Multiple sequence alignment - TraesCS6A01G108900

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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 TraesCS6A01G108900 chr6A 100.000 5523 0 0 1 5523 77779314 77784836 0.000000e+00 10200.0
1 TraesCS6A01G108900 chr6A 81.688 1540 181 42 3224 4709 73555907 73557399 0.000000e+00 1188.0
2 TraesCS6A01G108900 chr6A 80.655 641 77 26 2003 2618 73543288 73543906 2.350000e-123 453.0
3 TraesCS6A01G108900 chr6A 85.128 195 23 4 1393 1583 73542765 73542957 1.570000e-45 195.0
4 TraesCS6A01G108900 chr6A 90.099 101 10 0 1706 1806 73543029 73543129 1.250000e-26 132.0
5 TraesCS6A01G108900 chr6A 100.000 40 0 0 5335 5374 77784601 77784640 2.130000e-09 75.0
6 TraesCS6A01G108900 chr6A 100.000 40 0 0 5288 5327 77784648 77784687 2.130000e-09 75.0
7 TraesCS6A01G108900 chr6B 88.248 2825 249 56 33 2802 135111386 135114182 0.000000e+00 3301.0
8 TraesCS6A01G108900 chr6B 92.449 1907 116 11 2981 4870 135114453 135116348 0.000000e+00 2699.0
9 TraesCS6A01G108900 chr6B 82.991 1511 174 32 3224 4698 130828474 130829937 0.000000e+00 1290.0
10 TraesCS6A01G108900 chr6B 80.063 632 81 26 2003 2609 130823645 130824256 1.420000e-115 427.0
11 TraesCS6A01G108900 chr6B 82.051 234 28 11 997 1229 130822737 130822957 2.630000e-43 187.0
12 TraesCS6A01G108900 chr6B 91.000 100 9 0 1707 1806 130823365 130823464 9.650000e-28 135.0
13 TraesCS6A01G108900 chr6B 85.567 97 5 5 2898 2985 135114334 135114430 5.890000e-15 93.5
14 TraesCS6A01G108900 chr6D 90.072 2216 128 48 642 2809 61134325 61136496 0.000000e+00 2789.0
15 TraesCS6A01G108900 chr6D 91.755 1128 67 8 3745 4871 61137517 61138619 0.000000e+00 1544.0
16 TraesCS6A01G108900 chr6D 82.480 1524 182 33 3224 4709 58239086 58240562 0.000000e+00 1256.0
17 TraesCS6A01G108900 chr6D 93.249 711 40 6 2987 3693 61136788 61137494 0.000000e+00 1040.0
18 TraesCS6A01G108900 chr6D 90.137 365 33 3 5160 5523 61140493 61140855 6.480000e-129 472.0
19 TraesCS6A01G108900 chr6D 80.546 586 72 22 2053 2618 58235149 58235712 3.980000e-111 412.0
20 TraesCS6A01G108900 chr6D 86.770 257 29 4 177 428 61132836 61133092 1.170000e-71 281.0
21 TraesCS6A01G108900 chr6D 92.169 166 9 3 4881 5046 61139782 61139943 1.200000e-56 231.0
22 TraesCS6A01G108900 chr6D 84.579 214 30 2 441 651 61133694 61133907 5.610000e-50 209.0
23 TraesCS6A01G108900 chr6D 81.624 234 29 11 997 1229 58234187 58234407 1.220000e-41 182.0
24 TraesCS6A01G108900 chr6D 87.970 133 14 2 1674 1806 58234777 58234907 7.410000e-34 156.0
25 TraesCS6A01G108900 chr6D 92.079 101 7 1 2801 2901 61136547 61136646 2.070000e-29 141.0
26 TraesCS6A01G108900 chr6D 90.000 90 5 3 2898 2985 61136673 61136760 4.520000e-21 113.0
27 TraesCS6A01G108900 chr6D 100.000 40 0 0 5288 5327 61140667 61140706 2.130000e-09 75.0
28 TraesCS6A01G108900 chr5D 88.794 1749 178 13 3037 4776 218053958 218055697 0.000000e+00 2128.0
29 TraesCS6A01G108900 chr5D 82.743 1101 115 39 1401 2485 218052272 218053313 0.000000e+00 911.0
30 TraesCS6A01G108900 chr5D 83.256 430 44 17 998 1416 218051807 218052219 2.430000e-98 370.0
31 TraesCS6A01G108900 chr5A 88.393 1749 184 14 3037 4776 290928392 290930130 0.000000e+00 2087.0
32 TraesCS6A01G108900 chr5A 82.490 1205 127 40 1407 2596 290925492 290926627 0.000000e+00 979.0
33 TraesCS6A01G108900 chr5A 83.102 432 38 20 998 1416 290925025 290925434 1.460000e-95 361.0
34 TraesCS6A01G108900 chr5B 87.208 1243 127 11 3630 4863 234303455 234304674 0.000000e+00 1386.0
35 TraesCS6A01G108900 chr5B 84.474 979 98 29 1451 2427 234296023 234296949 0.000000e+00 917.0
36 TraesCS6A01G108900 chr5B 89.761 586 56 4 3048 3630 234302758 234303342 0.000000e+00 747.0
37 TraesCS6A01G108900 chr5B 82.326 430 45 19 998 1416 234295503 234295912 1.470000e-90 344.0
38 TraesCS6A01G108900 chr3D 85.567 97 13 1 5328 5424 508395283 508395188 3.520000e-17 100.0
39 TraesCS6A01G108900 chr3D 83.696 92 11 4 5327 5417 26207425 26207337 3.550000e-12 84.2
40 TraesCS6A01G108900 chr3B 85.000 100 8 6 5328 5424 671153834 671153739 1.640000e-15 95.3
41 TraesCS6A01G108900 chr3B 88.679 53 6 0 5064 5116 472915485 472915537 1.280000e-06 65.8
42 TraesCS6A01G108900 chr4A 82.243 107 15 4 5321 5424 42265415 42265520 7.620000e-14 89.8
43 TraesCS6A01G108900 chr7A 97.222 36 1 0 5327 5362 427616314 427616349 1.660000e-05 62.1
44 TraesCS6A01G108900 chr7A 100.000 28 0 0 5288 5315 427616322 427616349 1.000000e-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 TraesCS6A01G108900 chr6A 77779314 77784836 5522 False 3450.000000 10200 100.000000 1 5523 3 chr6A.!!$F3 5522
1 TraesCS6A01G108900 chr6A 73555907 73557399 1492 False 1188.000000 1188 81.688000 3224 4709 1 chr6A.!!$F1 1485
2 TraesCS6A01G108900 chr6A 73542765 73543906 1141 False 260.000000 453 85.294000 1393 2618 3 chr6A.!!$F2 1225
3 TraesCS6A01G108900 chr6B 135111386 135116348 4962 False 2031.166667 3301 88.754667 33 4870 3 chr6B.!!$F3 4837
4 TraesCS6A01G108900 chr6B 130828474 130829937 1463 False 1290.000000 1290 82.991000 3224 4698 1 chr6B.!!$F1 1474
5 TraesCS6A01G108900 chr6B 130822737 130824256 1519 False 249.666667 427 84.371333 997 2609 3 chr6B.!!$F2 1612
6 TraesCS6A01G108900 chr6D 61132836 61140855 8019 False 689.500000 2789 91.081000 177 5523 10 chr6D.!!$F2 5346
7 TraesCS6A01G108900 chr6D 58234187 58240562 6375 False 501.500000 1256 83.155000 997 4709 4 chr6D.!!$F1 3712
8 TraesCS6A01G108900 chr5D 218051807 218055697 3890 False 1136.333333 2128 84.931000 998 4776 3 chr5D.!!$F1 3778
9 TraesCS6A01G108900 chr5A 290925025 290930130 5105 False 1142.333333 2087 84.661667 998 4776 3 chr5A.!!$F1 3778
10 TraesCS6A01G108900 chr5B 234302758 234304674 1916 False 1066.500000 1386 88.484500 3048 4863 2 chr5B.!!$F2 1815
11 TraesCS6A01G108900 chr5B 234295503 234296949 1446 False 630.500000 917 83.400000 998 2427 2 chr5B.!!$F1 1429

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
847 1904 0.040336 TCCGATTATCTCTCGCGCAC 60.040 55.0 8.75 0.0 34.84 5.34 F
1405 2504 0.302890 CGTCGATGCCTGATTTGCTC 59.697 55.0 0.00 0.0 0.00 4.26 F
1442 2616 0.454452 GCGCTGAAAATTCACCGGTC 60.454 55.0 2.59 0.0 36.91 4.79 F
2467 3749 0.457509 CAATGAGAGCTGCGTCGTCT 60.458 55.0 0.00 0.0 0.00 4.18 F
3833 9370 0.034059 ACCGAGTGCTGAGAACCTTG 59.966 55.0 0.00 0.0 0.00 3.61 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2186 3447 3.663025 TGCATGATTTCGTCTGAACAGA 58.337 40.909 0.00 0.00 32.71 3.41 R
3318 8704 0.030092 TAGGGCCCTGGCTTGTATCT 60.030 55.000 35.81 5.66 41.60 1.98 R
3369 8755 3.244976 CCCAGCATAAAGTTTCTTTGCG 58.755 45.455 10.61 7.30 38.32 4.85 R
4342 9907 0.108138 CCCTCACACACCCGATTCTC 60.108 60.000 0.00 0.00 0.00 2.87 R
5258 12456 0.036875 GCCACTGGCTAGAAAGGTGT 59.963 55.000 13.28 0.00 46.69 4.16 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
18 19 1.542175 TCCCCCATCTCTACTCCGG 59.458 63.158 0.00 0.00 0.00 5.14
19 20 2.210711 CCCCCATCTCTACTCCGGC 61.211 68.421 0.00 0.00 0.00 6.13
20 21 2.210711 CCCCATCTCTACTCCGGCC 61.211 68.421 0.00 0.00 0.00 6.13
21 22 2.565645 CCCATCTCTACTCCGGCCG 61.566 68.421 21.04 21.04 0.00 6.13
22 23 2.565645 CCATCTCTACTCCGGCCGG 61.566 68.421 39.13 39.13 0.00 6.13
23 24 1.828660 CATCTCTACTCCGGCCGGT 60.829 63.158 41.57 27.50 36.47 5.28
24 25 0.536687 CATCTCTACTCCGGCCGGTA 60.537 60.000 41.57 27.12 36.47 4.02
25 26 0.250814 ATCTCTACTCCGGCCGGTAG 60.251 60.000 41.57 34.98 37.38 3.18
26 27 1.153005 CTCTACTCCGGCCGGTAGT 60.153 63.158 41.57 37.85 37.33 2.73
27 28 1.445716 CTCTACTCCGGCCGGTAGTG 61.446 65.000 37.90 30.55 37.33 2.74
28 29 1.751927 CTACTCCGGCCGGTAGTGT 60.752 63.158 37.90 32.58 36.47 3.55
29 30 1.722636 CTACTCCGGCCGGTAGTGTC 61.723 65.000 37.90 0.71 36.47 3.67
30 31 4.189188 CTCCGGCCGGTAGTGTCG 62.189 72.222 41.57 15.89 36.47 4.35
31 32 4.720902 TCCGGCCGGTAGTGTCGA 62.721 66.667 41.57 19.37 36.47 4.20
36 37 2.202440 CCGGTAGTGTCGACGCAG 60.202 66.667 29.21 16.93 0.00 5.18
41 42 1.068748 GGTAGTGTCGACGCAGAAGAA 60.069 52.381 29.21 6.11 0.00 2.52
44 45 1.371267 TGTCGACGCAGAAGAACCG 60.371 57.895 11.62 0.00 0.00 4.44
49 50 2.358737 CGCAGAAGAACCGGGCTT 60.359 61.111 6.32 9.23 0.00 4.35
50 51 2.680913 CGCAGAAGAACCGGGCTTG 61.681 63.158 15.46 5.44 0.00 4.01
51 52 2.335712 GCAGAAGAACCGGGCTTGG 61.336 63.158 15.46 9.15 0.00 3.61
63 64 3.760035 GCTTGGGTCGGCTCGAGA 61.760 66.667 18.75 0.00 36.23 4.04
66 67 1.005394 TTGGGTCGGCTCGAGAAAC 60.005 57.895 18.75 10.06 36.23 2.78
74 75 1.715993 GGCTCGAGAAACTTGGAGAC 58.284 55.000 18.75 0.00 0.00 3.36
86 87 1.535896 CTTGGAGACGACGACTCTCAA 59.464 52.381 22.92 21.44 36.61 3.02
87 88 0.873054 TGGAGACGACGACTCTCAAC 59.127 55.000 22.92 9.95 36.61 3.18
102 103 2.030540 TCTCAACGGTGGTAGTTTCGAG 60.031 50.000 0.00 0.00 0.00 4.04
156 158 2.093606 TCACCCAAATCCATACGCGTAA 60.094 45.455 24.55 7.41 0.00 3.18
159 161 3.199677 CCCAAATCCATACGCGTAAGAA 58.800 45.455 24.55 11.49 43.02 2.52
160 162 3.001939 CCCAAATCCATACGCGTAAGAAC 59.998 47.826 24.55 0.00 43.02 3.01
169 171 1.204467 ACGCGTAAGAACCCGGAATTA 59.796 47.619 11.67 0.00 43.02 1.40
180 182 7.114866 AGAACCCGGAATTAAAAGTGAAAAA 57.885 32.000 0.73 0.00 0.00 1.94
183 185 6.822442 ACCCGGAATTAAAAGTGAAAAACAT 58.178 32.000 0.73 0.00 0.00 2.71
187 189 8.987890 CCGGAATTAAAAGTGAAAAACATCAAT 58.012 29.630 0.00 0.00 0.00 2.57
197 199 7.205297 AGTGAAAAACATCAATGAAACCTCAG 58.795 34.615 0.00 0.00 34.23 3.35
207 209 1.939934 TGAAACCTCAGCGACAAACTG 59.060 47.619 0.00 0.00 36.44 3.16
222 224 2.673368 CAAACTGAGCTCGGATGGTTAC 59.327 50.000 29.29 0.00 0.00 2.50
251 253 0.967380 GTGGAACCAGCCCATCAAGG 60.967 60.000 0.00 0.00 35.91 3.61
266 268 5.358160 CCCATCAAGGTTCAAGAATTAGACC 59.642 44.000 0.00 0.00 33.75 3.85
290 292 2.100749 ACACTGATGAGAACGTGTGTCA 59.899 45.455 0.00 0.00 38.99 3.58
317 319 2.626840 GTTCTCATGACCTTCTGGAGC 58.373 52.381 0.00 0.00 37.04 4.70
318 320 1.942776 TCTCATGACCTTCTGGAGCA 58.057 50.000 0.00 0.00 37.04 4.26
319 321 1.829849 TCTCATGACCTTCTGGAGCAG 59.170 52.381 0.00 0.00 37.04 4.24
327 329 2.303549 CTTCTGGAGCAGGGCTACCG 62.304 65.000 0.00 0.00 39.07 4.02
332 334 2.606519 AGCAGGGCTACCGACCAA 60.607 61.111 0.00 0.00 42.67 3.67
338 340 2.202756 GCTACCGACCAAGGCTCG 60.203 66.667 0.00 4.74 33.69 5.03
351 353 1.280457 AGGCTCGAATCCTGGTTCTT 58.720 50.000 5.19 0.00 31.53 2.52
373 561 3.537206 AAAAGGCTCCTCGCAGCGT 62.537 57.895 15.93 0.00 40.68 5.07
377 565 0.896019 AGGCTCCTCGCAGCGTATAT 60.896 55.000 15.93 0.00 40.68 0.86
387 575 4.174762 TCGCAGCGTATATTTGTGTTGTA 58.825 39.130 15.93 0.00 0.00 2.41
416 604 3.224606 CGTGTTCGCTGCATATACTTG 57.775 47.619 0.00 0.00 0.00 3.16
420 608 1.205064 CGCTGCATATACTTGCGCC 59.795 57.895 4.18 0.00 45.77 6.53
423 611 1.498043 CTGCATATACTTGCGCCGCA 61.498 55.000 8.16 8.16 45.77 5.69
439 627 3.726517 CACAAGCCAGCGTTCGGG 61.727 66.667 0.00 0.00 0.00 5.14
447 1042 2.203437 AGCGTTCGGGGCCTTTTT 60.203 55.556 0.84 0.00 0.00 1.94
470 1065 3.053693 TCCACCTTATAATGCAGTGCCTT 60.054 43.478 13.72 11.97 0.00 4.35
485 1080 4.952335 CAGTGCCTTTGGGATATCTTTCTT 59.048 41.667 2.05 0.00 33.58 2.52
557 1160 7.923414 AGATTTATTTAGTCTTTCAACGGCT 57.077 32.000 0.00 0.00 0.00 5.52
562 1165 2.492019 AGTCTTTCAACGGCTTTTGC 57.508 45.000 0.00 0.00 46.64 3.68
570 1173 2.548057 TCAACGGCTTTTGCTTAGTGAG 59.452 45.455 0.00 0.00 46.54 3.51
574 1177 2.784347 GGCTTTTGCTTAGTGAGAGGT 58.216 47.619 0.00 0.00 46.54 3.85
578 1181 2.724977 TTGCTTAGTGAGAGGTGACG 57.275 50.000 0.00 0.00 0.00 4.35
582 1185 2.438411 CTTAGTGAGAGGTGACGTCCT 58.562 52.381 14.12 3.89 40.97 3.85
585 1188 3.088789 AGTGAGAGGTGACGTCCTATT 57.911 47.619 14.12 0.00 38.02 1.73
586 1189 2.755655 AGTGAGAGGTGACGTCCTATTG 59.244 50.000 14.12 0.00 38.02 1.90
588 1191 3.381908 GTGAGAGGTGACGTCCTATTGAT 59.618 47.826 14.12 0.00 38.02 2.57
590 1193 4.466370 TGAGAGGTGACGTCCTATTGATTT 59.534 41.667 14.12 0.00 38.02 2.17
593 1196 5.046591 AGAGGTGACGTCCTATTGATTTTCA 60.047 40.000 14.12 0.00 38.02 2.69
609 1212 0.317160 TTCAAGATGTGACGTCGGCT 59.683 50.000 11.62 2.29 35.39 5.52
615 1218 1.852895 GATGTGACGTCGGCTCAATAC 59.147 52.381 11.62 1.10 0.00 1.89
619 1222 0.454600 GACGTCGGCTCAATACCTCA 59.545 55.000 0.00 0.00 0.00 3.86
670 1700 3.308053 CCGTGCAATGATAAGACTGAGTG 59.692 47.826 0.00 0.00 0.00 3.51
673 1703 5.230936 CGTGCAATGATAAGACTGAGTGTAG 59.769 44.000 0.00 0.00 0.00 2.74
675 1705 4.509600 GCAATGATAAGACTGAGTGTAGGC 59.490 45.833 0.00 0.00 0.00 3.93
697 1727 2.529151 GGCACCTGCGATTAATTTGTG 58.471 47.619 0.00 0.00 43.26 3.33
746 1778 4.157958 GGCGTACGACGACGAGCT 62.158 66.667 21.65 0.00 46.05 4.09
747 1779 2.938002 GCGTACGACGACGAGCTG 60.938 66.667 21.65 2.00 46.05 4.24
794 1851 2.202878 CGACCCAGCGTACCATGG 60.203 66.667 11.19 11.19 36.27 3.66
804 1861 1.147153 GTACCATGGGCTCAGCTCC 59.853 63.158 18.09 0.00 0.00 4.70
805 1862 1.306911 TACCATGGGCTCAGCTCCA 60.307 57.895 18.09 9.08 34.50 3.86
806 1863 1.626356 TACCATGGGCTCAGCTCCAC 61.626 60.000 18.09 0.00 33.27 4.02
807 1864 2.677289 CCATGGGCTCAGCTCCACT 61.677 63.158 8.86 0.00 33.27 4.00
809 1866 3.341202 ATGGGCTCAGCTCCACTGC 62.341 63.158 8.86 0.00 46.76 4.40
810 1867 3.715097 GGGCTCAGCTCCACTGCT 61.715 66.667 0.00 0.00 46.76 4.24
811 1868 2.125188 GGCTCAGCTCCACTGCTC 60.125 66.667 0.00 0.00 46.76 4.26
843 1900 3.998341 ACTACTCTCCGATTATCTCTCGC 59.002 47.826 0.00 0.00 34.84 5.03
846 1903 0.238553 CTCCGATTATCTCTCGCGCA 59.761 55.000 8.75 0.00 34.84 6.09
847 1904 0.040336 TCCGATTATCTCTCGCGCAC 60.040 55.000 8.75 0.00 34.84 5.34
848 1905 0.317854 CCGATTATCTCTCGCGCACA 60.318 55.000 8.75 0.00 34.84 4.57
849 1906 1.048494 CGATTATCTCTCGCGCACAG 58.952 55.000 8.75 1.89 0.00 3.66
850 1907 0.781191 GATTATCTCTCGCGCACAGC 59.219 55.000 8.75 0.00 43.95 4.40
894 1957 0.679321 CTGCTGCCTCCCCTTTCTTC 60.679 60.000 0.00 0.00 0.00 2.87
898 1961 2.238701 GCCTCCCCTTTCTTCCCCA 61.239 63.158 0.00 0.00 0.00 4.96
899 1962 2.002625 CCTCCCCTTTCTTCCCCAG 58.997 63.158 0.00 0.00 0.00 4.45
904 1967 1.464722 CCTTTCTTCCCCAGCCCAA 59.535 57.895 0.00 0.00 0.00 4.12
924 1987 3.430497 CCCTCCCCCTCCTCGAGA 61.430 72.222 15.71 0.00 0.00 4.04
964 2027 2.202676 CGCCTCCAGTCGAGAAGC 60.203 66.667 0.00 0.00 41.63 3.86
969 2032 2.232298 CTCCAGTCGAGAAGCCCACC 62.232 65.000 0.00 0.00 41.63 4.61
985 2052 4.218722 CCACCATTGGCGGTAGAC 57.781 61.111 1.54 0.00 37.07 2.59
987 2054 1.813753 CACCATTGGCGGTAGACGG 60.814 63.158 1.54 0.00 44.51 4.79
988 2055 2.288025 ACCATTGGCGGTAGACGGT 61.288 57.895 1.54 0.00 44.51 4.83
1405 2504 0.302890 CGTCGATGCCTGATTTGCTC 59.697 55.000 0.00 0.00 0.00 4.26
1442 2616 0.454452 GCGCTGAAAATTCACCGGTC 60.454 55.000 2.59 0.00 36.91 4.79
1593 2780 2.544685 CATCCAAGGTCTCGACACATC 58.455 52.381 0.00 0.00 0.00 3.06
1607 2794 2.276740 CATCCCCTTCCCCTGCAC 59.723 66.667 0.00 0.00 0.00 4.57
1818 3008 6.018994 GGCTGTGAGTACAAAAATATCCTACG 60.019 42.308 0.00 0.00 36.14 3.51
1823 3013 7.438459 GTGAGTACAAAAATATCCTACGCATCT 59.562 37.037 0.00 0.00 0.00 2.90
1830 3020 8.916654 CAAAAATATCCTACGCATCTACTACTG 58.083 37.037 0.00 0.00 0.00 2.74
1869 3059 2.159142 GGCAGTAGTATTGTACGGCAGT 60.159 50.000 8.13 0.00 43.49 4.40
1875 3065 7.646314 CAGTAGTATTGTACGGCAGTAGTATT 58.354 38.462 0.00 0.00 31.03 1.89
1879 3069 7.646314 AGTATTGTACGGCAGTAGTATTGTAG 58.354 38.462 0.00 0.00 32.77 2.74
1921 3123 4.790766 GCTCTCCAAATGTGTGTGTGAAAG 60.791 45.833 0.00 0.00 0.00 2.62
2007 3254 1.542492 CACAGCTTGCCCTCATCTTT 58.458 50.000 0.00 0.00 0.00 2.52
2156 3416 5.033522 AGCCCTTCTTCTACTGGTAAGAAT 58.966 41.667 0.00 0.00 40.08 2.40
2160 3420 7.445945 CCCTTCTTCTACTGGTAAGAATATGG 58.554 42.308 0.00 0.00 40.08 2.74
2185 3446 5.593968 TGCCATTGTGCATATGAAAATCTC 58.406 37.500 6.97 0.00 36.04 2.75
2186 3447 5.361571 TGCCATTGTGCATATGAAAATCTCT 59.638 36.000 6.97 0.00 36.04 3.10
2230 3496 7.125507 TGCAAATCAATATGTAGTCCCCATTTT 59.874 33.333 0.00 0.00 0.00 1.82
2233 3499 5.701224 TCAATATGTAGTCCCCATTTTCCC 58.299 41.667 0.00 0.00 0.00 3.97
2246 3513 4.325344 CCCATTTTCCCACAGGATAAGTCT 60.325 45.833 0.00 0.00 43.54 3.24
2392 3660 5.391310 GCAATGCATAAGATATCTTGGTCCG 60.391 44.000 25.22 11.26 37.40 4.79
2414 3682 5.335897 CCGGTAAGATCATTTGCATAATGGG 60.336 44.000 16.44 7.68 0.00 4.00
2463 3745 1.661341 ATTCCAATGAGAGCTGCGTC 58.339 50.000 0.00 0.00 0.00 5.19
2465 3747 1.446792 CCAATGAGAGCTGCGTCGT 60.447 57.895 0.00 0.00 0.00 4.34
2466 3748 1.416813 CCAATGAGAGCTGCGTCGTC 61.417 60.000 0.00 0.00 0.00 4.20
2467 3749 0.457509 CAATGAGAGCTGCGTCGTCT 60.458 55.000 0.00 0.00 0.00 4.18
2734 7785 8.792830 TTGATAAAGGAGTTAGGAAACAGATG 57.207 34.615 0.00 0.00 38.12 2.90
2768 7819 9.927081 ATAGGAAGATGTTGATATGGTTTTCTT 57.073 29.630 0.00 0.00 0.00 2.52
2852 7961 2.420547 GCATCTACATGAGGGCAAGTGA 60.421 50.000 0.00 0.00 30.57 3.41
2877 7987 3.297134 TCCTTGGTCTCTGCACTTTTT 57.703 42.857 0.00 0.00 0.00 1.94
2949 8183 7.095523 GCACACACATGCTTCTCAAATTTATTT 60.096 33.333 0.00 0.00 42.62 1.40
3045 8398 4.744631 GCAAATCGTTGGTCAAAGTTTCAT 59.255 37.500 0.00 0.00 35.10 2.57
3172 8526 5.005779 GCCAACATGTTCAGATTAGTCGTAG 59.994 44.000 8.48 0.00 0.00 3.51
3175 8529 5.907207 ACATGTTCAGATTAGTCGTAGCAT 58.093 37.500 0.00 0.00 0.00 3.79
3298 8684 7.998964 TCATTAAAGAGGGAAAGATTATCCACC 59.001 37.037 0.00 0.00 38.80 4.61
3369 8755 7.520686 CAAAATGGATTTTTGTTATGAGCACC 58.479 34.615 3.28 0.00 45.99 5.01
3412 8798 4.037446 GGCAGGTTGTTTGATAACTCACAA 59.963 41.667 0.00 0.00 35.24 3.33
3431 8817 5.299028 TCACAAAATTTTACTGCTGCTGAGA 59.701 36.000 13.69 0.00 0.00 3.27
3439 8827 3.475566 ACTGCTGCTGAGAACTGTTAA 57.524 42.857 13.69 0.00 0.00 2.01
3630 9021 4.278669 ACCACCATCGTATCTAAGTGCTAG 59.721 45.833 0.00 0.00 0.00 3.42
3678 9204 9.275398 ACACTCGGTGATTTGTTACTTAAATAA 57.725 29.630 10.46 0.00 36.96 1.40
3823 9360 2.224426 TGGACATTACAAACCGAGTGCT 60.224 45.455 0.00 0.00 0.00 4.40
3833 9370 0.034059 ACCGAGTGCTGAGAACCTTG 59.966 55.000 0.00 0.00 0.00 3.61
4023 9567 5.454062 AGACTACTATGAAGATCCAGTGCT 58.546 41.667 0.00 0.00 0.00 4.40
4048 9592 1.283793 CAAACAGAACCCTGCTGCG 59.716 57.895 0.00 0.00 44.16 5.18
4049 9593 1.898574 AAACAGAACCCTGCTGCGG 60.899 57.895 0.26 0.26 44.16 5.69
4075 9625 0.479815 TCATGCCATCCAATCCTCCC 59.520 55.000 0.00 0.00 0.00 4.30
4147 9712 4.141892 CCATCTTCTCAGACTGAAGCTGAT 60.142 45.833 6.61 5.55 41.20 2.90
4186 9751 1.600636 TGTGGAGAAAGCAAGGCCG 60.601 57.895 0.00 0.00 0.00 6.13
4228 9793 2.677875 GGTCTGCAAAGCCCCAGG 60.678 66.667 0.00 0.00 0.00 4.45
4330 9895 0.770499 TGTCCCTGAAATGGAGCACA 59.230 50.000 0.00 0.00 28.45 4.57
4362 9927 1.078426 GAATCGGGTGTGTGAGGGG 60.078 63.158 0.00 0.00 0.00 4.79
4366 9931 1.004200 CGGGTGTGTGAGGGGTTAC 60.004 63.158 0.00 0.00 0.00 2.50
4459 10044 1.826921 GAGGGTGCCATCATGCCTG 60.827 63.158 0.00 0.00 0.00 4.85
4490 10075 4.813526 CGACGTCGCCTCTCGTGG 62.814 72.222 26.59 0.00 40.39 4.94
4587 10189 1.818959 TTGATGGGTGCTGCAAAGGC 61.819 55.000 2.77 0.00 41.68 4.35
4592 10199 1.980772 GGTGCTGCAAAGGCCAGAT 60.981 57.895 5.01 0.00 40.13 2.90
4634 10242 5.611374 TCCTATGTTCCTCGAATCCATTTC 58.389 41.667 0.00 0.00 0.00 2.17
4651 10259 5.605908 TCCATTTCTAGCTCAGATGGATCTT 59.394 40.000 11.85 0.00 37.47 2.40
4718 10326 2.102252 GTGTGATTGTGCCTTTTTCCCA 59.898 45.455 0.00 0.00 0.00 4.37
4799 10407 3.853475 ACGGTACTGTAGTATGTTTGCC 58.147 45.455 5.26 0.00 32.54 4.52
4831 10440 6.147864 TCAGAAAACATTCAGGGACAAAAG 57.852 37.500 0.00 0.00 0.00 2.27
4834 10443 4.590850 AAACATTCAGGGACAAAAGCTC 57.409 40.909 0.00 0.00 0.00 4.09
4871 10480 7.551262 TCGAATTTAAGGAAAATCAAGGATCGA 59.449 33.333 0.00 0.00 37.17 3.59
4872 10481 8.181573 CGAATTTAAGGAAAATCAAGGATCGAA 58.818 33.333 0.00 0.00 36.76 3.71
4879 10488 8.000780 AGGAAAATCAAGGATCGAATTTAAGG 57.999 34.615 0.00 0.00 0.00 2.69
4887 11649 3.815962 GGATCGAATTTAAGGAAGCTCCC 59.184 47.826 0.00 0.00 37.19 4.30
4898 11660 1.352687 GGAAGCTCCCTCTGGAACTTT 59.647 52.381 0.00 0.00 45.10 2.66
4900 11662 1.352687 AAGCTCCCTCTGGAACTTTCC 59.647 52.381 0.59 0.59 43.08 3.13
4909 11671 2.068915 GGAACTTTCCGGGGGTGTA 58.931 57.895 0.00 0.00 37.65 2.90
4914 11676 1.614226 TTTCCGGGGGTGTAGGGAG 60.614 63.158 0.00 0.00 0.00 4.30
4915 11677 3.629035 TTCCGGGGGTGTAGGGAGG 62.629 68.421 0.00 0.00 0.00 4.30
4917 11679 4.084147 CGGGGGTGTAGGGAGGGA 62.084 72.222 0.00 0.00 0.00 4.20
4937 11699 0.804989 CACTCCAACGGCCAGATTTC 59.195 55.000 2.24 0.00 0.00 2.17
5096 12170 2.940994 TGAGTTCCCCGTTGATTTCA 57.059 45.000 0.00 0.00 0.00 2.69
5137 12283 6.776116 TCTTAGATATTTGGACTCTTAGGCGA 59.224 38.462 0.00 0.00 0.00 5.54
5142 12288 1.142097 GGACTCTTAGGCGACAGGC 59.858 63.158 0.00 0.00 44.19 4.85
5156 12302 1.218047 CAGGCGACAAGATCCGGAA 59.782 57.895 9.01 0.00 0.00 4.30
5171 12369 0.895530 CGGAAGCTCTAGACCAACCA 59.104 55.000 0.00 0.00 0.00 3.67
5172 12370 1.134965 CGGAAGCTCTAGACCAACCAG 60.135 57.143 0.00 0.00 0.00 4.00
5207 12405 2.702478 CTCATCTGTTAGGGATGGCTCA 59.298 50.000 0.00 0.00 40.44 4.26
5231 12429 6.652205 AAGGGAGGATAAAATGAACCACTA 57.348 37.500 0.00 0.00 0.00 2.74
5292 12490 3.433031 CCAGTGGCGGACCTAAAATCATA 60.433 47.826 0.00 0.00 36.63 2.15
5293 12491 4.196193 CAGTGGCGGACCTAAAATCATAA 58.804 43.478 0.00 0.00 36.63 1.90
5294 12492 4.821805 CAGTGGCGGACCTAAAATCATAAT 59.178 41.667 0.00 0.00 36.63 1.28
5295 12493 5.049405 CAGTGGCGGACCTAAAATCATAATC 60.049 44.000 0.00 0.00 36.63 1.75
5296 12494 4.215613 GTGGCGGACCTAAAATCATAATCC 59.784 45.833 0.00 0.00 36.63 3.01
5298 12496 5.308497 TGGCGGACCTAAAATCATAATCCTA 59.692 40.000 0.00 0.00 36.63 2.94
5300 12498 5.351740 GCGGACCTAAAATCATAATCCTAGC 59.648 44.000 0.00 0.00 0.00 3.42
5301 12499 6.464222 CGGACCTAAAATCATAATCCTAGCA 58.536 40.000 0.00 0.00 0.00 3.49
5302 12500 6.934645 CGGACCTAAAATCATAATCCTAGCAA 59.065 38.462 0.00 0.00 0.00 3.91
5303 12501 7.444183 CGGACCTAAAATCATAATCCTAGCAAA 59.556 37.037 0.00 0.00 0.00 3.68
5304 12502 9.301897 GGACCTAAAATCATAATCCTAGCAAAT 57.698 33.333 0.00 0.00 0.00 2.32
5318 12516 7.916914 TCCTAGCAAATACTCCTTAAACAAC 57.083 36.000 0.00 0.00 0.00 3.32
5319 12517 7.455058 TCCTAGCAAATACTCCTTAAACAACA 58.545 34.615 0.00 0.00 0.00 3.33
5321 12519 8.739972 CCTAGCAAATACTCCTTAAACAACATT 58.260 33.333 0.00 0.00 0.00 2.71
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 1.542175 CCGGAGTAGAGATGGGGGA 59.458 63.158 0.00 0.00 0.00 4.81
1 2 2.210711 GCCGGAGTAGAGATGGGGG 61.211 68.421 5.05 0.00 0.00 5.40
2 3 2.210711 GGCCGGAGTAGAGATGGGG 61.211 68.421 5.05 0.00 0.00 4.96
3 4 2.565645 CGGCCGGAGTAGAGATGGG 61.566 68.421 20.10 0.00 0.00 4.00
4 5 2.565645 CCGGCCGGAGTAGAGATGG 61.566 68.421 41.82 6.81 37.50 3.51
5 6 3.043419 CCGGCCGGAGTAGAGATG 58.957 66.667 41.82 7.45 37.50 2.90
15 16 4.487412 GTCGACACTACCGGCCGG 62.487 72.222 42.17 42.17 42.03 6.13
16 17 4.824166 CGTCGACACTACCGGCCG 62.824 72.222 21.04 21.04 0.00 6.13
18 19 4.409218 TGCGTCGACACTACCGGC 62.409 66.667 17.16 9.32 0.00 6.13
19 20 2.191354 TTCTGCGTCGACACTACCGG 62.191 60.000 17.16 0.00 0.00 5.28
20 21 0.793478 CTTCTGCGTCGACACTACCG 60.793 60.000 17.16 0.89 0.00 4.02
21 22 0.520404 TCTTCTGCGTCGACACTACC 59.480 55.000 17.16 0.00 0.00 3.18
22 23 1.977412 GTTCTTCTGCGTCGACACTAC 59.023 52.381 17.16 2.09 0.00 2.73
23 24 1.068748 GGTTCTTCTGCGTCGACACTA 60.069 52.381 17.16 0.00 0.00 2.74
24 25 0.318784 GGTTCTTCTGCGTCGACACT 60.319 55.000 17.16 0.00 0.00 3.55
25 26 1.606350 CGGTTCTTCTGCGTCGACAC 61.606 60.000 17.16 6.48 0.00 3.67
26 27 1.371267 CGGTTCTTCTGCGTCGACA 60.371 57.895 17.16 0.00 0.00 4.35
27 28 2.087009 CCGGTTCTTCTGCGTCGAC 61.087 63.158 5.18 5.18 0.00 4.20
28 29 2.257371 CCGGTTCTTCTGCGTCGA 59.743 61.111 0.00 0.00 0.00 4.20
29 30 2.809601 CCCGGTTCTTCTGCGTCG 60.810 66.667 0.00 0.00 0.00 5.12
30 31 3.119096 GCCCGGTTCTTCTGCGTC 61.119 66.667 0.00 0.00 0.00 5.19
31 32 3.178540 AAGCCCGGTTCTTCTGCGT 62.179 57.895 0.00 0.00 0.00 5.24
36 37 1.674651 GACCCAAGCCCGGTTCTTC 60.675 63.158 0.00 0.00 32.27 2.87
49 50 1.469335 AAGTTTCTCGAGCCGACCCA 61.469 55.000 7.81 0.00 0.00 4.51
50 51 1.014564 CAAGTTTCTCGAGCCGACCC 61.015 60.000 7.81 0.00 0.00 4.46
51 52 1.014564 CCAAGTTTCTCGAGCCGACC 61.015 60.000 7.81 0.00 0.00 4.79
58 59 1.069432 CGTCGTCTCCAAGTTTCTCGA 60.069 52.381 0.00 0.00 0.00 4.04
63 64 1.955080 AGAGTCGTCGTCTCCAAGTTT 59.045 47.619 14.60 0.00 32.93 2.66
66 67 1.157585 TGAGAGTCGTCGTCTCCAAG 58.842 55.000 14.60 0.00 39.91 3.61
74 75 1.442184 CCACCGTTGAGAGTCGTCG 60.442 63.158 0.00 0.00 0.00 5.12
86 87 1.901591 TCTCTCGAAACTACCACCGT 58.098 50.000 0.00 0.00 0.00 4.83
87 88 3.243336 CTTTCTCTCGAAACTACCACCG 58.757 50.000 0.00 0.00 35.41 4.94
102 103 2.124903 TGTTCAACGAGTCGCTTTCTC 58.875 47.619 13.59 0.00 0.00 2.87
110 111 4.965062 TCACAAAACTTGTTCAACGAGTC 58.035 39.130 11.07 0.00 41.82 3.36
156 158 6.718522 TTTTCACTTTTAATTCCGGGTTCT 57.281 33.333 0.00 0.00 0.00 3.01
159 161 6.223351 TGTTTTTCACTTTTAATTCCGGGT 57.777 33.333 0.00 0.00 0.00 5.28
160 162 6.926272 TGATGTTTTTCACTTTTAATTCCGGG 59.074 34.615 0.00 0.00 0.00 5.73
169 171 8.791327 AGGTTTCATTGATGTTTTTCACTTTT 57.209 26.923 0.00 0.00 0.00 2.27
180 182 2.744202 GTCGCTGAGGTTTCATTGATGT 59.256 45.455 0.00 0.00 31.68 3.06
183 185 2.542020 TGTCGCTGAGGTTTCATTGA 57.458 45.000 0.00 0.00 31.68 2.57
187 189 1.939934 CAGTTTGTCGCTGAGGTTTCA 59.060 47.619 0.00 0.00 36.12 2.69
197 199 0.737715 ATCCGAGCTCAGTTTGTCGC 60.738 55.000 15.40 0.00 0.00 5.19
207 209 1.557651 GAACGTAACCATCCGAGCTC 58.442 55.000 2.73 2.73 0.00 4.09
251 253 6.223852 TCAGTGTCAGGTCTAATTCTTGAAC 58.776 40.000 0.00 0.00 0.00 3.18
266 268 2.728318 CACACGTTCTCATCAGTGTCAG 59.272 50.000 0.00 0.00 44.83 3.51
313 315 3.851128 GGTCGGTAGCCCTGCTCC 61.851 72.222 0.00 0.00 40.44 4.70
317 319 2.584608 CCTTGGTCGGTAGCCCTG 59.415 66.667 0.00 0.00 0.00 4.45
318 320 3.400054 GCCTTGGTCGGTAGCCCT 61.400 66.667 0.00 0.00 0.00 5.19
319 321 3.387225 GAGCCTTGGTCGGTAGCCC 62.387 68.421 0.00 0.00 0.00 5.19
327 329 0.462759 CCAGGATTCGAGCCTTGGTC 60.463 60.000 6.21 0.00 32.12 4.02
332 334 1.280457 AAGAACCAGGATTCGAGCCT 58.720 50.000 3.28 3.28 35.75 4.58
362 550 2.159156 ACACAAATATACGCTGCGAGGA 60.159 45.455 30.47 13.57 0.00 3.71
369 557 5.163794 GGCTTGTACAACACAAATATACGCT 60.164 40.000 3.59 0.00 46.37 5.07
373 561 5.163804 CGCTGGCTTGTACAACACAAATATA 60.164 40.000 3.59 0.00 46.37 0.86
377 565 1.064803 CGCTGGCTTGTACAACACAAA 59.935 47.619 3.59 0.00 46.37 2.83
408 596 0.937304 CTTGTGCGGCGCAAGTATAT 59.063 50.000 35.89 0.00 44.10 0.86
430 618 2.203437 AAAAAGGCCCCGAACGCT 60.203 55.556 0.00 0.00 0.00 5.07
447 1042 3.053693 AGGCACTGCATTATAAGGTGGAA 60.054 43.478 2.82 0.00 37.18 3.53
450 1045 4.440525 CCAAAGGCACTGCATTATAAGGTG 60.441 45.833 0.50 0.00 40.86 4.00
470 1065 5.880332 CGACCAAAGAAGAAAGATATCCCAA 59.120 40.000 0.00 0.00 0.00 4.12
533 1133 7.923414 AGCCGTTGAAAGACTAAATAAATCT 57.077 32.000 0.00 0.00 0.00 2.40
534 1134 8.965986 AAAGCCGTTGAAAGACTAAATAAATC 57.034 30.769 0.00 0.00 0.00 2.17
535 1135 9.191995 CAAAAGCCGTTGAAAGACTAAATAAAT 57.808 29.630 0.00 0.00 0.00 1.40
536 1136 7.168469 GCAAAAGCCGTTGAAAGACTAAATAAA 59.832 33.333 1.25 0.00 0.00 1.40
539 1142 4.982295 GCAAAAGCCGTTGAAAGACTAAAT 59.018 37.500 1.25 0.00 0.00 1.40
542 1145 3.211045 AGCAAAAGCCGTTGAAAGACTA 58.789 40.909 1.25 0.00 0.00 2.59
555 1158 3.187432 GTCACCTCTCACTAAGCAAAAGC 59.813 47.826 0.00 0.00 0.00 3.51
556 1159 3.430218 CGTCACCTCTCACTAAGCAAAAG 59.570 47.826 0.00 0.00 0.00 2.27
557 1160 3.181469 ACGTCACCTCTCACTAAGCAAAA 60.181 43.478 0.00 0.00 0.00 2.44
562 1165 2.438411 AGGACGTCACCTCTCACTAAG 58.562 52.381 18.91 0.00 34.98 2.18
570 1173 5.175859 TGAAAATCAATAGGACGTCACCTC 58.824 41.667 18.91 0.00 41.00 3.85
574 1177 6.878923 ACATCTTGAAAATCAATAGGACGTCA 59.121 34.615 18.91 0.00 35.59 4.35
578 1181 7.148407 ACGTCACATCTTGAAAATCAATAGGAC 60.148 37.037 0.00 0.00 35.59 3.85
582 1185 6.183360 CCGACGTCACATCTTGAAAATCAATA 60.183 38.462 17.16 0.00 35.59 1.90
585 1188 3.431912 CCGACGTCACATCTTGAAAATCA 59.568 43.478 17.16 0.00 35.39 2.57
586 1189 3.725010 GCCGACGTCACATCTTGAAAATC 60.725 47.826 17.16 0.00 35.39 2.17
588 1191 1.529438 GCCGACGTCACATCTTGAAAA 59.471 47.619 17.16 0.00 35.39 2.29
590 1193 0.317160 AGCCGACGTCACATCTTGAA 59.683 50.000 17.16 0.00 35.39 2.69
593 1196 0.317160 TTGAGCCGACGTCACATCTT 59.683 50.000 17.16 0.00 0.00 2.40
615 1218 3.773418 TCTCTATCGGTACCTCTGAGG 57.227 52.381 22.00 22.00 42.49 3.86
619 1222 5.489637 ACATCCTATCTCTATCGGTACCTCT 59.510 44.000 10.90 0.00 0.00 3.69
627 1230 3.119316 GGGTGCACATCCTATCTCTATCG 60.119 52.174 20.43 0.00 0.00 2.92
662 1692 2.184579 GCCCGCCTACACTCAGTC 59.815 66.667 0.00 0.00 0.00 3.51
663 1693 2.603473 TGCCCGCCTACACTCAGT 60.603 61.111 0.00 0.00 0.00 3.41
664 1694 2.125512 GTGCCCGCCTACACTCAG 60.126 66.667 0.00 0.00 33.92 3.35
673 1703 4.849310 TAATCGCAGGTGCCCGCC 62.849 66.667 0.00 0.00 37.91 6.13
675 1705 0.738389 AAATTAATCGCAGGTGCCCG 59.262 50.000 0.00 0.00 37.91 6.13
711 1743 2.954611 GCAGTTGGGCGAGGTTTC 59.045 61.111 0.00 0.00 0.00 2.78
722 1754 3.823421 CGTCGTACGCCGCAGTTG 61.823 66.667 11.24 0.00 33.65 3.16
730 1762 2.938002 CAGCTCGTCGTCGTACGC 60.938 66.667 11.24 4.96 42.21 4.42
741 1773 4.717629 TTGTCCCGTCGCAGCTCG 62.718 66.667 0.00 0.00 40.15 5.03
742 1774 1.959226 TTTTGTCCCGTCGCAGCTC 60.959 57.895 0.00 0.00 0.00 4.09
743 1775 2.110213 TTTTGTCCCGTCGCAGCT 59.890 55.556 0.00 0.00 0.00 4.24
745 1777 2.549282 CGTTTTGTCCCGTCGCAG 59.451 61.111 0.00 0.00 0.00 5.18
746 1778 3.641986 GCGTTTTGTCCCGTCGCA 61.642 61.111 0.00 0.00 45.01 5.10
747 1779 3.641986 TGCGTTTTGTCCCGTCGC 61.642 61.111 0.00 0.00 45.70 5.19
753 1793 1.278637 CGGACTGTGCGTTTTGTCC 59.721 57.895 13.79 0.00 43.86 4.02
806 1863 5.140747 AGAGTAGTTTACTGTTGGAGCAG 57.859 43.478 0.00 0.00 39.59 4.24
807 1864 4.021368 GGAGAGTAGTTTACTGTTGGAGCA 60.021 45.833 0.00 0.00 39.59 4.26
808 1865 4.496360 GGAGAGTAGTTTACTGTTGGAGC 58.504 47.826 0.00 0.00 39.59 4.70
809 1866 4.458295 TCGGAGAGTAGTTTACTGTTGGAG 59.542 45.833 0.00 0.00 39.59 3.86
810 1867 4.401022 TCGGAGAGTAGTTTACTGTTGGA 58.599 43.478 0.00 0.00 39.59 3.53
811 1868 4.778534 TCGGAGAGTAGTTTACTGTTGG 57.221 45.455 0.00 0.00 39.59 3.77
851 1908 4.794648 TTTATGCCCGCCTGCGCT 62.795 61.111 9.73 0.00 38.24 5.92
852 1909 3.137637 AATTTATGCCCGCCTGCGC 62.138 57.895 5.91 0.00 38.24 6.09
860 1922 1.068127 CAGCAGCTGGAATTTATGCCC 59.932 52.381 17.12 0.00 37.61 5.36
924 1987 2.044946 GGGATGGCCGTGCTCTTT 60.045 61.111 16.82 0.00 33.83 2.52
969 2032 1.813753 CCGTCTACCGCCAATGGTG 60.814 63.158 5.73 5.73 43.68 4.17
982 2049 5.045012 TCCATGTATACTGTCTACCGTCT 57.955 43.478 4.17 0.00 0.00 4.18
983 2050 4.215827 CCTCCATGTATACTGTCTACCGTC 59.784 50.000 4.17 0.00 0.00 4.79
984 2051 4.142790 CCTCCATGTATACTGTCTACCGT 58.857 47.826 4.17 0.00 0.00 4.83
985 2052 4.023107 CACCTCCATGTATACTGTCTACCG 60.023 50.000 4.17 0.00 0.00 4.02
986 2053 4.281182 CCACCTCCATGTATACTGTCTACC 59.719 50.000 4.17 0.00 0.00 3.18
987 2054 5.138276 TCCACCTCCATGTATACTGTCTAC 58.862 45.833 4.17 0.00 0.00 2.59
988 2055 5.133830 TCTCCACCTCCATGTATACTGTCTA 59.866 44.000 4.17 0.00 0.00 2.59
1108 2175 3.771160 ATTCGCTTCGCCTCCGGT 61.771 61.111 0.00 0.00 34.56 5.28
1405 2504 1.369625 GCCCGTAACCATCAAGACAG 58.630 55.000 0.00 0.00 0.00 3.51
1442 2616 3.754965 TGACCAATCCAAACCAGAGAAG 58.245 45.455 0.00 0.00 0.00 2.85
1593 2780 3.350163 ATGGTGCAGGGGAAGGGG 61.350 66.667 0.00 0.00 0.00 4.79
1607 2794 0.099968 CTTGTGCTGGCGATTGATGG 59.900 55.000 0.00 0.00 0.00 3.51
1677 2867 9.382275 GGGTTAAAATTACGGAGAATTACAGTA 57.618 33.333 0.00 0.00 0.00 2.74
1682 2872 7.148272 CGTTGGGGTTAAAATTACGGAGAATTA 60.148 37.037 0.00 0.00 0.00 1.40
1691 2881 4.811908 ACATGCGTTGGGGTTAAAATTAC 58.188 39.130 0.00 0.00 0.00 1.89
1693 2883 4.202264 TGAACATGCGTTGGGGTTAAAATT 60.202 37.500 0.00 0.00 34.75 1.82
1869 3059 8.311836 AGAAAAGCAGCAAGTACTACAATACTA 58.688 33.333 0.00 0.00 34.18 1.82
1875 3065 5.351465 GCATAGAAAAGCAGCAAGTACTACA 59.649 40.000 0.00 0.00 0.00 2.74
1879 3069 4.633565 AGAGCATAGAAAAGCAGCAAGTAC 59.366 41.667 0.00 0.00 0.00 2.73
1921 3123 5.297569 ACTGATACTGGGAAGCTTATTCC 57.702 43.478 0.00 2.24 37.86 3.01
2031 3288 6.662865 AGAATATGACAGACGGATCTCAAT 57.337 37.500 0.00 0.00 30.42 2.57
2036 3293 6.971602 TCTACAAGAATATGACAGACGGATC 58.028 40.000 0.00 0.00 0.00 3.36
2041 3298 9.202273 GGATCAATCTACAAGAATATGACAGAC 57.798 37.037 0.00 0.00 0.00 3.51
2156 3416 4.759893 TGCACAATGGCAGCCATA 57.240 50.000 27.91 8.68 44.40 2.74
2185 3446 3.681417 TGCATGATTTCGTCTGAACAGAG 59.319 43.478 4.67 0.82 38.27 3.35
2186 3447 3.663025 TGCATGATTTCGTCTGAACAGA 58.337 40.909 0.00 0.00 32.71 3.41
2230 3496 6.884472 TTTATCAAGACTTATCCTGTGGGA 57.116 37.500 0.00 0.00 46.81 4.37
2233 3499 9.294030 GCAAAATTTATCAAGACTTATCCTGTG 57.706 33.333 0.00 0.00 0.00 3.66
2246 3513 6.507900 TCAGTTTCCGTGCAAAATTTATCAA 58.492 32.000 0.00 0.00 0.00 2.57
2392 3660 6.449698 CACCCATTATGCAAATGATCTTACC 58.550 40.000 17.70 0.00 0.00 2.85
2414 3682 6.823689 TCAGTAAGAAAGGATAAAGATGGCAC 59.176 38.462 0.00 0.00 0.00 5.01
2463 3745 6.093404 TGAATTTAGCACTCTGAAGTAGACG 58.907 40.000 0.00 0.00 33.25 4.18
2465 3747 8.314021 TGAATGAATTTAGCACTCTGAAGTAGA 58.686 33.333 0.00 0.00 33.25 2.59
2466 3748 8.484641 TGAATGAATTTAGCACTCTGAAGTAG 57.515 34.615 0.00 0.00 33.25 2.57
2467 3749 8.721478 GTTGAATGAATTTAGCACTCTGAAGTA 58.279 33.333 0.00 0.00 33.25 2.24
2768 7819 9.288576 CTTGCCTAACTAAATATCATCATTCCA 57.711 33.333 0.00 0.00 0.00 3.53
2852 7961 1.834263 GTGCAGAGACCAAGGATAGGT 59.166 52.381 0.00 0.00 43.46 3.08
3172 8526 6.563422 TCTAAACTTTCATGTGGCAATATGC 58.437 36.000 7.83 0.00 44.08 3.14
3175 8529 7.994425 TCTTCTAAACTTTCATGTGGCAATA 57.006 32.000 0.00 0.00 0.00 1.90
3298 8684 4.148079 TCTAGTGCCTCACCAGATATCTG 58.852 47.826 23.53 23.53 43.40 2.90
3309 8695 2.432146 CTGGCTTGTATCTAGTGCCTCA 59.568 50.000 0.00 0.00 43.57 3.86
3318 8704 0.030092 TAGGGCCCTGGCTTGTATCT 60.030 55.000 35.81 5.66 41.60 1.98
3369 8755 3.244976 CCCAGCATAAAGTTTCTTTGCG 58.755 45.455 10.61 7.30 38.32 4.85
3412 8798 5.300286 ACAGTTCTCAGCAGCAGTAAAATTT 59.700 36.000 0.00 0.00 0.00 1.82
3420 8806 3.397482 ACTTAACAGTTCTCAGCAGCAG 58.603 45.455 0.00 0.00 0.00 4.24
3439 8827 8.135529 GTGAAGCTAACCTTTGAAAACATAACT 58.864 33.333 0.00 0.00 32.78 2.24
3555 8945 0.798776 CAGTAAACCTTCCAGCAGCG 59.201 55.000 0.00 0.00 0.00 5.18
3640 9147 2.851195 ACCGAGTGTGAAATCTTTGCT 58.149 42.857 0.00 0.00 0.00 3.91
3651 9158 6.533819 TTAAGTAACAAATCACCGAGTGTG 57.466 37.500 4.33 0.00 46.88 3.82
3823 9360 2.727123 TGAAGTTGCCAAGGTTCTCA 57.273 45.000 2.19 0.00 0.00 3.27
3833 9370 4.256920 TCTAGAAAGCTCATGAAGTTGCC 58.743 43.478 0.00 0.00 0.00 4.52
4023 9567 4.458989 CAGCAGGGTTCTGTTTGCTATTAA 59.541 41.667 0.00 0.00 44.49 1.40
4049 9593 1.612676 TTGGATGGCATGATAGCAGC 58.387 50.000 3.81 0.00 35.83 5.25
4050 9594 2.753452 GGATTGGATGGCATGATAGCAG 59.247 50.000 3.81 0.00 35.83 4.24
4075 9625 3.084786 GTTGGAAGGGAGAATCAGTTGG 58.915 50.000 0.00 0.00 36.25 3.77
4147 9712 3.021695 ACGGAGATTATCGTTGACCTCA 58.978 45.455 0.00 0.00 36.04 3.86
4186 9751 4.200092 CTGATAAGGTTCTTTGGTAGGCC 58.800 47.826 0.00 0.00 0.00 5.19
4213 9778 2.240918 ATCCCTGGGGCTTTGCAGA 61.241 57.895 14.00 0.00 34.68 4.26
4228 9793 3.432051 CTGGGAGACGCCGACATCC 62.432 68.421 0.00 0.00 37.63 3.51
4330 9895 2.604046 CGATTCTCGGACCATTTCCT 57.396 50.000 0.00 0.00 43.25 3.36
4342 9907 0.108138 CCCTCACACACCCGATTCTC 60.108 60.000 0.00 0.00 0.00 2.87
4348 9913 1.004200 GTAACCCCTCACACACCCG 60.004 63.158 0.00 0.00 0.00 5.28
4362 9927 4.513318 GCATTCTGAGCTCTATTGGGTAAC 59.487 45.833 16.19 0.00 0.00 2.50
4366 9931 3.204306 TGCATTCTGAGCTCTATTGGG 57.796 47.619 16.19 1.54 0.00 4.12
4483 10068 2.747460 GCCTGCATTGCCACGAGA 60.747 61.111 6.12 0.00 0.00 4.04
4490 10075 3.145551 CAGGGAGGCCTGCATTGC 61.146 66.667 26.95 8.45 0.00 3.56
4587 10189 1.338973 ACAGCAAGCACAAACATCTGG 59.661 47.619 0.00 0.00 0.00 3.86
4592 10199 2.999355 GGAAAAACAGCAAGCACAAACA 59.001 40.909 0.00 0.00 0.00 2.83
4634 10242 4.262121 CCTCACAAGATCCATCTGAGCTAG 60.262 50.000 0.00 0.00 39.26 3.42
4651 10259 5.400066 TTCGAACTCATACAATCCTCACA 57.600 39.130 0.00 0.00 0.00 3.58
4718 10326 6.594788 ATTTCTGCAATAGTGACATTTGGT 57.405 33.333 0.00 0.00 0.00 3.67
4799 10407 7.040478 TCCCTGAATGTTTTCTGATTGTTGTAG 60.040 37.037 0.00 0.00 33.84 2.74
4831 10440 4.376340 AAATTCGATCATGGTTTGGAGC 57.624 40.909 0.00 0.00 0.00 4.70
4834 10443 6.449635 TCCTTAAATTCGATCATGGTTTGG 57.550 37.500 0.00 0.00 0.00 3.28
4871 10480 3.852578 TCCAGAGGGAGCTTCCTTAAATT 59.147 43.478 16.96 0.00 38.64 1.82
4872 10481 3.464828 TCCAGAGGGAGCTTCCTTAAAT 58.535 45.455 16.96 0.00 38.64 1.40
4873 10482 2.915869 TCCAGAGGGAGCTTCCTTAAA 58.084 47.619 16.96 0.00 38.64 1.52
4874 10483 2.572104 GTTCCAGAGGGAGCTTCCTTAA 59.428 50.000 16.96 5.01 46.01 1.85
4875 10484 2.188817 GTTCCAGAGGGAGCTTCCTTA 58.811 52.381 16.96 0.00 46.01 2.69
4876 10485 0.988063 GTTCCAGAGGGAGCTTCCTT 59.012 55.000 16.96 2.11 46.01 3.36
4877 10486 2.690367 GTTCCAGAGGGAGCTTCCT 58.310 57.895 15.58 15.58 46.01 3.36
4898 11660 4.084147 CCTCCCTACACCCCCGGA 62.084 72.222 0.73 0.00 0.00 5.14
4900 11662 4.084147 TCCCTCCCTACACCCCCG 62.084 72.222 0.00 0.00 0.00 5.73
4903 11665 0.976590 GAGTGTCCCTCCCTACACCC 60.977 65.000 0.00 0.00 45.70 4.61
4904 11666 2.593128 GAGTGTCCCTCCCTACACC 58.407 63.158 0.00 0.00 45.70 4.16
4914 11676 3.901797 CTGGCCGTTGGAGTGTCCC 62.902 68.421 0.00 0.00 35.03 4.46
4915 11677 2.185310 ATCTGGCCGTTGGAGTGTCC 62.185 60.000 0.00 0.00 36.96 4.02
4916 11678 0.321653 AATCTGGCCGTTGGAGTGTC 60.322 55.000 0.00 0.00 0.00 3.67
4917 11679 0.110486 AAATCTGGCCGTTGGAGTGT 59.890 50.000 0.00 0.00 0.00 3.55
4927 11689 1.133668 AGCCCACATAGAAATCTGGCC 60.134 52.381 0.00 0.00 38.15 5.36
5054 12071 8.415950 TCAAATCAATTTGGTGGTACTATGTT 57.584 30.769 13.88 0.00 45.39 2.71
5055 12072 7.669722 ACTCAAATCAATTTGGTGGTACTATGT 59.330 33.333 13.88 0.00 45.39 2.29
5056 12073 8.055279 ACTCAAATCAATTTGGTGGTACTATG 57.945 34.615 13.88 0.00 45.39 2.23
5057 12074 8.650143 AACTCAAATCAATTTGGTGGTACTAT 57.350 30.769 13.88 0.00 45.39 2.12
5058 12075 7.175990 GGAACTCAAATCAATTTGGTGGTACTA 59.824 37.037 13.88 0.00 45.39 1.82
5059 12076 6.015434 GGAACTCAAATCAATTTGGTGGTACT 60.015 38.462 13.88 0.00 45.39 2.73
5060 12077 6.156519 GGAACTCAAATCAATTTGGTGGTAC 58.843 40.000 13.88 5.21 45.39 3.34
5062 12079 4.040339 GGGAACTCAAATCAATTTGGTGGT 59.960 41.667 13.88 7.39 45.39 4.16
5077 12151 2.940994 TGAAATCAACGGGGAACTCA 57.059 45.000 0.00 0.00 0.00 3.41
5084 12158 4.989279 AATCCTCAATGAAATCAACGGG 57.011 40.909 0.00 0.00 0.00 5.28
5086 12160 8.915871 ATAACAAATCCTCAATGAAATCAACG 57.084 30.769 0.00 0.00 0.00 4.10
5114 12188 6.322969 TGTCGCCTAAGAGTCCAAATATCTAA 59.677 38.462 0.00 0.00 0.00 2.10
5137 12283 1.541310 TTCCGGATCTTGTCGCCTGT 61.541 55.000 4.15 0.00 0.00 4.00
5142 12288 0.457851 AGAGCTTCCGGATCTTGTCG 59.542 55.000 4.15 0.00 37.40 4.35
5144 12290 2.691011 GTCTAGAGCTTCCGGATCTTGT 59.309 50.000 11.21 3.95 41.35 3.16
5156 12302 1.077993 ACTCCTGGTTGGTCTAGAGCT 59.922 52.381 21.80 0.00 37.07 4.09
5171 12369 6.865834 ACAGATGAGACTTAAATCACTCCT 57.134 37.500 0.00 0.00 0.00 3.69
5172 12370 7.708752 CCTAACAGATGAGACTTAAATCACTCC 59.291 40.741 0.00 0.00 0.00 3.85
5207 12405 5.903923 AGTGGTTCATTTTATCCTCCCTTT 58.096 37.500 0.00 0.00 0.00 3.11
5258 12456 0.036875 GCCACTGGCTAGAAAGGTGT 59.963 55.000 13.28 0.00 46.69 4.16
5278 12476 8.691661 TTTGCTAGGATTATGATTTTAGGTCC 57.308 34.615 0.00 0.00 0.00 4.46
5292 12490 8.957466 GTTGTTTAAGGAGTATTTGCTAGGATT 58.043 33.333 0.00 0.00 0.00 3.01
5293 12491 8.107095 TGTTGTTTAAGGAGTATTTGCTAGGAT 58.893 33.333 0.00 0.00 0.00 3.24
5294 12492 7.455058 TGTTGTTTAAGGAGTATTTGCTAGGA 58.545 34.615 0.00 0.00 0.00 2.94
5295 12493 7.681939 TGTTGTTTAAGGAGTATTTGCTAGG 57.318 36.000 0.00 0.00 0.00 3.02
5426 12625 7.487829 GTGCTAATCTTCACTAGAAAGAGACAG 59.512 40.741 14.56 12.15 36.22 3.51
5428 12627 7.543756 AGTGCTAATCTTCACTAGAAAGAGAC 58.456 38.462 14.56 8.29 41.32 3.36
5483 12682 4.419522 AACACAAGTGAGTTGACAACAC 57.580 40.909 20.08 14.31 38.60 3.32
5491 12690 7.535997 GGAAAAGAACTAAACACAAGTGAGTT 58.464 34.615 7.28 6.36 37.41 3.01


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

AutoCloner maintained by Alex Coulton.