551 47.826 0.00 0.00 38.04 2.74
2031 3256 2.623416 GGCAAGCTGTGGAACTTTTACT 59.377 45.455 0.00 0.00 38.04 2.24
2032 3257 2.288213 GGGCAAGCTGTGGAACTTTTAC 60.288 50.000 0.00 0.00 38.04 2.01
2033 3258 1.960689 GGGCAAGCTGTGGAACTTTTA 59.039 47.619 0.00 0.00 38.04 1.52
2034 3259 0.752658 GGGCAAGCTGTGGAACTTTT 59.247 50.000 0.00 0.00 38.04 2.27
2078 3335 6.145858 TGACAGATGGATTTCAAAATTTTGCG 59.854 34.615 23.36 4.14 38.05 4.85
2211 3474 1.270274 TGCACAATGGCAGTCATGTTC 59.730 47.619 0.00 0.00 39.25 3.18
2212 3475 1.330234 TGCACAATGGCAGTCATGTT 58.670 45.000 0.00 0.00 39.25 2.71
2213 3476 3.039452 TGCACAATGGCAGTCATGT 57.961 47.368 0.00 0.00 39.25 3.21
2278 3542 6.556874 AGACTTATCTTCTAGGAAATGGGGAG 59.443 42.308 0.00 0.00 0.00 4.30
2292 3562 9.214953 CGTGCAAAATTTATCAGACTTATCTTC 57.785 33.333 0.00 0.00 30.42 2.87
2465 3738 8.860780 AGAAAAGGATAAAGATAGCATCCATC 57.139 34.615 2.90 0.00 40.67 3.51
2525 3812 6.457934 CGCTGAATGAATTTAGCACTCTGAAT 60.458 38.462 16.96 0.00 46.17 2.57
2551 3838 2.555757 AGGCTTGCTGATGAAACTTGAC 59.444 45.455 0.00 0.00 0.00 3.18
2561 3848 2.042831 GCAACCGAGGCTTGCTGAT 61.043 57.895 16.52 0.00 40.79 2.90
2628 3917 4.791676 CGTTCTCATCATGAGCAAAACATG 59.208 41.667 10.10 0.00 43.95 3.21
2642 3931 3.181510 GCAACATAACCCACGTTCTCATC 60.182 47.826 0.00 0.00 33.17 2.92
2664 3953 1.382522 CCTTGATTCGACACCCATGG 58.617 55.000 4.14 4.14 0.00 3.66
2860 7918 8.964533 ACATCTGAGATATCCTTACCAACTAT 57.035 34.615 0.00 0.00 0.00 2.12
2932 7992 2.681778 CAGAGACCGAGGCTGGGT 60.682 66.667 22.03 22.03 41.48 4.51
2936 7996 2.601666 TGTGCAGAGACCGAGGCT 60.602 61.111 0.00 0.00 0.00 4.58
3036 8200 6.435277 ACCAATAAATCTGAGAAGCATGTGTT 59.565 34.615 0.00 0.00 0.00 3.32
3120 8310 7.195646 ACAAATTGATACCATTGATAAGTGCG 58.804 34.615 0.00 0.00 0.00 5.34
3238 8515 0.995024 ATGCACAGGCTAGGGAGTTT 59.005 50.000 0.00 0.00 41.91 2.66
3267 8545 6.980593 TGTGGTTAAGATGAACAATTGAAGG 58.019 36.000 13.59 0.00 0.00 3.46
3295 8573 6.046593 ACGACTAATCTGAACTTGTTGAACA 58.953 36.000 0.00 0.00 0.00 3.18
3297 8575 7.707464 TGTTACGACTAATCTGAACTTGTTGAA 59.293 33.333 0.00 0.00 0.00 2.69
3298 8576 7.204604 TGTTACGACTAATCTGAACTTGTTGA 58.795 34.615 0.00 0.00 0.00 3.18
3304 8583 7.360946 GGCAATTTGTTACGACTAATCTGAACT 60.361 37.037 0.00 0.00 31.47 3.01
3335 8614 7.643764 TGCTCAACGATTTTCTTCTAAACTTTG 59.356 33.333 0.00 0.00 0.00 2.77
3576 8887 3.988976 AACATGACCTGACAGTGCTAT 57.011 42.857 0.00 0.00 0.00 2.97
3577 8888 3.769739 AAACATGACCTGACAGTGCTA 57.230 42.857 0.00 0.00 0.00 3.49
3586 8899 4.321230 GCTAACCTTCCAAAACATGACCTG 60.321 45.833 0.00 0.00 0.00 4.00
3588 8901 3.826729 AGCTAACCTTCCAAAACATGACC 59.173 43.478 0.00 0.00 0.00 4.02
3629 8944 9.730705 TCTTTCTGGATATAGAAATAAGCATGG 57.269 33.333 0.00 0.00 43.52 3.66
3859 9311 8.565896 AGCACAAGAACAAAATGATGAGTATA 57.434 30.769 0.00 0.00 0.00 1.47
3868 9320 6.020121 CAGTGAGAAAGCACAAGAACAAAATG 60.020 38.462 0.00 0.00 41.19 2.32
3973 9425 3.003480 GTTGCTAAGATTCTCCGCACTT 58.997 45.455 8.76 0.00 0.00 3.16
4086 9545 7.596749 AAGTGAATCGTCTTACATTTGGTAG 57.403 36.000 0.00 0.00 32.49 3.18
4128 9587 3.381949 GTGGATGAGCGTACCTGAATAC 58.618 50.000 0.00 0.00 0.00 1.89
4175 9634 4.042934 AGGGTTCTGTTTGCTATTAGGTGT 59.957 41.667 0.00 0.00 0.00 4.16
4243 9711 3.274288 GGCTTCTTCTACCATGTTGGAG 58.726 50.000 0.00 0.00 40.96 3.86
4296 9779 3.136443 ACGGAGATTATCATCCTTGCCAA 59.864 43.478 0.00 0.00 33.12 4.52
4299 9782 3.496130 CACACGGAGATTATCATCCTTGC 59.504 47.826 13.07 0.00 38.16 4.01
4301 9784 3.967326 TCCACACGGAGATTATCATCCTT 59.033 43.478 0.00 0.00 35.91 3.36
4364 9850 1.683011 GGCATCTCTAGGGCTTTGCAA 60.683 52.381 12.25 0.00 0.00 4.08
4677 10200 3.620374 CACAGCTATTGCCTAAGACACAG 59.380 47.826 0.00 0.00 40.80 3.66
4680 10203 3.981071 ACACAGCTATTGCCTAAGACA 57.019 42.857 0.00 0.00 40.80 3.41
4765 10296 6.260050 GCTACAAATGGATTCGAGGAACATAA 59.740 38.462 0.00 0.00 0.00 1.90
4809 10340 7.304735 TCAACCAAATTCGAACTCATACAATG 58.695 34.615 0.00 0.00 0.00 2.82
4837 10368 2.668279 GCAATCACACATTGTCGGTTCC 60.668 50.000 0.00 0.00 0.00 3.62
4842 10373 0.794229 GGCGCAATCACACATTGTCG 60.794 55.000 10.83 0.00 34.34 4.35
4869 10400 3.689347 TCTGCAATAGTGACATTTGGCT 58.311 40.909 0.00 0.00 0.00 4.75
4931 10462 6.381707 TGGTAAGCAATGATACTACAGTACCA 59.618 38.462 0.00 0.00 32.72 3.25
4945 10476 6.215121 TGTTTTCTGATTGTGGTAAGCAATG 58.785 36.000 0.00 0.00 36.77 2.82
4946 10477 6.403866 TGTTTTCTGATTGTGGTAAGCAAT 57.596 33.333 0.00 0.00 39.04 3.56
4955 10486 5.009911 TGTCCCTGAATGTTTTCTGATTGTG 59.990 40.000 0.00 0.00 33.84 3.33
4997 10529 9.798994 CTGATCCTTGATTTTCCTTAAATTCAG 57.201 33.333 0.00 0.00 36.71 3.02
4998 10530 8.253113 GCTGATCCTTGATTTTCCTTAAATTCA 58.747 33.333 0.00 0.00 36.59 2.57
5046 10578 1.616159 GCCCTCTTTTTGCACTACCA 58.384 50.000 0.00 0.00 0.00 3.25
5049 10581 2.170166 CATGGCCCTCTTTTTGCACTA 58.830 47.619 0.00 0.00 0.00 2.74
5114 10646 4.750098 CGTATGTGGTTCATAGTGGAATCC 59.250 45.833 0.00 0.00 39.36 3.01
5233 10765 8.393959 TCTCATTTTCTAAATCCTACTCCCTT 57.606 34.615 0.00 0.00 0.00 3.95
5237 10769 8.723942 TGCTTCTCATTTTCTAAATCCTACTC 57.276 34.615 0.00 0.00 0.00 2.59
5246 10778 9.393249 CGTTTGTATTTGCTTCTCATTTTCTAA 57.607 29.630 0.00 0.00 0.00 2.10
5247 10779 8.779303 TCGTTTGTATTTGCTTCTCATTTTCTA 58.221 29.630 0.00 0.00 0.00 2.10
5249 10781 7.803189 TCTCGTTTGTATTTGCTTCTCATTTTC 59.197 33.333 0.00 0.00 0.00 2.29
5285 10877 7.173971 AGAGATGTTCTTAAGAGCCTCGCTC 62.174 48.000 19.02 16.48 44.06 5.03
5289 10881 5.068460 TGCTAGAGATGTTCTTAAGAGCCTC 59.932 44.000 15.74 14.86 34.33 4.70
5290 10882 4.959210 TGCTAGAGATGTTCTTAAGAGCCT 59.041 41.667 15.74 6.83 34.33 4.58
5291 10883 5.068460 TCTGCTAGAGATGTTCTTAAGAGCC 59.932 44.000 15.74 7.01 34.33 4.70
5318 10910 1.129917 TCCAAGGTGGACGTTTACCA 58.870 50.000 20.08 7.56 42.67 3.25
5327 10919 5.452077 CCGTAAACAATTTTTCCAAGGTGGA 60.452 40.000 0.00 0.00 46.61 4.02
5331 10923 6.809689 GGATACCGTAAACAATTTTTCCAAGG 59.190 38.462 0.00 0.00 0.00 3.61
5358 10950 3.769536 CCGTCCTGCAATAAACATTTCC 58.230 45.455 0.00 0.00 0.00 3.13
5363 10955 1.302383 CCGCCGTCCTGCAATAAACA 61.302 55.000 0.00 0.00 0.00 2.83
5379 10971 3.701604 ATTCCGTCTCAGCGTCCGC 62.702 63.158 2.94 2.94 42.33 5.54
5393 10985 5.930569 GGTATACGTTTACCTGATCCATTCC 59.069 44.000 23.23 0.00 38.89 3.01
5398 10990 3.243501 TGCGGTATACGTTTACCTGATCC 60.244 47.826 26.13 13.33 46.52 3.36
5403 10995 6.088016 TGAATATGCGGTATACGTTTACCT 57.912 37.500 26.13 14.47 46.52 3.08
5404 10996 6.768029 TTGAATATGCGGTATACGTTTACC 57.232 37.500 21.34 21.34 46.52 2.85
5648 12691 1.887198 CACTGTTCGAGGAGTACCAGT 59.113 52.381 0.00 0.00 38.94 4.00
5781 13295 0.250770 GGAGGAACTTCAACCGCCTT 60.251 55.000 0.00 0.00 41.55 4.35


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

AutoCloner maintained by Alex Coulton.