Multiple sequence alignment - TraesCS1D01G026600

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 TraesCS1D01G026600 chr1D 100.000 3879 0 0 1 3879 10765303 10761425 0.000000e+00 7164.0
1 TraesCS1D01G026600 chr1D 91.297 2884 170 37 1001 3842 10843827 10846671 0.000000e+00 3860.0
2 TraesCS1D01G026600 chr1D 94.384 1282 68 3 1626 2903 10775142 10773861 0.000000e+00 1965.0
3 TraesCS1D01G026600 chr1D 88.812 1582 134 20 1586 3131 10836395 10837969 0.000000e+00 1901.0
4 TraesCS1D01G026600 chr1D 93.394 878 45 2 3002 3879 10773847 10772983 0.000000e+00 1288.0
5 TraesCS1D01G026600 chr1D 87.531 409 32 9 863 1262 10894019 10894417 4.570000e-124 455.0
6 TraesCS1D01G026600 chr1D 80.038 521 64 31 1090 1592 10930002 10930500 2.220000e-92 350.0
7 TraesCS1D01G026600 chr1D 80.569 211 24 10 1389 1592 10836331 10836531 3.120000e-31 147.0
8 TraesCS1D01G026600 chr1D 85.714 84 8 2 1389 1472 10776416 10776337 6.910000e-13 86.1
9 TraesCS1D01G026600 chr1D 88.889 54 2 1 3826 3879 10846713 10846762 3.240000e-06 63.9
10 TraesCS1D01G026600 chr1A 95.248 1957 71 12 942 2885 13228961 13230908 0.000000e+00 3079.0
11 TraesCS1D01G026600 chr1A 95.412 1809 62 11 1090 2886 13009797 13007998 0.000000e+00 2861.0
12 TraesCS1D01G026600 chr1A 91.273 2097 132 25 949 3004 22791311 22789225 0.000000e+00 2811.0
13 TraesCS1D01G026600 chr1A 91.213 1912 119 25 1001 2897 13212431 13214308 0.000000e+00 2555.0
14 TraesCS1D01G026600 chr1A 94.022 803 46 2 3002 3803 13214328 13215129 0.000000e+00 1216.0
15 TraesCS1D01G026600 chr1A 93.351 752 40 4 3002 3749 13230940 13231685 0.000000e+00 1103.0
16 TraesCS1D01G026600 chr1A 90.044 683 45 13 2998 3678 22778886 22778225 0.000000e+00 863.0
17 TraesCS1D01G026600 chr1A 84.141 908 91 26 3002 3879 22760262 22759378 0.000000e+00 830.0
18 TraesCS1D01G026600 chr1A 94.266 436 22 3 3445 3879 13007698 13007265 0.000000e+00 664.0
19 TraesCS1D01G026600 chr1A 89.241 474 36 9 809 1275 22773487 22773022 2.600000e-161 579.0
20 TraesCS1D01G026600 chr1A 91.371 394 33 1 1 393 545878778 545879171 4.410000e-149 538.0
21 TraesCS1D01G026600 chr1A 87.137 482 45 9 808 1285 13266645 13267113 7.380000e-147 531.0
22 TraesCS1D01G026600 chr1A 87.556 450 30 9 377 806 13266159 13266602 7.480000e-137 497.0
23 TraesCS1D01G026600 chr1A 79.231 520 75 27 1090 1592 22761955 22761452 8.030000e-87 331.0
24 TraesCS1D01G026600 chr1A 78.805 519 70 30 1090 1592 13272152 13272646 2.910000e-81 313.0
25 TraesCS1D01G026600 chr1A 88.000 150 14 1 1386 1535 13006084 13005939 1.430000e-39 174.0
26 TraesCS1D01G026600 chr1B 89.055 2010 155 38 949 2903 16225731 16223732 0.000000e+00 2433.0
27 TraesCS1D01G026600 chr1B 92.690 1409 88 7 1501 2897 39732725 39734130 0.000000e+00 2017.0
28 TraesCS1D01G026600 chr1B 92.274 1385 82 14 1586 2946 23775548 23776931 0.000000e+00 1941.0
29 TraesCS1D01G026600 chr1B 88.341 1278 121 14 1864 3131 39740193 39741452 0.000000e+00 1509.0
30 TraesCS1D01G026600 chr1B 91.827 881 51 9 3002 3879 16223718 16222856 0.000000e+00 1208.0
31 TraesCS1D01G026600 chr1B 91.922 718 51 3 3002 3718 23599380 23600091 0.000000e+00 998.0
32 TraesCS1D01G026600 chr1B 91.365 718 54 4 3002 3718 23898156 23898866 0.000000e+00 976.0
33 TraesCS1D01G026600 chr1B 84.572 888 84 29 3002 3869 16402091 16402945 0.000000e+00 832.0
34 TraesCS1D01G026600 chr1B 91.512 377 32 0 2 378 11868377 11868753 1.600000e-143 520.0
35 TraesCS1D01G026600 chr1B 86.966 468 52 8 2419 2881 39738825 39739288 5.750000e-143 518.0
36 TraesCS1D01G026600 chr1B 92.355 327 25 0 967 1293 39732105 39732431 2.110000e-127 466.0
37 TraesCS1D01G026600 chr1B 81.065 169 19 7 1389 1552 16400742 16400902 5.260000e-24 122.0
38 TraesCS1D01G026600 chr1B 84.553 123 10 3 1386 1503 39732491 39732609 3.170000e-21 113.0
39 TraesCS1D01G026600 chr6B 94.960 377 18 1 2 378 673860331 673860706 1.200000e-164 590.0
40 TraesCS1D01G026600 chr6B 94.709 378 20 0 1 378 717099150 717098773 4.320000e-164 588.0
41 TraesCS1D01G026600 chr6B 91.270 378 33 0 2 379 84671199 84670822 2.070000e-142 516.0
42 TraesCS1D01G026600 chr3B 94.444 378 21 0 1 378 141737990 141738367 2.010000e-162 582.0
43 TraesCS1D01G026600 chr3B 94.459 379 20 1 1 379 618670042 618669665 2.010000e-162 582.0
44 TraesCS1D01G026600 chr7B 93.103 377 26 0 2 378 242671822 242672198 1.570000e-153 553.0
45 TraesCS1D01G026600 chrUn 91.247 377 33 0 2 378 153247376 153247000 7.430000e-142 514.0


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 TraesCS1D01G026600 chr1D 10761425 10765303 3878 True 7164.000000 7164 100.000000 1 3879 1 chr1D.!!$R1 3878
1 TraesCS1D01G026600 chr1D 10843827 10846762 2935 False 1961.950000 3860 90.093000 1001 3879 2 chr1D.!!$F4 2878
2 TraesCS1D01G026600 chr1D 10772983 10776416 3433 True 1113.033333 1965 91.164000 1389 3879 3 chr1D.!!$R2 2490
3 TraesCS1D01G026600 chr1D 10836331 10837969 1638 False 1024.000000 1901 84.690500 1389 3131 2 chr1D.!!$F3 1742
4 TraesCS1D01G026600 chr1A 22789225 22791311 2086 True 2811.000000 2811 91.273000 949 3004 1 chr1A.!!$R3 2055
5 TraesCS1D01G026600 chr1A 13228961 13231685 2724 False 2091.000000 3079 94.299500 942 3749 2 chr1A.!!$F4 2807
6 TraesCS1D01G026600 chr1A 13212431 13215129 2698 False 1885.500000 2555 92.617500 1001 3803 2 chr1A.!!$F3 2802
7 TraesCS1D01G026600 chr1A 13005939 13009797 3858 True 1233.000000 2861 92.559333 1090 3879 3 chr1A.!!$R4 2789
8 TraesCS1D01G026600 chr1A 22778225 22778886 661 True 863.000000 863 90.044000 2998 3678 1 chr1A.!!$R2 680
9 TraesCS1D01G026600 chr1A 22759378 22761955 2577 True 580.500000 830 81.686000 1090 3879 2 chr1A.!!$R5 2789
10 TraesCS1D01G026600 chr1A 13266159 13267113 954 False 514.000000 531 87.346500 377 1285 2 chr1A.!!$F5 908
11 TraesCS1D01G026600 chr1B 23775548 23776931 1383 False 1941.000000 1941 92.274000 1586 2946 1 chr1B.!!$F3 1360
12 TraesCS1D01G026600 chr1B 16222856 16225731 2875 True 1820.500000 2433 90.441000 949 3879 2 chr1B.!!$R1 2930
13 TraesCS1D01G026600 chr1B 39738825 39741452 2627 False 1013.500000 1509 87.653500 1864 3131 2 chr1B.!!$F7 1267
14 TraesCS1D01G026600 chr1B 23599380 23600091 711 False 998.000000 998 91.922000 3002 3718 1 chr1B.!!$F2 716
15 TraesCS1D01G026600 chr1B 23898156 23898866 710 False 976.000000 976 91.365000 3002 3718 1 chr1B.!!$F4 716
16 TraesCS1D01G026600 chr1B 39732105 39734130 2025 False 865.333333 2017 89.866000 967 2897 3 chr1B.!!$F6 1930
17 TraesCS1D01G026600 chr1B 16400742 16402945 2203 False 477.000000 832 82.818500 1389 3869 2 chr1B.!!$F5 2480

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
34 35 0.036010 AGATCCACCCACGCTTGAAG 60.036 55.000 0.00 0.0 0.00 3.02 F
371 372 0.037326 AGCTTCGCGGAATTGTCTCA 60.037 50.000 6.13 0.0 0.00 3.27 F
372 373 0.796312 GCTTCGCGGAATTGTCTCAA 59.204 50.000 6.13 0.0 0.00 3.02 F
373 374 1.196808 GCTTCGCGGAATTGTCTCAAA 59.803 47.619 6.13 0.0 0.00 2.69 F
817 879 1.529438 TCACAATTTCGCAACTCGGTC 59.471 47.619 0.00 0.0 39.05 4.79 F
2557 4055 1.553706 AGCTCATTGAGGGGCTTTTG 58.446 50.000 15.28 0.0 0.00 2.44 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1453 1614 4.392940 ACTGAGATTTGCTGTTTACTGCT 58.607 39.130 12.05 0.0 40.79 4.24 R
1706 3159 4.795970 ACTTGACTTGCGAGTTAACTTG 57.204 40.909 17.30 17.3 38.05 3.16 R
1753 3211 6.458232 TTGTGTTTTCCCCATTTATATCCG 57.542 37.500 0.00 0.0 0.00 4.18 R
2128 3620 7.044181 CAGCACTAAGATGACTCCATTTAGAA 58.956 38.462 0.00 0.0 35.00 2.10 R
2745 4243 1.135141 GTTCAGCACAAACACCAGCAA 60.135 47.619 0.00 0.0 0.00 3.91 R
3399 5013 1.340114 CCTTCCTAGTTGAACCCAGGC 60.340 57.143 8.33 0.0 0.00 4.85 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
24 25 5.752036 TCAGATTCATATCAGATCCACCC 57.248 43.478 0.00 0.00 32.95 4.61
25 26 5.157395 TCAGATTCATATCAGATCCACCCA 58.843 41.667 0.00 0.00 32.95 4.51
26 27 5.012458 TCAGATTCATATCAGATCCACCCAC 59.988 44.000 0.00 0.00 32.95 4.61
27 28 3.751479 TTCATATCAGATCCACCCACG 57.249 47.619 0.00 0.00 0.00 4.94
28 29 1.344438 TCATATCAGATCCACCCACGC 59.656 52.381 0.00 0.00 0.00 5.34
29 30 1.345741 CATATCAGATCCACCCACGCT 59.654 52.381 0.00 0.00 0.00 5.07
31 32 0.107508 ATCAGATCCACCCACGCTTG 60.108 55.000 0.00 0.00 0.00 4.01
33 34 0.321564 CAGATCCACCCACGCTTGAA 60.322 55.000 0.00 0.00 0.00 2.69
34 35 0.036010 AGATCCACCCACGCTTGAAG 60.036 55.000 0.00 0.00 0.00 3.02
35 36 1.648467 GATCCACCCACGCTTGAAGC 61.648 60.000 7.20 7.20 38.02 3.86
36 37 3.365265 CCACCCACGCTTGAAGCC 61.365 66.667 12.13 0.00 38.18 4.35
37 38 3.365265 CACCCACGCTTGAAGCCC 61.365 66.667 12.13 0.00 38.18 5.19
38 39 3.570212 ACCCACGCTTGAAGCCCT 61.570 61.111 12.13 0.00 38.18 5.19
40 41 1.450312 CCCACGCTTGAAGCCCTAG 60.450 63.158 12.13 0.00 38.18 3.02
41 42 2.109126 CCACGCTTGAAGCCCTAGC 61.109 63.158 12.13 1.17 38.18 3.42
52 53 2.581074 GCCCTAGCTATACGGGAGG 58.419 63.158 18.52 5.18 40.55 4.30
53 54 1.605971 GCCCTAGCTATACGGGAGGC 61.606 65.000 18.52 7.80 40.55 4.70
54 55 0.039911 CCCTAGCTATACGGGAGGCT 59.960 60.000 10.45 0.00 40.55 4.58
55 56 1.550409 CCCTAGCTATACGGGAGGCTT 60.550 57.143 10.45 0.00 40.55 4.35
56 57 2.249139 CCTAGCTATACGGGAGGCTTT 58.751 52.381 0.00 0.00 36.40 3.51
57 58 2.028930 CCTAGCTATACGGGAGGCTTTG 60.029 54.545 0.00 0.00 36.40 2.77
58 59 0.759346 AGCTATACGGGAGGCTTTGG 59.241 55.000 0.00 0.00 0.00 3.28
59 60 0.885150 GCTATACGGGAGGCTTTGGC 60.885 60.000 0.00 0.00 37.82 4.52
60 61 0.759346 CTATACGGGAGGCTTTGGCT 59.241 55.000 0.00 0.00 42.48 4.75
61 62 1.141053 CTATACGGGAGGCTTTGGCTT 59.859 52.381 0.00 0.00 38.98 4.35
62 63 0.331616 ATACGGGAGGCTTTGGCTTT 59.668 50.000 0.00 0.00 38.98 3.51
64 65 2.639327 CGGGAGGCTTTGGCTTTGG 61.639 63.158 0.00 0.00 38.98 3.28
65 66 2.659016 GGAGGCTTTGGCTTTGGC 59.341 61.111 0.00 0.00 38.98 4.52
82 83 7.313951 GCTTTGGCCAATGATCTATATACTC 57.686 40.000 30.10 8.16 0.00 2.59
83 84 6.881065 GCTTTGGCCAATGATCTATATACTCA 59.119 38.462 30.10 5.46 0.00 3.41
84 85 7.065563 GCTTTGGCCAATGATCTATATACTCAG 59.934 40.741 30.10 15.19 0.00 3.35
85 86 7.797121 TTGGCCAATGATCTATATACTCAGA 57.203 36.000 16.05 0.00 0.00 3.27
86 87 7.797121 TGGCCAATGATCTATATACTCAGAA 57.203 36.000 0.61 0.00 0.00 3.02
88 89 9.492730 TGGCCAATGATCTATATACTCAGAATA 57.507 33.333 0.61 0.00 0.00 1.75
98 99 9.409918 TCTATATACTCAGAATATACAGGTGGC 57.590 37.037 0.00 0.00 0.00 5.01
100 101 8.671987 ATATACTCAGAATATACAGGTGGCTT 57.328 34.615 0.00 0.00 0.00 4.35
101 102 5.283457 ACTCAGAATATACAGGTGGCTTC 57.717 43.478 0.00 0.00 0.00 3.86
103 104 3.069586 TCAGAATATACAGGTGGCTTCCG 59.930 47.826 0.00 0.00 0.00 4.30
104 105 3.069586 CAGAATATACAGGTGGCTTCCGA 59.930 47.826 0.00 0.00 0.00 4.55
105 106 3.904339 AGAATATACAGGTGGCTTCCGAT 59.096 43.478 0.00 0.00 0.00 4.18
106 107 4.348168 AGAATATACAGGTGGCTTCCGATT 59.652 41.667 0.00 0.00 0.00 3.34
107 108 2.332063 ATACAGGTGGCTTCCGATTG 57.668 50.000 0.00 0.00 0.00 2.67
110 111 1.074775 AGGTGGCTTCCGATTGCAA 59.925 52.632 0.00 0.00 0.00 4.08
111 112 0.539438 AGGTGGCTTCCGATTGCAAA 60.539 50.000 1.71 0.00 0.00 3.68
115 116 2.083774 TGGCTTCCGATTGCAAAGTAG 58.916 47.619 1.71 0.00 0.00 2.57
118 119 2.159517 GCTTCCGATTGCAAAGTAGTGG 60.160 50.000 1.71 0.00 0.00 4.00
119 120 2.851263 TCCGATTGCAAAGTAGTGGT 57.149 45.000 1.71 0.00 0.00 4.16
121 122 1.468520 CCGATTGCAAAGTAGTGGTGG 59.531 52.381 1.71 0.00 0.00 4.61
122 123 2.422597 CGATTGCAAAGTAGTGGTGGA 58.577 47.619 1.71 0.00 0.00 4.02
123 124 2.811431 CGATTGCAAAGTAGTGGTGGAA 59.189 45.455 1.71 0.00 0.00 3.53
124 125 3.120199 CGATTGCAAAGTAGTGGTGGAAG 60.120 47.826 1.71 0.00 0.00 3.46
125 126 3.569194 TTGCAAAGTAGTGGTGGAAGA 57.431 42.857 0.00 0.00 0.00 2.87
126 127 2.846193 TGCAAAGTAGTGGTGGAAGAC 58.154 47.619 0.00 0.00 0.00 3.01
127 128 2.171659 TGCAAAGTAGTGGTGGAAGACA 59.828 45.455 0.00 0.00 0.00 3.41
128 129 3.181445 TGCAAAGTAGTGGTGGAAGACAT 60.181 43.478 0.00 0.00 0.00 3.06
129 130 3.437049 GCAAAGTAGTGGTGGAAGACATC 59.563 47.826 0.00 0.00 0.00 3.06
140 141 1.933247 GAAGACATCCAGAAGCGGAG 58.067 55.000 0.00 0.00 38.83 4.63
153 154 4.547859 CGGAGCTTGGCTTGCTAT 57.452 55.556 4.93 0.00 39.88 2.97
155 156 1.442526 CGGAGCTTGGCTTGCTATGG 61.443 60.000 4.93 0.00 39.88 2.74
158 159 1.140375 GCTTGGCTTGCTATGGTGC 59.860 57.895 0.00 0.00 0.00 5.01
159 160 1.597797 GCTTGGCTTGCTATGGTGCA 61.598 55.000 0.00 0.00 41.65 4.57
169 170 3.544684 TGCTATGGTGCAATAGTTCAGG 58.455 45.455 7.16 0.00 40.29 3.86
171 172 3.812053 GCTATGGTGCAATAGTTCAGGAG 59.188 47.826 7.16 0.00 33.42 3.69
172 173 4.443457 GCTATGGTGCAATAGTTCAGGAGA 60.443 45.833 7.16 0.00 33.42 3.71
173 174 4.785346 ATGGTGCAATAGTTCAGGAGAT 57.215 40.909 0.00 0.00 0.00 2.75
175 176 5.692115 TGGTGCAATAGTTCAGGAGATTA 57.308 39.130 0.00 0.00 0.00 1.75
176 177 5.674525 TGGTGCAATAGTTCAGGAGATTAG 58.325 41.667 0.00 0.00 0.00 1.73
177 178 5.425217 TGGTGCAATAGTTCAGGAGATTAGA 59.575 40.000 0.00 0.00 0.00 2.10
178 179 5.988561 GGTGCAATAGTTCAGGAGATTAGAG 59.011 44.000 0.00 0.00 0.00 2.43
181 182 8.580720 GTGCAATAGTTCAGGAGATTAGAGATA 58.419 37.037 0.00 0.00 0.00 1.98
188 189 9.739276 AGTTCAGGAGATTAGAGATATGTCTAG 57.261 37.037 9.35 0.00 33.97 2.43
191 192 9.733556 TCAGGAGATTAGAGATATGTCTAGTTC 57.266 37.037 9.35 10.42 33.97 3.01
192 193 9.739276 CAGGAGATTAGAGATATGTCTAGTTCT 57.261 37.037 17.37 17.37 33.97 3.01
201 202 9.249053 AGAGATATGTCTAGTTCTTTCACTTCA 57.751 33.333 0.00 0.00 33.97 3.02
203 204 9.814899 AGATATGTCTAGTTCTTTCACTTCATG 57.185 33.333 0.00 0.00 31.36 3.07
204 205 9.593134 GATATGTCTAGTTCTTTCACTTCATGT 57.407 33.333 0.00 0.00 0.00 3.21
231 232 9.815306 AATATAGTCTATGAAAGTAGGAGCTCA 57.185 33.333 17.19 0.00 0.00 4.26
232 233 5.845391 AGTCTATGAAAGTAGGAGCTCAC 57.155 43.478 17.19 6.03 0.00 3.51
233 234 5.265191 AGTCTATGAAAGTAGGAGCTCACA 58.735 41.667 17.19 0.00 0.00 3.58
234 235 5.896678 AGTCTATGAAAGTAGGAGCTCACAT 59.103 40.000 17.19 10.62 0.00 3.21
235 236 6.382570 AGTCTATGAAAGTAGGAGCTCACATT 59.617 38.462 17.19 5.18 0.00 2.71
236 237 7.044798 GTCTATGAAAGTAGGAGCTCACATTT 58.955 38.462 17.19 10.29 0.00 2.32
237 238 7.550906 GTCTATGAAAGTAGGAGCTCACATTTT 59.449 37.037 17.19 11.08 0.00 1.82
239 240 5.620206 TGAAAGTAGGAGCTCACATTTTGA 58.380 37.500 17.19 3.17 0.00 2.69
242 243 3.944015 AGTAGGAGCTCACATTTTGATGC 59.056 43.478 17.19 0.00 32.17 3.91
243 244 3.083122 AGGAGCTCACATTTTGATGCT 57.917 42.857 17.19 0.00 39.79 3.79
244 245 3.015327 AGGAGCTCACATTTTGATGCTC 58.985 45.455 17.19 12.17 45.42 4.26
245 246 2.751259 GGAGCTCACATTTTGATGCTCA 59.249 45.455 17.19 0.00 46.60 4.26
249 250 4.219944 AGCTCACATTTTGATGCTCACAAT 59.780 37.500 0.00 0.00 35.17 2.71
251 252 5.407387 GCTCACATTTTGATGCTCACAATTT 59.593 36.000 0.00 0.00 32.17 1.82
252 253 6.587226 GCTCACATTTTGATGCTCACAATTTA 59.413 34.615 0.00 0.00 32.17 1.40
254 255 6.587226 TCACATTTTGATGCTCACAATTTAGC 59.413 34.615 0.00 0.00 39.25 3.09
255 256 5.574055 ACATTTTGATGCTCACAATTTAGCG 59.426 36.000 0.00 0.00 41.77 4.26
256 257 5.369685 TTTTGATGCTCACAATTTAGCGA 57.630 34.783 0.00 0.00 41.77 4.93
257 258 5.369685 TTTGATGCTCACAATTTAGCGAA 57.630 34.783 0.00 0.00 41.77 4.70
258 259 4.604843 TGATGCTCACAATTTAGCGAAG 57.395 40.909 0.00 0.00 41.77 3.79
271 272 4.291047 CGAAGCATGCACTCACCT 57.709 55.556 21.98 0.00 0.00 4.00
272 273 2.548178 CGAAGCATGCACTCACCTT 58.452 52.632 21.98 2.69 0.00 3.50
273 274 0.167470 CGAAGCATGCACTCACCTTG 59.833 55.000 21.98 0.00 0.00 3.61
274 275 0.524862 GAAGCATGCACTCACCTTGG 59.475 55.000 21.98 0.00 0.00 3.61
276 277 1.303561 GCATGCACTCACCTTGGGA 60.304 57.895 14.21 0.00 0.00 4.37
277 278 1.310933 GCATGCACTCACCTTGGGAG 61.311 60.000 14.21 0.00 39.30 4.30
286 287 4.410400 CCTTGGGAGGTGGCCGTC 62.410 72.222 0.00 0.00 38.32 4.79
287 288 3.636231 CTTGGGAGGTGGCCGTCA 61.636 66.667 0.00 0.00 0.00 4.35
288 289 2.933287 TTGGGAGGTGGCCGTCAT 60.933 61.111 0.00 0.00 0.00 3.06
289 290 3.266686 TTGGGAGGTGGCCGTCATG 62.267 63.158 0.00 0.00 0.00 3.07
290 291 3.717294 GGGAGGTGGCCGTCATGT 61.717 66.667 0.00 0.00 0.00 3.21
292 293 1.303317 GGAGGTGGCCGTCATGTTT 60.303 57.895 0.00 0.00 0.00 2.83
293 294 1.586154 GGAGGTGGCCGTCATGTTTG 61.586 60.000 0.00 0.00 0.00 2.93
294 295 1.586154 GAGGTGGCCGTCATGTTTGG 61.586 60.000 0.00 0.00 0.00 3.28
295 296 1.901464 GGTGGCCGTCATGTTTGGT 60.901 57.895 0.00 0.00 0.00 3.67
296 297 1.460273 GGTGGCCGTCATGTTTGGTT 61.460 55.000 0.00 0.00 0.00 3.67
298 299 1.199097 GTGGCCGTCATGTTTGGTTAG 59.801 52.381 0.00 0.00 0.00 2.34
300 301 0.170339 GCCGTCATGTTTGGTTAGGC 59.830 55.000 0.00 0.00 36.32 3.93
301 302 0.808755 CCGTCATGTTTGGTTAGGCC 59.191 55.000 0.00 0.00 37.90 5.19
309 310 2.041430 TGGTTAGGCCATCCGGGA 59.959 61.111 5.01 0.00 43.61 5.14
310 311 1.616930 TGGTTAGGCCATCCGGGAA 60.617 57.895 5.01 0.00 43.61 3.97
311 312 1.208844 TGGTTAGGCCATCCGGGAAA 61.209 55.000 5.01 0.00 43.61 3.13
313 314 1.411074 GGTTAGGCCATCCGGGAAATT 60.411 52.381 5.01 0.00 40.01 1.82
314 315 2.384828 GTTAGGCCATCCGGGAAATTT 58.615 47.619 5.01 0.00 40.01 1.82
315 316 2.764010 GTTAGGCCATCCGGGAAATTTT 59.236 45.455 5.01 0.00 40.01 1.82
316 317 1.951209 AGGCCATCCGGGAAATTTTT 58.049 45.000 5.01 0.00 40.01 1.94
334 335 3.278668 TTTTGTCCGTCCCTGTAAACA 57.721 42.857 0.00 0.00 0.00 2.83
335 336 3.495434 TTTGTCCGTCCCTGTAAACAT 57.505 42.857 0.00 0.00 0.00 2.71
339 340 2.482721 GTCCGTCCCTGTAAACATTGTG 59.517 50.000 0.00 0.00 0.00 3.33
340 341 2.369203 TCCGTCCCTGTAAACATTGTGA 59.631 45.455 0.00 0.00 0.00 3.58
341 342 2.482721 CCGTCCCTGTAAACATTGTGAC 59.517 50.000 0.00 0.00 0.00 3.67
342 343 2.156891 CGTCCCTGTAAACATTGTGACG 59.843 50.000 8.54 8.54 38.42 4.35
343 344 3.395639 GTCCCTGTAAACATTGTGACGA 58.604 45.455 0.00 0.00 0.00 4.20
344 345 3.810941 GTCCCTGTAAACATTGTGACGAA 59.189 43.478 0.00 0.00 0.00 3.85
349 350 7.392113 TCCCTGTAAACATTGTGACGAATTAAT 59.608 33.333 0.00 0.00 0.00 1.40
350 351 8.670135 CCCTGTAAACATTGTGACGAATTAATA 58.330 33.333 0.00 0.00 0.00 0.98
357 358 8.895932 ACATTGTGACGAATTAATAAAGCTTC 57.104 30.769 0.00 0.00 0.00 3.86
359 360 5.556470 TGTGACGAATTAATAAAGCTTCGC 58.444 37.500 0.00 0.00 43.07 4.70
360 361 4.660465 GTGACGAATTAATAAAGCTTCGCG 59.340 41.667 0.00 0.00 43.07 5.87
361 362 4.191662 ACGAATTAATAAAGCTTCGCGG 57.808 40.909 6.13 0.00 43.07 6.46
362 363 3.866910 ACGAATTAATAAAGCTTCGCGGA 59.133 39.130 6.13 0.00 43.07 5.54
364 365 5.007332 ACGAATTAATAAAGCTTCGCGGAAT 59.993 36.000 6.13 0.00 43.07 3.01
365 366 5.907391 CGAATTAATAAAGCTTCGCGGAATT 59.093 36.000 6.13 2.88 34.78 2.17
366 367 6.129717 CGAATTAATAAAGCTTCGCGGAATTG 60.130 38.462 6.13 0.00 34.78 2.32
367 368 5.554822 TTAATAAAGCTTCGCGGAATTGT 57.445 34.783 6.13 0.00 0.00 2.71
369 370 1.523758 AAAGCTTCGCGGAATTGTCT 58.476 45.000 6.13 0.00 0.00 3.41
371 372 0.037326 AGCTTCGCGGAATTGTCTCA 60.037 50.000 6.13 0.00 0.00 3.27
372 373 0.796312 GCTTCGCGGAATTGTCTCAA 59.204 50.000 6.13 0.00 0.00 3.02
373 374 1.196808 GCTTCGCGGAATTGTCTCAAA 59.803 47.619 6.13 0.00 0.00 2.69
374 375 2.350388 GCTTCGCGGAATTGTCTCAAAA 60.350 45.455 6.13 0.00 0.00 2.44
375 376 3.851838 GCTTCGCGGAATTGTCTCAAAAA 60.852 43.478 6.13 0.00 0.00 1.94
399 400 4.962155 AGTGTTTCTGGTTTCTGGTCTAG 58.038 43.478 0.00 0.00 0.00 2.43
408 409 7.664758 TCTGGTTTCTGGTCTAGTTTACTTAC 58.335 38.462 0.00 0.00 0.00 2.34
585 606 9.723447 AATTGTTCGTGTTTTCAAAAAGTTTTT 57.277 22.222 7.79 7.79 0.00 1.94
642 663 6.767524 TGTCTCCTGCTTTTGAAAAAGTTA 57.232 33.333 15.08 6.10 45.48 2.24
817 879 1.529438 TCACAATTTCGCAACTCGGTC 59.471 47.619 0.00 0.00 39.05 4.79
832 894 3.138304 CTCGGTCTCCTACTCTGATCTG 58.862 54.545 0.00 0.00 0.00 2.90
842 904 6.929625 TCCTACTCTGATCTGAGAAAACAAG 58.070 40.000 29.89 17.32 37.50 3.16
933 995 4.874977 GCGGCGAGTAGGAGGTGC 62.875 72.222 12.98 0.00 0.00 5.01
935 997 4.208686 GGCGAGTAGGAGGTGCCG 62.209 72.222 0.00 0.00 43.43 5.69
937 999 4.208686 CGAGTAGGAGGTGCCGGC 62.209 72.222 22.73 22.73 43.43 6.13
938 1000 3.851128 GAGTAGGAGGTGCCGGCC 61.851 72.222 26.77 15.53 43.43 6.13
1450 1611 7.234661 TGCCATGTTCATTATTGATGCATAT 57.765 32.000 0.00 0.00 35.64 1.78
1451 1612 8.350852 TGCCATGTTCATTATTGATGCATATA 57.649 30.769 0.00 0.00 35.64 0.86
1452 1613 8.973182 TGCCATGTTCATTATTGATGCATATAT 58.027 29.630 0.00 0.00 35.64 0.86
1567 1846 8.567285 AAATTAACTTTCTACAGATGGTGAGG 57.433 34.615 0.00 0.00 0.00 3.86
1706 3159 5.911752 TGGTGAGATGATAGCTTTCTCTTC 58.088 41.667 5.74 2.88 37.40 2.87
2056 3542 4.256110 CAGCATCTCAACAAGGTACATCA 58.744 43.478 0.00 0.00 0.00 3.07
2128 3620 9.533253 GCATTTAATATCAACTGTTAATTGGCT 57.467 29.630 0.00 0.00 29.56 4.75
2557 4055 1.553706 AGCTCATTGAGGGGCTTTTG 58.446 50.000 15.28 0.00 0.00 2.44
2745 4243 7.066887 TGTGATGTTTCGCATAAATAATGAGGT 59.933 33.333 0.00 0.00 37.45 3.85
2951 4475 8.489489 AGTGATGTAATGGATCAAGTAGATGTT 58.511 33.333 0.00 0.00 37.00 2.71
2981 4509 7.952671 ACTGAGTTATATCGTGGTGTAATGAT 58.047 34.615 0.00 0.00 0.00 2.45
2984 4512 6.759272 AGTTATATCGTGGTGTAATGATGCT 58.241 36.000 0.00 0.00 0.00 3.79
3145 4743 9.899661 ATTATGTATTATGGTGGCGTGTTATAT 57.100 29.630 0.00 0.00 0.00 0.86
3399 5013 5.292765 TCTGAACTAACTTCTGAAGCACAG 58.707 41.667 17.00 13.09 46.97 3.66
3448 5068 5.249393 AGACACCTTCATGTTATCAGTCCTT 59.751 40.000 0.00 0.00 31.24 3.36
3532 5154 2.558359 GTTGCCTGTTCAAGCCAATACT 59.442 45.455 0.00 0.00 0.00 2.12
3709 5336 6.090088 GTGGATATGCTAATTGACGACATCTC 59.910 42.308 0.00 0.00 0.00 2.75
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 6.171921 GGGTGGATCTGATATGAATCTGAAG 58.828 44.000 0.00 0.00 41.63 3.02
1 2 5.608015 TGGGTGGATCTGATATGAATCTGAA 59.392 40.000 0.00 0.00 41.63 3.02
2 3 5.012458 GTGGGTGGATCTGATATGAATCTGA 59.988 44.000 0.00 0.00 42.25 3.27
3 4 5.243981 GTGGGTGGATCTGATATGAATCTG 58.756 45.833 0.00 0.00 32.93 2.90
5 6 4.248859 CGTGGGTGGATCTGATATGAATC 58.751 47.826 0.00 0.00 0.00 2.52
6 7 3.557898 GCGTGGGTGGATCTGATATGAAT 60.558 47.826 0.00 0.00 0.00 2.57
7 8 2.224281 GCGTGGGTGGATCTGATATGAA 60.224 50.000 0.00 0.00 0.00 2.57
10 11 1.722034 AGCGTGGGTGGATCTGATAT 58.278 50.000 0.00 0.00 0.00 1.63
11 12 1.138859 CAAGCGTGGGTGGATCTGATA 59.861 52.381 0.00 0.00 0.00 2.15
12 13 0.107508 CAAGCGTGGGTGGATCTGAT 60.108 55.000 0.00 0.00 0.00 2.90
13 14 1.191489 TCAAGCGTGGGTGGATCTGA 61.191 55.000 0.00 0.00 0.00 3.27
14 15 0.321564 TTCAAGCGTGGGTGGATCTG 60.322 55.000 0.00 0.00 0.00 2.90
17 18 1.675641 GCTTCAAGCGTGGGTGGAT 60.676 57.895 0.00 0.00 0.00 3.41
18 19 2.281484 GCTTCAAGCGTGGGTGGA 60.281 61.111 0.00 0.00 0.00 4.02
19 20 3.365265 GGCTTCAAGCGTGGGTGG 61.365 66.667 2.54 0.00 43.62 4.61
20 21 2.463589 TAGGGCTTCAAGCGTGGGTG 62.464 60.000 2.54 0.00 43.62 4.61
22 23 1.450312 CTAGGGCTTCAAGCGTGGG 60.450 63.158 2.54 0.00 43.62 4.61
23 24 2.109126 GCTAGGGCTTCAAGCGTGG 61.109 63.158 2.54 0.00 43.62 4.94
24 25 3.490890 GCTAGGGCTTCAAGCGTG 58.509 61.111 2.54 0.00 43.62 5.34
34 35 1.605971 GCCTCCCGTATAGCTAGGGC 61.606 65.000 11.02 6.43 44.70 5.19
35 36 0.039911 AGCCTCCCGTATAGCTAGGG 59.960 60.000 9.81 9.81 46.40 3.53
36 37 1.926108 AAGCCTCCCGTATAGCTAGG 58.074 55.000 0.00 0.00 34.49 3.02
37 38 2.028930 CCAAAGCCTCCCGTATAGCTAG 60.029 54.545 0.00 0.00 34.49 3.42
38 39 1.968493 CCAAAGCCTCCCGTATAGCTA 59.032 52.381 0.00 0.00 34.49 3.32
40 41 0.885150 GCCAAAGCCTCCCGTATAGC 60.885 60.000 0.00 0.00 0.00 2.97
41 42 0.759346 AGCCAAAGCCTCCCGTATAG 59.241 55.000 0.00 0.00 41.25 1.31
43 44 0.331616 AAAGCCAAAGCCTCCCGTAT 59.668 50.000 0.00 0.00 41.25 3.06
44 45 0.608035 CAAAGCCAAAGCCTCCCGTA 60.608 55.000 0.00 0.00 41.25 4.02
45 46 1.903404 CAAAGCCAAAGCCTCCCGT 60.903 57.895 0.00 0.00 41.25 5.28
46 47 2.639327 CCAAAGCCAAAGCCTCCCG 61.639 63.158 0.00 0.00 41.25 5.14
48 49 2.659016 GCCAAAGCCAAAGCCTCC 59.341 61.111 0.00 0.00 41.25 4.30
58 59 6.881065 TGAGTATATAGATCATTGGCCAAAGC 59.119 38.462 24.71 10.14 38.76 3.51
59 60 8.316946 TCTGAGTATATAGATCATTGGCCAAAG 58.683 37.037 24.71 19.38 0.00 2.77
60 61 8.206126 TCTGAGTATATAGATCATTGGCCAAA 57.794 34.615 24.71 7.42 0.00 3.28
61 62 7.797121 TCTGAGTATATAGATCATTGGCCAA 57.203 36.000 23.00 23.00 0.00 4.52
62 63 7.797121 TTCTGAGTATATAGATCATTGGCCA 57.203 36.000 0.00 0.00 0.00 5.36
72 73 9.409918 GCCACCTGTATATTCTGAGTATATAGA 57.590 37.037 18.89 6.03 29.66 1.98
73 74 9.415008 AGCCACCTGTATATTCTGAGTATATAG 57.585 37.037 13.49 13.49 0.00 1.31
74 75 9.769677 AAGCCACCTGTATATTCTGAGTATATA 57.230 33.333 3.62 1.00 0.00 0.86
75 76 8.671987 AAGCCACCTGTATATTCTGAGTATAT 57.328 34.615 3.62 0.00 0.00 0.86
77 78 6.014156 GGAAGCCACCTGTATATTCTGAGTAT 60.014 42.308 0.00 0.00 0.00 2.12
78 79 5.304614 GGAAGCCACCTGTATATTCTGAGTA 59.695 44.000 0.00 0.00 0.00 2.59
81 82 3.069586 CGGAAGCCACCTGTATATTCTGA 59.930 47.826 0.00 0.00 0.00 3.27
82 83 3.069586 TCGGAAGCCACCTGTATATTCTG 59.930 47.826 0.00 0.00 0.00 3.02
83 84 3.305720 TCGGAAGCCACCTGTATATTCT 58.694 45.455 0.00 0.00 0.00 2.40
84 85 3.746045 TCGGAAGCCACCTGTATATTC 57.254 47.619 0.00 0.00 0.00 1.75
85 86 4.389374 CAATCGGAAGCCACCTGTATATT 58.611 43.478 0.00 0.00 0.00 1.28
86 87 3.807209 GCAATCGGAAGCCACCTGTATAT 60.807 47.826 0.00 0.00 0.00 0.86
88 89 1.747206 GCAATCGGAAGCCACCTGTAT 60.747 52.381 0.00 0.00 0.00 2.29
90 91 1.675641 GCAATCGGAAGCCACCTGT 60.676 57.895 0.00 0.00 0.00 4.00
91 92 1.243342 TTGCAATCGGAAGCCACCTG 61.243 55.000 0.00 0.00 0.00 4.00
93 94 0.109132 CTTTGCAATCGGAAGCCACC 60.109 55.000 0.00 0.00 0.00 4.61
95 96 2.083774 CTACTTTGCAATCGGAAGCCA 58.916 47.619 0.00 0.00 0.00 4.75
96 97 2.084546 ACTACTTTGCAATCGGAAGCC 58.915 47.619 0.00 0.00 0.00 4.35
98 99 3.074412 ACCACTACTTTGCAATCGGAAG 58.926 45.455 0.00 0.00 0.00 3.46
100 101 2.422597 CACCACTACTTTGCAATCGGA 58.577 47.619 0.00 0.00 0.00 4.55
101 102 1.468520 CCACCACTACTTTGCAATCGG 59.531 52.381 0.00 0.00 0.00 4.18
103 104 4.072131 TCTTCCACCACTACTTTGCAATC 58.928 43.478 0.00 0.00 0.00 2.67
104 105 3.821033 GTCTTCCACCACTACTTTGCAAT 59.179 43.478 0.00 0.00 0.00 3.56
105 106 3.211045 GTCTTCCACCACTACTTTGCAA 58.789 45.455 0.00 0.00 0.00 4.08
106 107 2.171659 TGTCTTCCACCACTACTTTGCA 59.828 45.455 0.00 0.00 0.00 4.08
107 108 2.846193 TGTCTTCCACCACTACTTTGC 58.154 47.619 0.00 0.00 0.00 3.68
110 111 3.983044 GGATGTCTTCCACCACTACTT 57.017 47.619 0.00 0.00 44.74 2.24
121 122 1.933247 CTCCGCTTCTGGATGTCTTC 58.067 55.000 0.00 0.00 37.41 2.87
122 123 0.107945 GCTCCGCTTCTGGATGTCTT 60.108 55.000 0.00 0.00 37.41 3.01
123 124 0.975040 AGCTCCGCTTCTGGATGTCT 60.975 55.000 0.00 0.00 33.89 3.41
124 125 0.107945 AAGCTCCGCTTCTGGATGTC 60.108 55.000 0.00 0.00 46.77 3.06
125 126 0.392193 CAAGCTCCGCTTCTGGATGT 60.392 55.000 0.00 0.00 46.77 3.06
126 127 1.094073 CCAAGCTCCGCTTCTGGATG 61.094 60.000 0.00 0.00 46.77 3.51
127 128 1.222936 CCAAGCTCCGCTTCTGGAT 59.777 57.895 0.00 0.00 46.77 3.41
128 129 2.665000 CCAAGCTCCGCTTCTGGA 59.335 61.111 0.00 0.00 46.77 3.86
129 130 3.130160 GCCAAGCTCCGCTTCTGG 61.130 66.667 0.00 0.35 46.77 3.86
130 131 1.673665 AAGCCAAGCTCCGCTTCTG 60.674 57.895 13.08 0.00 46.77 3.02
131 132 1.673665 CAAGCCAAGCTCCGCTTCT 60.674 57.895 15.37 0.00 46.77 2.85
132 133 2.873288 CAAGCCAAGCTCCGCTTC 59.127 61.111 15.37 0.00 46.77 3.86
134 135 2.262774 ATAGCAAGCCAAGCTCCGCT 62.263 55.000 15.22 15.22 45.12 5.52
135 136 1.821332 ATAGCAAGCCAAGCTCCGC 60.821 57.895 0.00 3.46 42.32 5.54
136 137 1.442526 CCATAGCAAGCCAAGCTCCG 61.443 60.000 0.00 0.00 42.32 4.63
137 138 0.394899 ACCATAGCAAGCCAAGCTCC 60.395 55.000 0.00 0.00 42.32 4.70
140 141 1.140375 GCACCATAGCAAGCCAAGC 59.860 57.895 0.00 0.00 0.00 4.01
141 142 2.570365 TGCACCATAGCAAGCCAAG 58.430 52.632 0.00 0.00 42.46 3.61
142 143 4.839262 TGCACCATAGCAAGCCAA 57.161 50.000 0.00 0.00 42.46 4.52
148 149 3.199727 TCCTGAACTATTGCACCATAGCA 59.800 43.478 5.49 0.00 43.99 3.49
149 150 3.808728 TCCTGAACTATTGCACCATAGC 58.191 45.455 5.49 0.00 0.00 2.97
150 151 5.282055 TCTCCTGAACTATTGCACCATAG 57.718 43.478 4.21 4.21 0.00 2.23
151 152 5.894298 ATCTCCTGAACTATTGCACCATA 57.106 39.130 0.00 0.00 0.00 2.74
152 153 4.785346 ATCTCCTGAACTATTGCACCAT 57.215 40.909 0.00 0.00 0.00 3.55
153 154 4.574674 AATCTCCTGAACTATTGCACCA 57.425 40.909 0.00 0.00 0.00 4.17
155 156 6.810911 TCTCTAATCTCCTGAACTATTGCAC 58.189 40.000 0.00 0.00 0.00 4.57
162 163 9.739276 CTAGACATATCTCTAATCTCCTGAACT 57.261 37.037 0.00 0.00 36.29 3.01
163 164 9.515226 ACTAGACATATCTCTAATCTCCTGAAC 57.485 37.037 0.00 0.00 36.29 3.18
165 166 9.733556 GAACTAGACATATCTCTAATCTCCTGA 57.266 37.037 0.00 0.00 36.29 3.86
166 167 9.739276 AGAACTAGACATATCTCTAATCTCCTG 57.261 37.037 0.00 0.00 36.29 3.86
175 176 9.249053 TGAAGTGAAAGAACTAGACATATCTCT 57.751 33.333 0.00 0.00 36.29 3.10
177 178 9.814899 CATGAAGTGAAAGAACTAGACATATCT 57.185 33.333 0.00 0.00 39.15 1.98
178 179 9.593134 ACATGAAGTGAAAGAACTAGACATATC 57.407 33.333 0.00 0.00 0.00 1.63
181 182 9.950496 ATTACATGAAGTGAAAGAACTAGACAT 57.050 29.630 0.00 0.00 0.00 3.06
206 207 9.238368 GTGAGCTCCTACTTTCATAGACTATAT 57.762 37.037 12.15 0.00 0.00 0.86
208 209 7.063593 TGTGAGCTCCTACTTTCATAGACTAT 58.936 38.462 12.15 0.00 0.00 2.12
209 210 6.424032 TGTGAGCTCCTACTTTCATAGACTA 58.576 40.000 12.15 0.00 0.00 2.59
210 211 5.265191 TGTGAGCTCCTACTTTCATAGACT 58.735 41.667 12.15 0.00 0.00 3.24
212 213 6.798427 AATGTGAGCTCCTACTTTCATAGA 57.202 37.500 12.15 0.00 0.00 1.98
213 214 7.550551 TCAAAATGTGAGCTCCTACTTTCATAG 59.449 37.037 12.15 0.87 0.00 2.23
214 215 7.394016 TCAAAATGTGAGCTCCTACTTTCATA 58.606 34.615 12.15 0.00 0.00 2.15
215 216 6.240894 TCAAAATGTGAGCTCCTACTTTCAT 58.759 36.000 12.15 2.18 0.00 2.57
216 217 5.620206 TCAAAATGTGAGCTCCTACTTTCA 58.380 37.500 12.15 0.00 0.00 2.69
217 218 6.549952 CATCAAAATGTGAGCTCCTACTTTC 58.450 40.000 12.15 0.00 40.43 2.62
219 220 4.397417 GCATCAAAATGTGAGCTCCTACTT 59.603 41.667 12.15 0.00 40.43 2.24
221 222 3.944015 AGCATCAAAATGTGAGCTCCTAC 59.056 43.478 12.15 4.05 40.43 3.18
222 223 4.194640 GAGCATCAAAATGTGAGCTCCTA 58.805 43.478 12.15 0.00 43.94 2.94
223 224 3.015327 GAGCATCAAAATGTGAGCTCCT 58.985 45.455 12.15 0.00 43.94 3.69
224 225 2.751259 TGAGCATCAAAATGTGAGCTCC 59.249 45.455 12.15 3.09 45.97 4.70
239 240 2.749076 TGCTTCGCTAAATTGTGAGCAT 59.251 40.909 7.73 0.00 38.69 3.79
242 243 3.103738 GCATGCTTCGCTAAATTGTGAG 58.896 45.455 11.37 0.00 0.00 3.51
243 244 2.487372 TGCATGCTTCGCTAAATTGTGA 59.513 40.909 20.33 0.00 0.00 3.58
244 245 2.595536 GTGCATGCTTCGCTAAATTGTG 59.404 45.455 20.33 0.00 0.00 3.33
245 246 2.489329 AGTGCATGCTTCGCTAAATTGT 59.511 40.909 20.33 0.00 0.00 2.71
249 250 1.464608 GTGAGTGCATGCTTCGCTAAA 59.535 47.619 20.33 0.00 0.00 1.85
251 252 0.740868 GGTGAGTGCATGCTTCGCTA 60.741 55.000 24.96 3.15 0.00 4.26
252 253 2.037136 GGTGAGTGCATGCTTCGCT 61.037 57.895 24.96 16.22 0.00 4.93
254 255 0.167470 CAAGGTGAGTGCATGCTTCG 59.833 55.000 20.33 0.38 0.00 3.79
255 256 0.524862 CCAAGGTGAGTGCATGCTTC 59.475 55.000 20.33 16.42 0.00 3.86
256 257 0.896940 CCCAAGGTGAGTGCATGCTT 60.897 55.000 20.33 7.15 0.00 3.91
257 258 1.303888 CCCAAGGTGAGTGCATGCT 60.304 57.895 20.33 0.00 0.00 3.79
258 259 1.303561 TCCCAAGGTGAGTGCATGC 60.304 57.895 11.82 11.82 0.00 4.06
259 260 0.679002 CCTCCCAAGGTGAGTGCATG 60.679 60.000 0.00 0.00 37.94 4.06
260 261 1.687612 CCTCCCAAGGTGAGTGCAT 59.312 57.895 0.00 0.00 37.94 3.96
261 262 3.160585 CCTCCCAAGGTGAGTGCA 58.839 61.111 0.00 0.00 37.94 4.57
270 271 2.971598 ATGACGGCCACCTCCCAAG 61.972 63.158 2.24 0.00 0.00 3.61
271 272 2.933287 ATGACGGCCACCTCCCAA 60.933 61.111 2.24 0.00 0.00 4.12
272 273 3.716195 CATGACGGCCACCTCCCA 61.716 66.667 2.24 0.00 0.00 4.37
273 274 2.764637 AAACATGACGGCCACCTCCC 62.765 60.000 2.24 0.00 0.00 4.30
274 275 1.303317 AAACATGACGGCCACCTCC 60.303 57.895 2.24 0.00 0.00 4.30
276 277 1.603455 CCAAACATGACGGCCACCT 60.603 57.895 2.24 0.00 0.00 4.00
277 278 1.460273 AACCAAACATGACGGCCACC 61.460 55.000 2.24 0.00 0.00 4.61
278 279 1.199097 CTAACCAAACATGACGGCCAC 59.801 52.381 2.24 0.00 0.00 5.01
279 280 1.529226 CTAACCAAACATGACGGCCA 58.471 50.000 2.24 0.00 0.00 5.36
280 281 0.808755 CCTAACCAAACATGACGGCC 59.191 55.000 0.00 0.00 0.00 6.13
281 282 0.170339 GCCTAACCAAACATGACGGC 59.830 55.000 0.00 0.00 0.00 5.68
282 283 0.808755 GGCCTAACCAAACATGACGG 59.191 55.000 0.00 0.00 38.86 4.79
293 294 0.185175 ATTTCCCGGATGGCCTAACC 59.815 55.000 0.73 3.67 39.84 2.85
294 295 2.067365 AATTTCCCGGATGGCCTAAC 57.933 50.000 0.73 0.00 0.00 2.34
295 296 2.838637 AAATTTCCCGGATGGCCTAA 57.161 45.000 0.73 0.00 0.00 2.69
296 297 2.838637 AAAATTTCCCGGATGGCCTA 57.161 45.000 0.73 0.00 0.00 3.93
313 314 3.618351 TGTTTACAGGGACGGACAAAAA 58.382 40.909 0.00 0.00 0.00 1.94
314 315 3.278668 TGTTTACAGGGACGGACAAAA 57.721 42.857 0.00 0.00 0.00 2.44
315 316 3.495434 ATGTTTACAGGGACGGACAAA 57.505 42.857 0.00 0.00 0.00 2.83
316 317 3.142951 CAATGTTTACAGGGACGGACAA 58.857 45.455 0.00 0.00 0.00 3.18
319 320 2.369203 TCACAATGTTTACAGGGACGGA 59.631 45.455 0.00 0.00 0.00 4.69
320 321 2.482721 GTCACAATGTTTACAGGGACGG 59.517 50.000 0.00 0.00 0.00 4.79
321 322 2.156891 CGTCACAATGTTTACAGGGACG 59.843 50.000 11.00 11.00 40.45 4.79
322 323 3.395639 TCGTCACAATGTTTACAGGGAC 58.604 45.455 0.00 0.00 0.00 4.46
323 324 3.755112 TCGTCACAATGTTTACAGGGA 57.245 42.857 0.00 0.00 0.00 4.20
324 325 5.371115 AATTCGTCACAATGTTTACAGGG 57.629 39.130 0.00 0.00 0.00 4.45
330 331 9.691362 AAGCTTTATTAATTCGTCACAATGTTT 57.309 25.926 0.00 0.00 0.00 2.83
331 332 9.341899 GAAGCTTTATTAATTCGTCACAATGTT 57.658 29.630 0.00 0.00 0.00 2.71
332 333 7.692291 CGAAGCTTTATTAATTCGTCACAATGT 59.308 33.333 0.00 0.00 39.62 2.71
333 334 8.028433 CGAAGCTTTATTAATTCGTCACAATG 57.972 34.615 0.00 0.00 39.62 2.82
373 374 5.480422 AGACCAGAAACCAGAAACACTTTTT 59.520 36.000 0.00 0.00 0.00 1.94
374 375 5.016831 AGACCAGAAACCAGAAACACTTTT 58.983 37.500 0.00 0.00 0.00 2.27
375 376 4.600062 AGACCAGAAACCAGAAACACTTT 58.400 39.130 0.00 0.00 0.00 2.66
585 606 6.864342 TCCCAACATTTTTCGAAAAACACTA 58.136 32.000 32.14 15.07 40.33 2.74
706 727 7.846485 TGCGAACAATTTGTAAAAGGAAAATC 58.154 30.769 1.76 0.00 0.00 2.17
755 776 9.525409 TTCGTCCGTTTTATAAAAATGGAAAAA 57.475 25.926 24.25 19.64 36.82 1.94
756 777 9.525409 TTTCGTCCGTTTTATAAAAATGGAAAA 57.475 25.926 24.25 20.22 36.82 2.29
773 794 8.293867 TGAATAAATTTTGAGAATTTCGTCCGT 58.706 29.630 0.00 0.00 32.64 4.69
806 827 0.099082 GAGTAGGAGACCGAGTTGCG 59.901 60.000 0.00 0.00 40.47 4.85
817 879 6.522625 TGTTTTCTCAGATCAGAGTAGGAG 57.477 41.667 14.13 0.86 36.97 3.69
916 978 4.874977 GCACCTCCTACTCGCCGC 62.875 72.222 0.00 0.00 0.00 6.53
1450 1611 7.331026 ACTGAGATTTGCTGTTTACTGCTATA 58.669 34.615 12.05 0.20 40.79 1.31
1451 1612 6.176183 ACTGAGATTTGCTGTTTACTGCTAT 58.824 36.000 12.05 6.51 40.79 2.97
1452 1613 5.551233 ACTGAGATTTGCTGTTTACTGCTA 58.449 37.500 12.05 3.09 40.79 3.49
1453 1614 4.392940 ACTGAGATTTGCTGTTTACTGCT 58.607 39.130 12.05 0.00 40.79 4.24
1567 1846 8.603242 TGTTAACTTCAAGAGGAAACTATCAC 57.397 34.615 7.22 0.00 44.43 3.06
1706 3159 4.795970 ACTTGACTTGCGAGTTAACTTG 57.204 40.909 17.30 17.30 38.05 3.16
1753 3211 6.458232 TTGTGTTTTCCCCATTTATATCCG 57.542 37.500 0.00 0.00 0.00 4.18
2128 3620 7.044181 CAGCACTAAGATGACTCCATTTAGAA 58.956 38.462 0.00 0.00 35.00 2.10
2557 4055 6.912591 CGATGCCAACTGTTATATTTCCTTTC 59.087 38.462 0.00 0.00 0.00 2.62
2745 4243 1.135141 GTTCAGCACAAACACCAGCAA 60.135 47.619 0.00 0.00 0.00 3.91
2951 4475 4.021229 ACCACGATATAACTCAGTCCACA 58.979 43.478 0.00 0.00 0.00 4.17
2981 4509 4.688879 CCACGATTAACTTAGTTCACAGCA 59.311 41.667 0.00 0.00 0.00 4.41
2984 4512 5.603596 ACACCACGATTAACTTAGTTCACA 58.396 37.500 0.00 0.00 0.00 3.58
3344 4958 3.271729 CCAAATGCAATGCAAAGCCATA 58.728 40.909 13.45 0.00 43.62 2.74
3399 5013 1.340114 CCTTCCTAGTTGAACCCAGGC 60.340 57.143 8.33 0.00 0.00 4.85
3569 5192 7.581476 TGGTGTCTTGAAGATCGTTTATTTTC 58.419 34.615 0.00 0.00 30.96 2.29
3574 5197 4.391830 GCATGGTGTCTTGAAGATCGTTTA 59.608 41.667 0.00 0.00 0.00 2.01
3782 5415 4.716784 TCAGTATGACAGGAAAGGCACTAT 59.283 41.667 0.00 0.00 42.56 2.12


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

AutoCloner maintained by Alex Coulton.