Multiple sequence alignment - TraesCS2D01G253800

Loading Multiple Alignment...

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 TraesCS2D01G253800 chr2D 100.000 4538 0 0 1 4538 306247824 306252361 0.000000e+00 8381
1 TraesCS2D01G253800 chr2D 89.535 172 15 2 4369 4538 553358802 553358632 9.890000e-52 215
2 TraesCS2D01G253800 chr2D 94.656 131 6 1 21 150 199858797 199858927 7.700000e-48 202
3 TraesCS2D01G253800 chr2A 95.430 3567 103 21 175 3705 385007450 385003908 0.000000e+00 5629
4 TraesCS2D01G253800 chr2A 97.187 391 10 1 4148 4538 385003450 385003061 0.000000e+00 660
5 TraesCS2D01G253800 chr2A 96.190 315 10 2 3820 4134 385003909 385003597 8.710000e-142 514
6 TraesCS2D01G253800 chr2A 93.478 138 8 1 4402 4538 235712056 235712193 2.140000e-48 204
7 TraesCS2D01G253800 chr2B 95.464 3549 89 22 175 3705 374204345 374207839 0.000000e+00 5596
8 TraesCS2D01G253800 chr2B 93.557 745 21 3 3820 4538 374207838 374208581 0.000000e+00 1085
9 TraesCS2D01G253800 chr2B 95.556 135 5 1 21 154 65430289 65430423 9.890000e-52 215
10 TraesCS2D01G253800 chr2B 96.748 123 3 1 3705 3827 409336449 409336570 2.140000e-48 204
11 TraesCS2D01G253800 chr5A 97.887 142 3 0 1915 2056 400867606 400867465 3.510000e-61 246
12 TraesCS2D01G253800 chr4D 94.853 136 6 1 17 151 42266291 42266426 1.280000e-50 211
13 TraesCS2D01G253800 chr4D 94.697 132 6 1 21 151 73211804 73211935 2.140000e-48 204
14 TraesCS2D01G253800 chr4B 94.776 134 6 1 21 153 621843759 621843626 1.650000e-49 207
15 TraesCS2D01G253800 chr4B 95.968 124 4 1 3705 3827 455621561 455621438 2.770000e-47 200
16 TraesCS2D01G253800 chr4B 92.754 138 6 4 3705 3839 304887967 304888103 3.580000e-46 196
17 TraesCS2D01G253800 chr7D 94.118 136 7 1 21 155 511939905 511940040 5.950000e-49 206
18 TraesCS2D01G253800 chr6B 98.276 116 2 0 3705 3820 697123537 697123652 2.140000e-48 204
19 TraesCS2D01G253800 chr6B 94.030 134 7 1 21 153 122972106 122971973 7.700000e-48 202
20 TraesCS2D01G253800 chr6B 95.968 124 4 1 3705 3828 313699436 313699558 2.770000e-47 200
21 TraesCS2D01G253800 chr6A 94.697 132 6 1 21 151 68503592 68503461 2.140000e-48 204
22 TraesCS2D01G253800 chr5D 96.721 122 4 0 3705 3826 385791176 385791055 2.140000e-48 204
23 TraesCS2D01G253800 chr5D 97.479 119 2 1 3705 3823 548322912 548323029 7.700000e-48 202
24 TraesCS2D01G253800 chr5D 87.363 182 11 6 4369 4538 6115882 6116063 9.960000e-47 198
25 TraesCS2D01G253800 chr3A 98.276 116 2 0 3705 3820 402276750 402276865 2.140000e-48 204
26 TraesCS2D01G253800 chr1D 94.074 135 7 1 21 154 433907840 433907706 2.140000e-48 204
27 TraesCS2D01G253800 chr6D 95.652 115 5 0 3705 3819 459048299 459048413 7.750000e-43 185


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 TraesCS2D01G253800 chr2D 306247824 306252361 4537 False 8381.000000 8381 100.0000 1 4538 1 chr2D.!!$F2 4537
1 TraesCS2D01G253800 chr2A 385003061 385007450 4389 True 2267.666667 5629 96.2690 175 4538 3 chr2A.!!$R1 4363
2 TraesCS2D01G253800 chr2B 374204345 374208581 4236 False 3340.500000 5596 94.5105 175 4538 2 chr2B.!!$F3 4363

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
107 108 0.101579 ACCCAAACGGACAAAAAGCG 59.898 50.0 0.00 0.00 34.64 4.68 F
687 723 0.179051 TTTGCTTTGCTTTGCTGGGG 60.179 50.0 0.00 0.00 0.00 4.96 F
770 806 0.389948 TTCTTTCTCGCCTTCTCGCC 60.390 55.0 0.00 0.00 0.00 5.54 F
773 809 0.389948 TTTCTCGCCTTCTCGCCTTC 60.390 55.0 0.00 0.00 0.00 3.46 F
787 823 0.392327 GCCTTCAGGTTCCTGAGAGC 60.392 60.0 18.99 20.06 42.97 4.09 F
2457 2510 0.033504 GTTCTCCCACTCTTCGCACA 59.966 55.0 0.00 0.00 0.00 4.57 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1711 1764 0.755686 CCTGGATCCTCTTTCCTCGG 59.244 60.000 14.23 0.00 34.17 4.63 R
2361 2414 0.034198 TCCGTCGCAGATTGAAACCA 59.966 50.000 0.00 0.00 40.67 3.67 R
2362 2415 1.128692 CTTCCGTCGCAGATTGAAACC 59.871 52.381 0.00 0.00 40.67 3.27 R
2445 2498 2.031516 CCCAGCTGTGCGAAGAGTG 61.032 63.158 13.81 0.00 0.00 3.51 R
2622 2675 2.171448 ACCCTGGTGAGAATCTGTATGC 59.829 50.000 0.00 0.00 34.92 3.14 R
3751 3804 0.039180 GGGAAGGGTCCGACCATTTT 59.961 55.000 18.14 9.49 43.04 1.82 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
26 27 9.793252 GAATGCAAATCAATATACATATGGGTC 57.207 33.333 7.80 0.00 0.00 4.46
27 28 7.376435 TGCAAATCAATATACATATGGGTCG 57.624 36.000 7.80 0.00 0.00 4.79
28 29 6.374053 TGCAAATCAATATACATATGGGTCGG 59.626 38.462 7.80 0.00 0.00 4.79
29 30 6.677920 GCAAATCAATATACATATGGGTCGGC 60.678 42.308 7.80 0.00 0.00 5.54
30 31 4.118093 TCAATATACATATGGGTCGGCG 57.882 45.455 7.80 0.00 0.00 6.46
31 32 2.596904 ATATACATATGGGTCGGCGC 57.403 50.000 7.80 0.00 0.00 6.53
32 33 0.171679 TATACATATGGGTCGGCGCG 59.828 55.000 7.80 0.00 0.00 6.86
33 34 1.812686 ATACATATGGGTCGGCGCGT 61.813 55.000 8.43 3.65 0.00 6.01
34 35 2.018727 TACATATGGGTCGGCGCGTT 62.019 55.000 8.43 0.00 0.00 4.84
35 36 2.587753 ATATGGGTCGGCGCGTTG 60.588 61.111 8.43 0.00 0.00 4.10
36 37 4.823419 TATGGGTCGGCGCGTTGG 62.823 66.667 8.43 0.00 0.00 3.77
54 55 3.215245 GCACACTGCCAACCCAAA 58.785 55.556 0.00 0.00 37.42 3.28
55 56 1.747774 GCACACTGCCAACCCAAAT 59.252 52.632 0.00 0.00 37.42 2.32
56 57 0.600782 GCACACTGCCAACCCAAATG 60.601 55.000 0.00 0.00 37.42 2.32
57 58 0.600782 CACACTGCCAACCCAAATGC 60.601 55.000 0.00 0.00 0.00 3.56
58 59 1.047596 ACACTGCCAACCCAAATGCA 61.048 50.000 0.00 0.00 0.00 3.96
59 60 0.106335 CACTGCCAACCCAAATGCAA 59.894 50.000 0.00 0.00 32.58 4.08
60 61 0.835941 ACTGCCAACCCAAATGCAAA 59.164 45.000 0.00 0.00 32.58 3.68
61 62 1.211457 ACTGCCAACCCAAATGCAAAA 59.789 42.857 0.00 0.00 32.58 2.44
62 63 1.603326 CTGCCAACCCAAATGCAAAAC 59.397 47.619 0.00 0.00 32.58 2.43
63 64 1.211457 TGCCAACCCAAATGCAAAACT 59.789 42.857 0.00 0.00 0.00 2.66
64 65 1.603326 GCCAACCCAAATGCAAAACTG 59.397 47.619 0.00 0.00 0.00 3.16
65 66 2.744494 GCCAACCCAAATGCAAAACTGA 60.744 45.455 0.00 0.00 0.00 3.41
66 67 3.132925 CCAACCCAAATGCAAAACTGAG 58.867 45.455 0.00 0.00 0.00 3.35
67 68 2.531522 ACCCAAATGCAAAACTGAGC 57.468 45.000 0.00 0.00 0.00 4.26
68 69 1.269726 ACCCAAATGCAAAACTGAGCG 60.270 47.619 0.00 0.00 0.00 5.03
69 70 1.421382 CCAAATGCAAAACTGAGCGG 58.579 50.000 0.00 0.00 0.00 5.52
70 71 1.000385 CCAAATGCAAAACTGAGCGGA 60.000 47.619 0.00 0.00 0.00 5.54
71 72 2.053627 CAAATGCAAAACTGAGCGGAC 58.946 47.619 0.00 0.00 0.00 4.79
72 73 0.238289 AATGCAAAACTGAGCGGACG 59.762 50.000 0.00 0.00 0.00 4.79
73 74 2.127232 GCAAAACTGAGCGGACGC 60.127 61.111 8.91 8.91 42.33 5.19
74 75 2.556287 CAAAACTGAGCGGACGCC 59.444 61.111 13.63 5.70 43.17 5.68
105 106 2.113910 CGACCCAAACGGACAAAAAG 57.886 50.000 0.00 0.00 34.64 2.27
106 107 1.847818 GACCCAAACGGACAAAAAGC 58.152 50.000 0.00 0.00 34.64 3.51
107 108 0.101579 ACCCAAACGGACAAAAAGCG 59.898 50.000 0.00 0.00 34.64 4.68
108 109 0.596341 CCCAAACGGACAAAAAGCGG 60.596 55.000 0.00 0.00 0.00 5.52
109 110 0.382515 CCAAACGGACAAAAAGCGGA 59.617 50.000 0.00 0.00 0.00 5.54
110 111 1.472990 CAAACGGACAAAAAGCGGAC 58.527 50.000 0.00 0.00 0.00 4.79
111 112 1.096416 AAACGGACAAAAAGCGGACA 58.904 45.000 0.00 0.00 0.00 4.02
112 113 1.096416 AACGGACAAAAAGCGGACAA 58.904 45.000 0.00 0.00 0.00 3.18
113 114 1.096416 ACGGACAAAAAGCGGACAAA 58.904 45.000 0.00 0.00 0.00 2.83
114 115 1.679153 ACGGACAAAAAGCGGACAAAT 59.321 42.857 0.00 0.00 0.00 2.32
115 116 2.050691 CGGACAAAAAGCGGACAAATG 58.949 47.619 0.00 0.00 0.00 2.32
116 117 1.792367 GGACAAAAAGCGGACAAATGC 59.208 47.619 0.00 0.00 0.00 3.56
117 118 1.451651 GACAAAAAGCGGACAAATGCG 59.548 47.619 0.00 0.00 43.57 4.73
123 124 4.160635 CGGACAAATGCGCCGTCC 62.161 66.667 19.71 19.71 44.79 4.79
124 125 4.160635 GGACAAATGCGCCGTCCG 62.161 66.667 16.42 0.29 39.86 4.79
125 126 3.419759 GACAAATGCGCCGTCCGT 61.420 61.111 4.18 0.00 39.71 4.69
126 127 2.961669 GACAAATGCGCCGTCCGTT 61.962 57.895 4.18 0.00 39.71 4.44
127 128 2.254051 CAAATGCGCCGTCCGTTT 59.746 55.556 4.18 0.00 39.71 3.60
128 129 2.080062 CAAATGCGCCGTCCGTTTG 61.080 57.895 4.18 3.18 39.71 2.93
129 130 3.262142 AAATGCGCCGTCCGTTTGG 62.262 57.895 4.18 0.00 39.71 3.28
153 154 2.854522 CCCGTTGGGTTGCTCTTAG 58.145 57.895 0.00 0.00 38.25 2.18
154 155 0.323629 CCCGTTGGGTTGCTCTTAGA 59.676 55.000 0.00 0.00 38.25 2.10
155 156 1.271163 CCCGTTGGGTTGCTCTTAGAA 60.271 52.381 0.00 0.00 38.25 2.10
156 157 2.500229 CCGTTGGGTTGCTCTTAGAAA 58.500 47.619 0.00 0.00 0.00 2.52
157 158 2.882137 CCGTTGGGTTGCTCTTAGAAAA 59.118 45.455 0.00 0.00 0.00 2.29
158 159 3.316868 CCGTTGGGTTGCTCTTAGAAAAA 59.683 43.478 0.00 0.00 0.00 1.94
236 237 1.597854 CAGCCAAGAGACGGTGCAA 60.598 57.895 0.00 0.00 0.00 4.08
285 286 2.124819 CCCAGCTAGCCAGTGCAG 60.125 66.667 12.13 0.00 41.13 4.41
295 296 1.310216 GCCAGTGCAGTGCATCATCA 61.310 55.000 22.87 0.00 41.91 3.07
296 297 1.389555 CCAGTGCAGTGCATCATCAT 58.610 50.000 22.87 0.59 41.91 2.45
297 298 1.333931 CCAGTGCAGTGCATCATCATC 59.666 52.381 22.87 6.29 41.91 2.92
298 299 2.014128 CAGTGCAGTGCATCATCATCA 58.986 47.619 22.87 0.00 41.91 3.07
299 300 2.618709 CAGTGCAGTGCATCATCATCAT 59.381 45.455 22.87 0.00 41.91 2.45
300 301 2.879026 AGTGCAGTGCATCATCATCATC 59.121 45.455 22.87 3.88 41.91 2.92
313 314 7.414208 GCATCATCATCATCCAGCTAATAACAG 60.414 40.741 0.00 0.00 0.00 3.16
512 517 1.454479 CCTGCGCCTGATTTCCCAT 60.454 57.895 4.18 0.00 0.00 4.00
514 519 1.679139 CTGCGCCTGATTTCCCATTA 58.321 50.000 4.18 0.00 0.00 1.90
520 529 5.001232 GCGCCTGATTTCCCATTATACTAA 58.999 41.667 0.00 0.00 0.00 2.24
522 531 6.403636 GCGCCTGATTTCCCATTATACTAATG 60.404 42.308 0.00 0.81 0.00 1.90
616 625 1.212751 GGACGGCTTGCCATTTGTC 59.787 57.895 12.45 10.08 0.00 3.18
617 626 1.212751 GACGGCTTGCCATTTGTCC 59.787 57.895 12.45 0.00 0.00 4.02
639 660 0.679321 CTCTGGGCTTGGAGCTTTCC 60.679 60.000 0.00 0.00 41.99 3.13
679 715 3.650139 CTGCTCTTGATTTGCTTTGCTT 58.350 40.909 0.00 0.00 0.00 3.91
680 716 4.056050 CTGCTCTTGATTTGCTTTGCTTT 58.944 39.130 0.00 0.00 0.00 3.51
682 718 3.363673 GCTCTTGATTTGCTTTGCTTTGC 60.364 43.478 0.00 0.00 0.00 3.68
683 719 4.056050 CTCTTGATTTGCTTTGCTTTGCT 58.944 39.130 0.00 0.00 0.00 3.91
684 720 3.805422 TCTTGATTTGCTTTGCTTTGCTG 59.195 39.130 0.00 0.00 0.00 4.41
686 722 1.802365 GATTTGCTTTGCTTTGCTGGG 59.198 47.619 0.00 0.00 0.00 4.45
687 723 0.179051 TTTGCTTTGCTTTGCTGGGG 60.179 50.000 0.00 0.00 0.00 4.96
766 802 4.068599 CCTTTCTTTCTTTCTCGCCTTCT 58.931 43.478 0.00 0.00 0.00 2.85
767 803 4.153296 CCTTTCTTTCTTTCTCGCCTTCTC 59.847 45.833 0.00 0.00 0.00 2.87
768 804 2.947852 TCTTTCTTTCTCGCCTTCTCG 58.052 47.619 0.00 0.00 0.00 4.04
769 805 1.391826 CTTTCTTTCTCGCCTTCTCGC 59.608 52.381 0.00 0.00 0.00 5.03
770 806 0.389948 TTCTTTCTCGCCTTCTCGCC 60.390 55.000 0.00 0.00 0.00 5.54
771 807 1.216710 CTTTCTCGCCTTCTCGCCT 59.783 57.895 0.00 0.00 0.00 5.52
772 808 0.390472 CTTTCTCGCCTTCTCGCCTT 60.390 55.000 0.00 0.00 0.00 4.35
773 809 0.389948 TTTCTCGCCTTCTCGCCTTC 60.390 55.000 0.00 0.00 0.00 3.46
774 810 1.532604 TTCTCGCCTTCTCGCCTTCA 61.533 55.000 0.00 0.00 0.00 3.02
787 823 0.392327 GCCTTCAGGTTCCTGAGAGC 60.392 60.000 18.99 20.06 42.97 4.09
816 856 6.080648 TCTTGTTCTTGTTCTCTTACGCTA 57.919 37.500 0.00 0.00 0.00 4.26
831 871 1.765314 ACGCTAAATCTCTGGCCATCT 59.235 47.619 5.51 0.00 0.00 2.90
885 925 2.981560 AATGCGGTTCTGCTTGGCG 61.982 57.895 5.23 0.00 35.36 5.69
1092 1139 2.217038 GCCCCAGCCGATCCTCATA 61.217 63.158 0.00 0.00 0.00 2.15
1422 1475 1.304509 GGCTGCTCTCCAAGTTCAGC 61.305 60.000 0.00 4.14 46.68 4.26
1452 1505 4.411869 GGAGAGATTTCTTGGAGGGATTCT 59.588 45.833 0.00 0.00 32.53 2.40
1467 1520 3.868077 GGGATTCTCAGATCAACTCAACG 59.132 47.826 0.00 0.00 0.00 4.10
1711 1764 1.151668 GGGATGCATCGATGTACTGC 58.848 55.000 25.47 13.81 36.45 4.40
2041 2094 0.601046 CAACAAGACCGCTGCAGAGA 60.601 55.000 20.43 0.00 0.00 3.10
2115 2168 1.203441 TCCTTGATGCTGCCTCACCT 61.203 55.000 7.13 0.00 0.00 4.00
2146 2199 1.607467 CTTTGGGTTCAGCTGGGGG 60.607 63.158 15.13 0.00 0.00 5.40
2268 2321 1.426251 TTGGAGGCATCAGTGGTGGT 61.426 55.000 5.34 0.00 0.00 4.16
2311 2364 3.080300 CCAAGTGGGTGCTAATTGGTA 57.920 47.619 0.00 0.00 36.48 3.25
2351 2404 2.937469 TTTATCGCAATTGCTGGTGG 57.063 45.000 26.86 11.97 39.32 4.61
2361 2414 4.996758 GCAATTGCTGGTGGTCTTTATTTT 59.003 37.500 23.21 0.00 38.21 1.82
2362 2415 5.106987 GCAATTGCTGGTGGTCTTTATTTTG 60.107 40.000 23.21 0.00 38.21 2.44
2436 2489 2.100749 TCTCCATGGTGCTACACATACG 59.899 50.000 12.58 0.00 35.86 3.06
2445 2498 1.836383 CTACACATACGCGTTCTCCC 58.164 55.000 20.78 0.00 0.00 4.30
2457 2510 0.033504 GTTCTCCCACTCTTCGCACA 59.966 55.000 0.00 0.00 0.00 4.57
2478 2531 1.891722 CTGGGGCATTTGGGAGCAAC 61.892 60.000 0.00 0.00 0.00 4.17
2579 2632 1.144913 AGGCTTTGGCAAGGTCTACAA 59.855 47.619 15.33 0.00 40.87 2.41
2622 2675 0.397114 GGGTGGCAATTAAGAGGGGG 60.397 60.000 0.00 0.00 0.00 5.40
2623 2676 1.043116 GGTGGCAATTAAGAGGGGGC 61.043 60.000 0.00 0.00 0.00 5.80
2880 2933 1.610886 GGGCTTCACTACCTTCACACC 60.611 57.143 0.00 0.00 0.00 4.16
3189 3242 1.376942 CCTTGCTGACTGGGCTCTG 60.377 63.158 0.00 0.00 0.00 3.35
3257 3310 3.088532 TGGATGGAAATTACACACTGGC 58.911 45.455 0.00 0.00 0.00 4.85
3262 3315 1.127951 GAAATTACACACTGGCGTCCG 59.872 52.381 0.00 0.00 0.00 4.79
3269 3322 1.300620 CACTGGCGTCCGTCAAGAA 60.301 57.895 0.00 0.00 0.00 2.52
3272 3325 0.721718 CTGGCGTCCGTCAAGAAATC 59.278 55.000 0.00 0.00 0.00 2.17
3277 3330 1.808411 GTCCGTCAAGAAATCCAGCA 58.192 50.000 0.00 0.00 0.00 4.41
3464 3517 0.874390 GTGGCGTGCATCAAAGAAGA 59.126 50.000 0.00 0.00 0.00 2.87
3493 3546 2.997315 CTCGTCCAGGCTCCCACA 60.997 66.667 0.00 0.00 0.00 4.17
3552 3605 2.620585 GCCATGATACAGAAGGGCTTTC 59.379 50.000 0.32 0.32 38.37 2.62
3709 3762 9.584839 CAAAAATATTTCTGTTTTGCTAACAGC 57.415 29.630 20.58 0.00 45.34 4.40
3710 3763 7.889589 AAATATTTCTGTTTTGCTAACAGCC 57.110 32.000 20.58 0.00 45.34 4.85
3711 3764 6.840780 ATATTTCTGTTTTGCTAACAGCCT 57.159 33.333 20.58 12.89 45.34 4.58
3712 3765 4.568152 TTTCTGTTTTGCTAACAGCCTC 57.432 40.909 20.58 0.00 45.34 4.70
3713 3766 3.492102 TCTGTTTTGCTAACAGCCTCT 57.508 42.857 20.58 0.00 45.34 3.69
3714 3767 3.820557 TCTGTTTTGCTAACAGCCTCTT 58.179 40.909 20.58 0.00 45.34 2.85
3715 3768 3.565482 TCTGTTTTGCTAACAGCCTCTTG 59.435 43.478 20.58 4.23 45.34 3.02
3716 3769 2.034558 TGTTTTGCTAACAGCCTCTTGC 59.965 45.455 1.54 0.00 41.51 4.01
3717 3770 1.979855 TTTGCTAACAGCCTCTTGCA 58.020 45.000 0.00 0.00 44.83 4.08
3718 3771 1.527034 TTGCTAACAGCCTCTTGCAG 58.473 50.000 0.00 0.00 44.83 4.41
3719 3772 0.686789 TGCTAACAGCCTCTTGCAGA 59.313 50.000 0.00 0.00 44.83 4.26
3720 3773 1.072173 TGCTAACAGCCTCTTGCAGAA 59.928 47.619 0.00 0.00 44.83 3.02
3721 3774 2.154462 GCTAACAGCCTCTTGCAGAAA 58.846 47.619 0.00 0.00 44.83 2.52
3722 3775 2.751806 GCTAACAGCCTCTTGCAGAAAT 59.248 45.455 0.00 0.00 44.83 2.17
3723 3776 3.427233 GCTAACAGCCTCTTGCAGAAATG 60.427 47.826 0.00 0.00 44.83 2.32
3724 3777 2.283145 ACAGCCTCTTGCAGAAATGT 57.717 45.000 0.00 0.00 44.83 2.71
3725 3778 3.423539 ACAGCCTCTTGCAGAAATGTA 57.576 42.857 0.00 0.00 44.83 2.29
3726 3779 3.341823 ACAGCCTCTTGCAGAAATGTAG 58.658 45.455 0.00 0.00 44.83 2.74
3727 3780 2.681848 CAGCCTCTTGCAGAAATGTAGG 59.318 50.000 0.00 0.00 44.83 3.18
3728 3781 2.019984 GCCTCTTGCAGAAATGTAGGG 58.980 52.381 0.00 0.00 40.77 3.53
3729 3782 2.356125 GCCTCTTGCAGAAATGTAGGGA 60.356 50.000 0.00 0.00 40.77 4.20
3730 3783 3.873801 GCCTCTTGCAGAAATGTAGGGAA 60.874 47.826 0.00 0.00 40.77 3.97
3731 3784 4.335416 CCTCTTGCAGAAATGTAGGGAAA 58.665 43.478 0.00 0.00 0.00 3.13
3732 3785 4.397417 CCTCTTGCAGAAATGTAGGGAAAG 59.603 45.833 0.00 0.00 0.00 2.62
3733 3786 4.335416 TCTTGCAGAAATGTAGGGAAAGG 58.665 43.478 0.00 0.00 0.00 3.11
3734 3787 2.446435 TGCAGAAATGTAGGGAAAGGC 58.554 47.619 0.00 0.00 0.00 4.35
3735 3788 2.041620 TGCAGAAATGTAGGGAAAGGCT 59.958 45.455 0.00 0.00 0.00 4.58
3736 3789 2.424956 GCAGAAATGTAGGGAAAGGCTG 59.575 50.000 0.00 0.00 0.00 4.85
3737 3790 2.424956 CAGAAATGTAGGGAAAGGCTGC 59.575 50.000 0.00 0.00 0.00 5.25
3738 3791 1.401905 GAAATGTAGGGAAAGGCTGCG 59.598 52.381 0.00 0.00 0.00 5.18
3739 3792 0.328258 AATGTAGGGAAAGGCTGCGT 59.672 50.000 0.00 0.00 0.00 5.24
3740 3793 1.200519 ATGTAGGGAAAGGCTGCGTA 58.799 50.000 0.00 0.00 0.00 4.42
3741 3794 0.248289 TGTAGGGAAAGGCTGCGTAC 59.752 55.000 0.00 0.00 37.28 3.67
3742 3795 0.248289 GTAGGGAAAGGCTGCGTACA 59.752 55.000 0.00 0.00 36.89 2.90
3743 3796 0.978151 TAGGGAAAGGCTGCGTACAA 59.022 50.000 0.00 0.00 0.00 2.41
3744 3797 0.328258 AGGGAAAGGCTGCGTACAAT 59.672 50.000 0.00 0.00 0.00 2.71
3745 3798 1.557832 AGGGAAAGGCTGCGTACAATA 59.442 47.619 0.00 0.00 0.00 1.90
3746 3799 1.940613 GGGAAAGGCTGCGTACAATAG 59.059 52.381 0.00 0.00 0.00 1.73
3747 3800 2.419574 GGGAAAGGCTGCGTACAATAGA 60.420 50.000 0.00 0.00 0.00 1.98
3748 3801 2.608090 GGAAAGGCTGCGTACAATAGAC 59.392 50.000 0.00 0.00 0.00 2.59
3749 3802 2.311124 AAGGCTGCGTACAATAGACC 57.689 50.000 0.00 0.00 0.00 3.85
3750 3803 0.464452 AGGCTGCGTACAATAGACCC 59.536 55.000 0.00 0.00 0.00 4.46
3751 3804 0.177141 GGCTGCGTACAATAGACCCA 59.823 55.000 0.00 0.00 0.00 4.51
3752 3805 1.406341 GGCTGCGTACAATAGACCCAA 60.406 52.381 0.00 0.00 0.00 4.12
3753 3806 2.352388 GCTGCGTACAATAGACCCAAA 58.648 47.619 0.00 0.00 0.00 3.28
3754 3807 2.745281 GCTGCGTACAATAGACCCAAAA 59.255 45.455 0.00 0.00 0.00 2.44
3755 3808 3.377172 GCTGCGTACAATAGACCCAAAAT 59.623 43.478 0.00 0.00 0.00 1.82
3756 3809 4.730613 GCTGCGTACAATAGACCCAAAATG 60.731 45.833 0.00 0.00 0.00 2.32
3757 3810 3.692101 TGCGTACAATAGACCCAAAATGG 59.308 43.478 0.00 0.00 37.25 3.16
3758 3811 3.692593 GCGTACAATAGACCCAAAATGGT 59.307 43.478 0.00 0.00 42.79 3.55
3764 3817 2.563297 GACCCAAAATGGTCGGACC 58.437 57.895 20.36 20.36 44.98 4.46
3765 3818 0.963856 GACCCAAAATGGTCGGACCC 60.964 60.000 23.81 7.15 44.98 4.46
3766 3819 1.382629 CCCAAAATGGTCGGACCCT 59.617 57.895 23.81 12.03 37.50 4.34
3767 3820 0.251608 CCCAAAATGGTCGGACCCTT 60.252 55.000 23.81 17.44 37.50 3.95
3768 3821 1.173913 CCAAAATGGTCGGACCCTTC 58.826 55.000 23.81 0.00 37.50 3.46
3769 3822 1.173913 CAAAATGGTCGGACCCTTCC 58.826 55.000 23.81 0.00 37.50 3.46
3770 3823 0.039180 AAAATGGTCGGACCCTTCCC 59.961 55.000 23.81 0.00 38.99 3.97
3771 3824 1.859841 AAATGGTCGGACCCTTCCCC 61.860 60.000 23.81 0.00 38.99 4.81
3772 3825 3.572715 ATGGTCGGACCCTTCCCCA 62.573 63.158 23.81 4.19 38.99 4.96
3773 3826 3.400054 GGTCGGACCCTTCCCCAG 61.400 72.222 16.55 0.00 38.99 4.45
3774 3827 2.284405 GTCGGACCCTTCCCCAGA 60.284 66.667 0.00 0.00 38.99 3.86
3775 3828 2.284405 TCGGACCCTTCCCCAGAC 60.284 66.667 0.00 0.00 38.99 3.51
3776 3829 3.400054 CGGACCCTTCCCCAGACC 61.400 72.222 0.00 0.00 38.99 3.85
3777 3830 3.015753 GGACCCTTCCCCAGACCC 61.016 72.222 0.00 0.00 35.57 4.46
3778 3831 2.125225 GACCCTTCCCCAGACCCT 59.875 66.667 0.00 0.00 0.00 4.34
3779 3832 2.204151 ACCCTTCCCCAGACCCTG 60.204 66.667 0.00 0.00 0.00 4.45
3780 3833 3.732849 CCCTTCCCCAGACCCTGC 61.733 72.222 0.00 0.00 0.00 4.85
3781 3834 4.101448 CCTTCCCCAGACCCTGCG 62.101 72.222 0.00 0.00 0.00 5.18
3782 3835 4.785453 CTTCCCCAGACCCTGCGC 62.785 72.222 0.00 0.00 0.00 6.09
3797 3850 4.856801 CGCAAGCGGGGGCTACAT 62.857 66.667 6.55 0.00 35.56 2.29
3798 3851 3.211963 GCAAGCGGGGGCTACATG 61.212 66.667 0.00 0.00 0.00 3.21
3799 3852 3.211963 CAAGCGGGGGCTACATGC 61.212 66.667 0.00 0.00 41.94 4.06
3800 3853 3.727258 AAGCGGGGGCTACATGCA 61.727 61.111 0.00 0.00 45.15 3.96
3801 3854 3.995506 AAGCGGGGGCTACATGCAC 62.996 63.158 0.00 0.00 46.31 4.57
3802 3855 4.489771 GCGGGGGCTACATGCACT 62.490 66.667 0.00 0.00 46.25 4.40
3803 3856 2.514592 CGGGGGCTACATGCACTG 60.515 66.667 0.00 0.00 46.25 3.66
3804 3857 2.124151 GGGGGCTACATGCACTGG 60.124 66.667 0.00 0.00 46.25 4.00
3805 3858 2.124151 GGGGCTACATGCACTGGG 60.124 66.667 0.00 0.00 46.25 4.45
3806 3859 2.124151 GGGCTACATGCACTGGGG 60.124 66.667 0.00 0.00 43.01 4.96
3807 3860 2.830370 GGCTACATGCACTGGGGC 60.830 66.667 0.00 0.00 45.15 5.80
3808 3861 2.273449 GCTACATGCACTGGGGCT 59.727 61.111 0.00 0.00 42.31 5.19
3809 3862 2.117156 GCTACATGCACTGGGGCTG 61.117 63.158 0.00 0.00 42.31 4.85
3810 3863 2.045045 TACATGCACTGGGGCTGC 60.045 61.111 0.00 0.00 35.03 5.25
3811 3864 3.643595 TACATGCACTGGGGCTGCC 62.644 63.158 11.05 11.05 33.36 4.85
3963 4016 5.692115 TGAGCTGTCCCATATTTCAGTTA 57.308 39.130 0.00 0.00 0.00 2.24
4108 4163 6.808008 AAGACCATTATTTGCATATCGGAG 57.192 37.500 0.00 0.00 0.00 4.63
4115 4170 8.950210 CCATTATTTGCATATCGGAGACTTATT 58.050 33.333 0.00 0.00 42.51 1.40
4211 4399 6.052405 ACATAATCTGGTTTACGGTACCAA 57.948 37.500 13.54 0.00 44.63 3.67
4419 4631 2.813908 GTGTGCTTACCTCCCGCG 60.814 66.667 0.00 0.00 0.00 6.46
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 9.793252 GACCCATATGTATATTGATTTGCATTC 57.207 33.333 1.24 0.00 0.00 2.67
1 2 8.461222 CGACCCATATGTATATTGATTTGCATT 58.539 33.333 1.24 0.00 0.00 3.56
2 3 7.067372 CCGACCCATATGTATATTGATTTGCAT 59.933 37.037 1.24 0.00 0.00 3.96
3 4 6.374053 CCGACCCATATGTATATTGATTTGCA 59.626 38.462 1.24 0.00 0.00 4.08
4 5 6.677920 GCCGACCCATATGTATATTGATTTGC 60.678 42.308 1.24 0.00 0.00 3.68
5 6 6.456853 CGCCGACCCATATGTATATTGATTTG 60.457 42.308 1.24 0.00 0.00 2.32
6 7 5.584649 CGCCGACCCATATGTATATTGATTT 59.415 40.000 1.24 0.00 0.00 2.17
7 8 5.116180 CGCCGACCCATATGTATATTGATT 58.884 41.667 1.24 0.00 0.00 2.57
8 9 4.693283 CGCCGACCCATATGTATATTGAT 58.307 43.478 1.24 0.00 0.00 2.57
9 10 3.677700 GCGCCGACCCATATGTATATTGA 60.678 47.826 0.00 0.00 0.00 2.57
10 11 2.607635 GCGCCGACCCATATGTATATTG 59.392 50.000 0.00 0.00 0.00 1.90
11 12 2.737359 CGCGCCGACCCATATGTATATT 60.737 50.000 0.00 0.00 0.00 1.28
12 13 1.202371 CGCGCCGACCCATATGTATAT 60.202 52.381 0.00 0.00 0.00 0.86
13 14 0.171679 CGCGCCGACCCATATGTATA 59.828 55.000 0.00 0.00 0.00 1.47
14 15 1.080093 CGCGCCGACCCATATGTAT 60.080 57.895 0.00 0.00 0.00 2.29
15 16 2.018727 AACGCGCCGACCCATATGTA 62.019 55.000 5.73 0.00 0.00 2.29
16 17 3.379865 AACGCGCCGACCCATATGT 62.380 57.895 5.73 0.00 0.00 2.29
17 18 2.587753 AACGCGCCGACCCATATG 60.588 61.111 5.73 0.00 0.00 1.78
18 19 2.587753 CAACGCGCCGACCCATAT 60.588 61.111 5.73 0.00 0.00 1.78
19 20 4.823419 CCAACGCGCCGACCCATA 62.823 66.667 5.73 0.00 0.00 2.74
37 38 0.600782 CATTTGGGTTGGCAGTGTGC 60.601 55.000 0.00 0.00 44.08 4.57
38 39 0.600782 GCATTTGGGTTGGCAGTGTG 60.601 55.000 0.00 0.00 0.00 3.82
39 40 1.047596 TGCATTTGGGTTGGCAGTGT 61.048 50.000 0.00 0.00 0.00 3.55
40 41 0.106335 TTGCATTTGGGTTGGCAGTG 59.894 50.000 0.00 0.00 37.59 3.66
41 42 0.835941 TTTGCATTTGGGTTGGCAGT 59.164 45.000 0.00 0.00 37.59 4.40
42 43 1.603326 GTTTTGCATTTGGGTTGGCAG 59.397 47.619 0.00 0.00 37.59 4.85
43 44 1.211457 AGTTTTGCATTTGGGTTGGCA 59.789 42.857 0.00 0.00 0.00 4.92
44 45 1.603326 CAGTTTTGCATTTGGGTTGGC 59.397 47.619 0.00 0.00 0.00 4.52
45 46 3.132925 CTCAGTTTTGCATTTGGGTTGG 58.867 45.455 0.00 0.00 0.00 3.77
46 47 2.545106 GCTCAGTTTTGCATTTGGGTTG 59.455 45.455 0.00 0.00 0.00 3.77
47 48 2.802774 CGCTCAGTTTTGCATTTGGGTT 60.803 45.455 0.00 0.00 0.00 4.11
48 49 1.269726 CGCTCAGTTTTGCATTTGGGT 60.270 47.619 0.00 0.00 0.00 4.51
49 50 1.421382 CGCTCAGTTTTGCATTTGGG 58.579 50.000 0.00 0.00 0.00 4.12
50 51 1.000385 TCCGCTCAGTTTTGCATTTGG 60.000 47.619 0.00 0.00 0.00 3.28
51 52 2.053627 GTCCGCTCAGTTTTGCATTTG 58.946 47.619 0.00 0.00 0.00 2.32
52 53 1.334960 CGTCCGCTCAGTTTTGCATTT 60.335 47.619 0.00 0.00 0.00 2.32
53 54 0.238289 CGTCCGCTCAGTTTTGCATT 59.762 50.000 0.00 0.00 0.00 3.56
54 55 1.868997 CGTCCGCTCAGTTTTGCAT 59.131 52.632 0.00 0.00 0.00 3.96
55 56 2.892334 GCGTCCGCTCAGTTTTGCA 61.892 57.895 4.10 0.00 38.26 4.08
56 57 2.127232 GCGTCCGCTCAGTTTTGC 60.127 61.111 4.10 0.00 38.26 3.68
57 58 2.556287 GGCGTCCGCTCAGTTTTG 59.444 61.111 11.82 0.00 41.60 2.44
58 59 3.041940 CGGCGTCCGCTCAGTTTT 61.042 61.111 11.82 0.00 41.17 2.43
83 84 4.629523 TGTCCGTTTGGGTCGGCC 62.630 66.667 0.00 0.00 46.49 6.13
84 85 1.726533 TTTTGTCCGTTTGGGTCGGC 61.727 55.000 0.00 0.00 46.49 5.54
86 87 1.862411 GCTTTTTGTCCGTTTGGGTCG 60.862 52.381 0.00 0.00 37.00 4.79
87 88 1.847818 GCTTTTTGTCCGTTTGGGTC 58.152 50.000 0.00 0.00 37.00 4.46
88 89 0.101579 CGCTTTTTGTCCGTTTGGGT 59.898 50.000 0.00 0.00 37.00 4.51
89 90 0.596341 CCGCTTTTTGTCCGTTTGGG 60.596 55.000 0.00 0.00 35.24 4.12
90 91 0.382515 TCCGCTTTTTGTCCGTTTGG 59.617 50.000 0.00 0.00 0.00 3.28
91 92 1.202200 TGTCCGCTTTTTGTCCGTTTG 60.202 47.619 0.00 0.00 0.00 2.93
92 93 1.096416 TGTCCGCTTTTTGTCCGTTT 58.904 45.000 0.00 0.00 0.00 3.60
93 94 1.096416 TTGTCCGCTTTTTGTCCGTT 58.904 45.000 0.00 0.00 0.00 4.44
94 95 1.096416 TTTGTCCGCTTTTTGTCCGT 58.904 45.000 0.00 0.00 0.00 4.69
95 96 2.050691 CATTTGTCCGCTTTTTGTCCG 58.949 47.619 0.00 0.00 0.00 4.79
96 97 1.792367 GCATTTGTCCGCTTTTTGTCC 59.208 47.619 0.00 0.00 0.00 4.02
97 98 1.451651 CGCATTTGTCCGCTTTTTGTC 59.548 47.619 0.00 0.00 0.00 3.18
98 99 1.486439 CGCATTTGTCCGCTTTTTGT 58.514 45.000 0.00 0.00 0.00 2.83
99 100 0.161446 GCGCATTTGTCCGCTTTTTG 59.839 50.000 0.30 0.00 46.14 2.44
100 101 2.516486 GCGCATTTGTCCGCTTTTT 58.484 47.368 0.30 0.00 46.14 1.94
101 102 4.243383 GCGCATTTGTCCGCTTTT 57.757 50.000 0.30 0.00 46.14 2.27
105 106 4.811761 GACGGCGCATTTGTCCGC 62.812 66.667 10.83 0.00 46.49 5.54
107 108 4.160635 CGGACGGCGCATTTGTCC 62.161 66.667 22.73 22.73 46.91 4.02
108 109 2.452366 AAACGGACGGCGCATTTGTC 62.452 55.000 10.83 11.19 0.00 3.18
109 110 2.548295 AAACGGACGGCGCATTTGT 61.548 52.632 10.83 0.74 0.00 2.83
110 111 2.080062 CAAACGGACGGCGCATTTG 61.080 57.895 10.83 9.01 0.00 2.32
111 112 2.254051 CAAACGGACGGCGCATTT 59.746 55.556 10.83 0.00 0.00 2.32
112 113 3.732892 CCAAACGGACGGCGCATT 61.733 61.111 10.83 0.00 0.00 3.56
136 137 2.178912 TTCTAAGAGCAACCCAACGG 57.821 50.000 0.00 0.00 0.00 4.44
137 138 4.561735 TTTTTCTAAGAGCAACCCAACG 57.438 40.909 0.00 0.00 0.00 4.10
159 160 9.337396 ACAAACTCCTTTTTCTTTTCTGTTTTT 57.663 25.926 0.00 0.00 0.00 1.94
160 161 8.902540 ACAAACTCCTTTTTCTTTTCTGTTTT 57.097 26.923 0.00 0.00 0.00 2.43
161 162 8.902540 AACAAACTCCTTTTTCTTTTCTGTTT 57.097 26.923 0.00 0.00 0.00 2.83
162 163 8.773645 CAAACAAACTCCTTTTTCTTTTCTGTT 58.226 29.630 0.00 0.00 0.00 3.16
163 164 7.931407 ACAAACAAACTCCTTTTTCTTTTCTGT 59.069 29.630 0.00 0.00 0.00 3.41
164 165 8.223100 CACAAACAAACTCCTTTTTCTTTTCTG 58.777 33.333 0.00 0.00 0.00 3.02
165 166 7.095229 GCACAAACAAACTCCTTTTTCTTTTCT 60.095 33.333 0.00 0.00 0.00 2.52
166 167 7.015289 GCACAAACAAACTCCTTTTTCTTTTC 58.985 34.615 0.00 0.00 0.00 2.29
167 168 6.484977 TGCACAAACAAACTCCTTTTTCTTTT 59.515 30.769 0.00 0.00 0.00 2.27
168 169 5.994668 TGCACAAACAAACTCCTTTTTCTTT 59.005 32.000 0.00 0.00 0.00 2.52
169 170 5.546526 TGCACAAACAAACTCCTTTTTCTT 58.453 33.333 0.00 0.00 0.00 2.52
170 171 5.146010 TGCACAAACAAACTCCTTTTTCT 57.854 34.783 0.00 0.00 0.00 2.52
171 172 5.854431 TTGCACAAACAAACTCCTTTTTC 57.146 34.783 0.00 0.00 0.00 2.29
172 173 5.762711 ACTTTGCACAAACAAACTCCTTTTT 59.237 32.000 0.00 0.00 34.68 1.94
173 174 5.304778 ACTTTGCACAAACAAACTCCTTTT 58.695 33.333 0.00 0.00 34.68 2.27
285 286 2.505405 AGCTGGATGATGATGATGCAC 58.495 47.619 0.00 0.00 0.00 4.57
295 296 4.070716 GCTGCTGTTATTAGCTGGATGAT 58.929 43.478 0.00 0.00 44.01 2.45
296 297 3.135348 AGCTGCTGTTATTAGCTGGATGA 59.865 43.478 0.00 0.00 45.40 2.92
297 298 3.474600 AGCTGCTGTTATTAGCTGGATG 58.525 45.455 0.00 0.00 45.40 3.51
298 299 3.853355 AGCTGCTGTTATTAGCTGGAT 57.147 42.857 0.00 0.00 45.40 3.41
299 300 3.634397 AAGCTGCTGTTATTAGCTGGA 57.366 42.857 1.35 0.00 46.34 3.86
300 301 3.441572 ACAAAGCTGCTGTTATTAGCTGG 59.558 43.478 1.35 0.00 46.34 4.85
313 314 1.202452 AGCTCACCAAAACAAAGCTGC 60.202 47.619 0.00 0.00 41.54 5.25
512 517 6.816640 CCTTGCCGCTAATAGCATTAGTATAA 59.183 38.462 13.15 0.00 42.58 0.98
514 519 5.178797 CCTTGCCGCTAATAGCATTAGTAT 58.821 41.667 13.15 0.00 42.58 2.12
520 529 0.179020 TGCCTTGCCGCTAATAGCAT 60.179 50.000 13.15 0.00 42.58 3.79
522 531 0.029433 GTTGCCTTGCCGCTAATAGC 59.971 55.000 1.41 1.41 38.02 2.97
596 605 1.213537 CAAATGGCAAGCCGTCCTG 59.786 57.895 6.23 3.83 39.42 3.86
617 626 1.560866 AAGCTCCAAGCCCAGAGAGG 61.561 60.000 0.00 0.00 43.77 3.69
639 660 1.148759 GCTAGCGCCGGAAGAAGAAG 61.149 60.000 5.05 0.00 0.00 2.85
679 715 1.992277 GCTCTCTCTCCCCCAGCAA 60.992 63.158 0.00 0.00 0.00 3.91
680 716 2.364842 GCTCTCTCTCCCCCAGCA 60.365 66.667 0.00 0.00 0.00 4.41
682 718 3.535962 GCGCTCTCTCTCCCCCAG 61.536 72.222 0.00 0.00 0.00 4.45
683 719 4.067512 AGCGCTCTCTCTCCCCCA 62.068 66.667 2.64 0.00 0.00 4.96
684 720 3.223589 GAGCGCTCTCTCTCCCCC 61.224 72.222 29.88 0.00 36.42 5.40
743 779 2.155279 AGGCGAGAAAGAAAGAAAGGC 58.845 47.619 0.00 0.00 0.00 4.35
773 809 1.079543 CACGGCTCTCAGGAACCTG 60.080 63.158 14.01 14.01 44.86 4.00
774 810 1.122019 AACACGGCTCTCAGGAACCT 61.122 55.000 0.00 0.00 0.00 3.50
787 823 3.871594 AGAGAACAAGAACAAGAACACGG 59.128 43.478 0.00 0.00 0.00 4.94
816 856 3.205784 GCTACAGATGGCCAGAGATTT 57.794 47.619 13.05 0.00 0.00 2.17
831 871 9.650714 TTAACCTAGAGTGATAATAAGGCTACA 57.349 33.333 0.00 0.00 0.00 2.74
902 942 1.492319 TTTTTGCTCGTCCGTCGTGG 61.492 55.000 0.00 0.00 40.80 4.94
904 944 4.423764 TTTTTGCTCGTCCGTCGT 57.576 50.000 0.00 0.00 40.80 4.34
924 964 8.706322 ACTCAGGTCACCAGTTTTTATTTTAT 57.294 30.769 0.00 0.00 0.00 1.40
925 965 9.280174 CTACTCAGGTCACCAGTTTTTATTTTA 57.720 33.333 0.00 0.00 0.00 1.52
929 969 5.280521 CCCTACTCAGGTCACCAGTTTTTAT 60.281 44.000 0.00 0.00 40.79 1.40
930 970 4.041198 CCCTACTCAGGTCACCAGTTTTTA 59.959 45.833 0.00 0.00 40.79 1.52
945 985 2.037144 GGAGCGGATAAACCCTACTCA 58.963 52.381 0.00 0.00 33.77 3.41
1092 1139 1.745489 GGAATCCGAGCCGCAGTTT 60.745 57.895 0.00 0.00 0.00 2.66
1422 1475 2.263077 CAAGAAATCTCTCCGTGGACG 58.737 52.381 0.00 0.00 39.44 4.79
1452 1505 2.928301 GCTGCTCGTTGAGTTGATCTGA 60.928 50.000 0.00 0.00 31.39 3.27
1467 1520 1.416813 CCTTGACGATGACGCTGCTC 61.417 60.000 0.00 0.00 43.96 4.26
1661 1714 1.030457 GTACATGGTCTCGATCCCGT 58.970 55.000 0.00 4.87 37.05 5.28
1711 1764 0.755686 CCTGGATCCTCTTTCCTCGG 59.244 60.000 14.23 0.00 34.17 4.63
2041 2094 3.276857 CTCTGGCAAACACATCATAGCT 58.723 45.455 0.00 0.00 0.00 3.32
2115 2168 2.338809 ACCCAAAGAGTGTCCATCTGA 58.661 47.619 0.00 0.00 0.00 3.27
2268 2321 0.532573 TCCGTTTTGGTTTGCTTGCA 59.467 45.000 0.00 0.00 39.52 4.08
2311 2364 3.914426 AATTATCAGACCGGAAGCAGT 57.086 42.857 9.46 0.00 0.00 4.40
2351 2404 6.861055 TCGCAGATTGAAACCAAAATAAAGAC 59.139 34.615 0.00 0.00 0.00 3.01
2361 2414 0.034198 TCCGTCGCAGATTGAAACCA 59.966 50.000 0.00 0.00 40.67 3.67
2362 2415 1.128692 CTTCCGTCGCAGATTGAAACC 59.871 52.381 0.00 0.00 40.67 3.27
2436 2489 2.095252 GCGAAGAGTGGGAGAACGC 61.095 63.158 0.00 0.00 38.03 4.84
2445 2498 2.031516 CCCAGCTGTGCGAAGAGTG 61.032 63.158 13.81 0.00 0.00 3.51
2457 2510 2.361771 CTCCCAAATGCCCCAGCT 59.638 61.111 0.00 0.00 40.80 4.24
2478 2531 4.431131 AACCGCCTGCCCATCCTG 62.431 66.667 0.00 0.00 0.00 3.86
2579 2632 2.644798 GTGCCATCCTCCATTATACCCT 59.355 50.000 0.00 0.00 0.00 4.34
2622 2675 2.171448 ACCCTGGTGAGAATCTGTATGC 59.829 50.000 0.00 0.00 34.92 3.14
2623 2676 3.452264 TGACCCTGGTGAGAATCTGTATG 59.548 47.826 0.00 0.00 34.92 2.39
2835 2888 1.798223 GCTGCGCCGATACATATTTCA 59.202 47.619 4.18 0.00 0.00 2.69
2880 2933 0.834612 TTATACCCCTGTCAAGCCCG 59.165 55.000 0.00 0.00 0.00 6.13
3189 3242 1.109323 ACCTGTGCCTTTGCCTGTTC 61.109 55.000 0.00 0.00 36.33 3.18
3257 3310 0.721718 GCTGGATTTCTTGACGGACG 59.278 55.000 0.00 0.00 0.00 4.79
3262 3315 4.637534 TGCTATCTTGCTGGATTTCTTGAC 59.362 41.667 0.00 0.00 0.00 3.18
3269 3322 6.570692 CATTTTTCTGCTATCTTGCTGGATT 58.429 36.000 0.00 0.00 33.58 3.01
3272 3325 4.110482 GCATTTTTCTGCTATCTTGCTGG 58.890 43.478 0.00 0.00 39.12 4.85
3277 3330 3.131755 GCCAGGCATTTTTCTGCTATCTT 59.868 43.478 6.55 0.00 41.95 2.40
3297 3350 1.077429 GTTCACCCCCTCATCTGCC 60.077 63.158 0.00 0.00 0.00 4.85
3395 3448 2.704572 GAGGGTCTGAACAACCATCAG 58.295 52.381 2.34 0.00 44.86 2.90
3464 3517 0.904649 TGGACGAGTGGATTGCTCAT 59.095 50.000 0.00 0.00 33.45 2.90
3493 3546 3.896888 TCAACAACTTGCCCATCTGAATT 59.103 39.130 0.00 0.00 0.00 2.17
3552 3605 6.308766 CCCTATTCATTTTGCTTGAAACTTCG 59.691 38.462 0.00 0.00 36.72 3.79
3711 3764 4.335416 CCTTTCCCTACATTTCTGCAAGA 58.665 43.478 0.00 0.00 44.68 3.02
3712 3765 3.119352 GCCTTTCCCTACATTTCTGCAAG 60.119 47.826 0.00 0.00 0.00 4.01
3713 3766 2.825532 GCCTTTCCCTACATTTCTGCAA 59.174 45.455 0.00 0.00 0.00 4.08
3714 3767 2.041620 AGCCTTTCCCTACATTTCTGCA 59.958 45.455 0.00 0.00 0.00 4.41
3715 3768 2.424956 CAGCCTTTCCCTACATTTCTGC 59.575 50.000 0.00 0.00 0.00 4.26
3716 3769 2.424956 GCAGCCTTTCCCTACATTTCTG 59.575 50.000 0.00 0.00 0.00 3.02
3717 3770 2.728007 GCAGCCTTTCCCTACATTTCT 58.272 47.619 0.00 0.00 0.00 2.52
3718 3771 1.401905 CGCAGCCTTTCCCTACATTTC 59.598 52.381 0.00 0.00 0.00 2.17
3719 3772 1.271926 ACGCAGCCTTTCCCTACATTT 60.272 47.619 0.00 0.00 0.00 2.32
3720 3773 0.328258 ACGCAGCCTTTCCCTACATT 59.672 50.000 0.00 0.00 0.00 2.71
3721 3774 1.134491 GTACGCAGCCTTTCCCTACAT 60.134 52.381 0.00 0.00 0.00 2.29
3722 3775 0.248289 GTACGCAGCCTTTCCCTACA 59.752 55.000 0.00 0.00 0.00 2.74
3723 3776 0.248289 TGTACGCAGCCTTTCCCTAC 59.752 55.000 0.00 0.00 0.00 3.18
3724 3777 0.978151 TTGTACGCAGCCTTTCCCTA 59.022 50.000 0.00 0.00 0.00 3.53
3725 3778 0.328258 ATTGTACGCAGCCTTTCCCT 59.672 50.000 0.00 0.00 0.00 4.20
3726 3779 1.940613 CTATTGTACGCAGCCTTTCCC 59.059 52.381 0.00 0.00 0.00 3.97
3727 3780 2.608090 GTCTATTGTACGCAGCCTTTCC 59.392 50.000 0.00 0.00 0.00 3.13
3728 3781 2.608090 GGTCTATTGTACGCAGCCTTTC 59.392 50.000 0.00 0.00 0.00 2.62
3729 3782 2.629051 GGTCTATTGTACGCAGCCTTT 58.371 47.619 0.00 0.00 0.00 3.11
3730 3783 1.134491 GGGTCTATTGTACGCAGCCTT 60.134 52.381 0.00 0.00 0.00 4.35
3731 3784 0.464452 GGGTCTATTGTACGCAGCCT 59.536 55.000 0.00 0.00 0.00 4.58
3732 3785 0.177141 TGGGTCTATTGTACGCAGCC 59.823 55.000 0.00 0.00 35.18 4.85
3733 3786 2.018542 TTGGGTCTATTGTACGCAGC 57.981 50.000 0.00 0.00 40.36 5.25
3734 3787 4.201910 CCATTTTGGGTCTATTGTACGCAG 60.202 45.833 0.00 0.00 40.36 5.18
3735 3788 3.692101 CCATTTTGGGTCTATTGTACGCA 59.308 43.478 0.00 0.00 37.94 5.24
3736 3789 3.692593 ACCATTTTGGGTCTATTGTACGC 59.307 43.478 0.00 0.00 43.37 4.42
3747 3800 1.076014 GGGTCCGACCATTTTGGGT 59.924 57.895 19.43 0.00 43.37 4.51
3748 3801 0.251608 AAGGGTCCGACCATTTTGGG 60.252 55.000 19.43 0.00 39.55 4.12
3749 3802 1.173913 GAAGGGTCCGACCATTTTGG 58.826 55.000 18.14 0.00 43.04 3.28
3750 3803 1.173913 GGAAGGGTCCGACCATTTTG 58.826 55.000 18.14 0.00 43.04 2.44
3751 3804 0.039180 GGGAAGGGTCCGACCATTTT 59.961 55.000 18.14 9.49 43.04 1.82
3752 3805 1.689412 GGGAAGGGTCCGACCATTT 59.311 57.895 18.14 11.86 43.04 2.32
3753 3806 2.306384 GGGGAAGGGTCCGACCATT 61.306 63.158 17.19 17.19 46.04 3.16
3754 3807 2.691252 GGGGAAGGGTCCGACCAT 60.691 66.667 19.43 9.67 46.04 3.55
3755 3808 4.257810 TGGGGAAGGGTCCGACCA 62.258 66.667 19.43 0.00 46.04 4.02
3756 3809 3.400054 CTGGGGAAGGGTCCGACC 61.400 72.222 9.30 9.30 46.04 4.79
3757 3810 2.284405 TCTGGGGAAGGGTCCGAC 60.284 66.667 0.00 0.00 46.04 4.79
3758 3811 2.284405 GTCTGGGGAAGGGTCCGA 60.284 66.667 0.00 0.00 46.04 4.55
3759 3812 3.400054 GGTCTGGGGAAGGGTCCG 61.400 72.222 0.00 0.00 46.04 4.79
3760 3813 3.015753 GGGTCTGGGGAAGGGTCC 61.016 72.222 0.00 0.00 44.10 4.46
3761 3814 2.125225 AGGGTCTGGGGAAGGGTC 59.875 66.667 0.00 0.00 0.00 4.46
3762 3815 2.204151 CAGGGTCTGGGGAAGGGT 60.204 66.667 0.00 0.00 0.00 4.34
3763 3816 3.732849 GCAGGGTCTGGGGAAGGG 61.733 72.222 0.00 0.00 31.21 3.95
3764 3817 4.101448 CGCAGGGTCTGGGGAAGG 62.101 72.222 4.35 0.00 40.11 3.46
3765 3818 4.785453 GCGCAGGGTCTGGGGAAG 62.785 72.222 0.30 0.00 43.28 3.46
3780 3833 4.856801 ATGTAGCCCCCGCTTGCG 62.857 66.667 8.14 8.14 45.55 4.85
3781 3834 3.211963 CATGTAGCCCCCGCTTGC 61.212 66.667 0.00 0.00 45.55 4.01
3782 3835 3.211963 GCATGTAGCCCCCGCTTG 61.212 66.667 0.00 0.00 45.55 4.01
3783 3836 3.727258 TGCATGTAGCCCCCGCTT 61.727 61.111 0.00 0.00 45.55 4.68
3785 3838 4.489771 AGTGCATGTAGCCCCCGC 62.490 66.667 0.00 0.00 44.83 6.13
3786 3839 2.514592 CAGTGCATGTAGCCCCCG 60.515 66.667 0.00 0.00 44.83 5.73
3787 3840 2.124151 CCAGTGCATGTAGCCCCC 60.124 66.667 0.00 0.00 44.83 5.40
3788 3841 2.124151 CCCAGTGCATGTAGCCCC 60.124 66.667 0.00 0.00 44.83 5.80
3789 3842 2.124151 CCCCAGTGCATGTAGCCC 60.124 66.667 0.00 0.00 44.83 5.19
3790 3843 2.830370 GCCCCAGTGCATGTAGCC 60.830 66.667 0.00 0.00 44.83 3.93
3791 3844 2.117156 CAGCCCCAGTGCATGTAGC 61.117 63.158 0.00 0.00 45.96 3.58
3792 3845 2.117156 GCAGCCCCAGTGCATGTAG 61.117 63.158 0.00 0.00 40.86 2.74
3793 3846 2.045045 GCAGCCCCAGTGCATGTA 60.045 61.111 0.00 0.00 40.86 2.29
3862 3915 2.039818 TTTGGTTCCAGCGTGTTACA 57.960 45.000 0.00 0.00 0.00 2.41
3963 4016 7.218228 TGAACAAAATAGCTGAACATGACAT 57.782 32.000 0.00 0.00 0.00 3.06
4144 4199 5.314718 TCTAGGGTAGATATTCGGACACA 57.685 43.478 0.00 0.00 0.00 3.72
4202 4390 2.767505 CTTCTTGAAGCTTGGTACCGT 58.232 47.619 2.10 0.00 0.00 4.83
4205 4393 2.504367 TGGCTTCTTGAAGCTTGGTAC 58.496 47.619 27.48 14.68 44.86 3.34
4211 4399 1.339291 GTGCTTTGGCTTCTTGAAGCT 59.661 47.619 27.48 0.00 44.86 3.74
4493 4705 2.633967 TGCCCTCAGTTTTCATTGCATT 59.366 40.909 0.00 0.00 0.00 3.56


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

AutoCloner maintained by Alex Coulton.