Multiple sequence alignment - TraesCS4D01G299700

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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 TraesCS4D01G299700 chr4D 100.000 4247 0 0 1 4247 468601794 468597548 0.000000e+00 7843.0
1 TraesCS4D01G299700 chr4A 89.609 3580 208 87 771 4247 2942750 2946268 0.000000e+00 4399.0
2 TraesCS4D01G299700 chr4B 87.265 2230 166 53 106 2265 588202212 588200031 0.000000e+00 2436.0
3 TraesCS4D01G299700 chr4B 94.541 1264 43 19 2288 3532 588199965 588198709 0.000000e+00 1929.0
4 TraesCS4D01G299700 chr4B 95.188 478 15 5 3626 4102 588198348 588197878 0.000000e+00 749.0
5 TraesCS4D01G299700 chr4B 96.825 63 1 1 3567 3628 588198513 588198451 2.090000e-18 104.0
6 TraesCS4D01G299700 chr3B 83.776 1091 97 36 933 1975 509971996 509970938 0.000000e+00 961.0
7 TraesCS4D01G299700 chr1B 83.685 1091 97 38 933 1975 186139956 186141013 0.000000e+00 953.0
8 TraesCS4D01G299700 chr7B 83.532 1093 98 40 933 1975 707547497 707546437 0.000000e+00 946.0
9 TraesCS4D01G299700 chr7B 83.288 1095 98 38 933 1975 669096405 669095344 0.000000e+00 929.0
10 TraesCS4D01G299700 chrUn 83.333 1086 105 35 933 1975 65799397 65800449 0.000000e+00 933.0
11 TraesCS4D01G299700 chr6B 82.998 1094 103 42 933 1975 54643104 54644165 0.000000e+00 913.0
12 TraesCS4D01G299700 chr6B 82.597 1086 110 36 933 1975 9465362 9466411 0.000000e+00 885.0
13 TraesCS4D01G299700 chr6B 84.444 135 20 1 1821 1955 268046110 268045977 9.580000e-27 132.0
14 TraesCS4D01G299700 chr6B 80.702 114 16 5 2313 2422 68103978 68104089 2.720000e-12 84.2
15 TraesCS4D01G299700 chr2B 82.676 1091 108 36 933 1975 263969480 263970537 0.000000e+00 893.0
16 TraesCS4D01G299700 chr2B 88.889 81 8 1 2088 2167 220437996 220438076 9.720000e-17 99.0
17 TraesCS4D01G299700 chr5D 84.289 471 64 9 1676 2142 28564096 28564560 6.480000e-123 451.0
18 TraesCS4D01G299700 chr2D 83.898 472 69 6 1679 2147 530164745 530165212 1.080000e-120 444.0
19 TraesCS4D01G299700 chr2D 91.250 80 7 0 2088 2167 530165185 530165264 4.490000e-20 110.0
20 TraesCS4D01G299700 chr7A 85.128 390 51 6 1618 2005 651016205 651016589 3.980000e-105 392.0
21 TraesCS4D01G299700 chr7A 84.817 382 53 4 1618 1998 112624875 112625252 3.100000e-101 379.0
22 TraesCS4D01G299700 chr5A 85.079 382 52 4 1618 1998 494221235 494221612 6.660000e-103 385.0
23 TraesCS4D01G299700 chr5A 86.250 80 7 1 2088 2167 609691969 609692044 2.720000e-12 84.2
24 TraesCS4D01G299700 chr3D 93.103 145 10 0 1826 1970 35106498 35106354 3.330000e-51 213.0
25 TraesCS4D01G299700 chr3D 88.750 80 5 1 2088 2167 542663113 542663038 1.260000e-15 95.3
26 TraesCS4D01G299700 chr7D 86.992 123 16 0 1821 1943 552341036 552340914 5.730000e-29 139.0
27 TraesCS4D01G299700 chr6D 87.654 81 9 1 2088 2167 6085697 6085617 4.520000e-15 93.5
28 TraesCS4D01G299700 chr6A 81.481 108 15 4 2319 2422 17041902 17042008 2.720000e-12 84.2


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 TraesCS4D01G299700 chr4D 468597548 468601794 4246 True 7843.0 7843 100.00000 1 4247 1 chr4D.!!$R1 4246
1 TraesCS4D01G299700 chr4A 2942750 2946268 3518 False 4399.0 4399 89.60900 771 4247 1 chr4A.!!$F1 3476
2 TraesCS4D01G299700 chr4B 588197878 588202212 4334 True 1304.5 2436 93.45475 106 4102 4 chr4B.!!$R1 3996
3 TraesCS4D01G299700 chr3B 509970938 509971996 1058 True 961.0 961 83.77600 933 1975 1 chr3B.!!$R1 1042
4 TraesCS4D01G299700 chr1B 186139956 186141013 1057 False 953.0 953 83.68500 933 1975 1 chr1B.!!$F1 1042
5 TraesCS4D01G299700 chr7B 707546437 707547497 1060 True 946.0 946 83.53200 933 1975 1 chr7B.!!$R2 1042
6 TraesCS4D01G299700 chr7B 669095344 669096405 1061 True 929.0 929 83.28800 933 1975 1 chr7B.!!$R1 1042
7 TraesCS4D01G299700 chrUn 65799397 65800449 1052 False 933.0 933 83.33300 933 1975 1 chrUn.!!$F1 1042
8 TraesCS4D01G299700 chr6B 54643104 54644165 1061 False 913.0 913 82.99800 933 1975 1 chr6B.!!$F2 1042
9 TraesCS4D01G299700 chr6B 9465362 9466411 1049 False 885.0 885 82.59700 933 1975 1 chr6B.!!$F1 1042
10 TraesCS4D01G299700 chr2B 263969480 263970537 1057 False 893.0 893 82.67600 933 1975 1 chr2B.!!$F2 1042
11 TraesCS4D01G299700 chr2D 530164745 530165264 519 False 277.0 444 87.57400 1679 2167 2 chr2D.!!$F1 488

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
670 698 0.110486 TCCAACCACTGCTTTCTCCC 59.890 55.0 0.00 0.00 0.0 4.30 F
671 699 0.111253 CCAACCACTGCTTTCTCCCT 59.889 55.0 0.00 0.00 0.0 4.20 F
1180 1262 0.177836 GCCTTCTCTCTTCCTGCCTC 59.822 60.0 0.00 0.00 0.0 4.70 F
1808 1946 0.387622 TTGTGCTGCTCGTACGGTAC 60.388 55.0 16.52 8.25 32.7 3.34 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1497 1594 0.809385 ACGACACAGAGACCGTATGG 59.191 55.000 0.00 0.0 42.84 2.74 R
1603 1700 1.135257 GCAGTAAGAAGAGCGAGCAGA 60.135 52.381 0.00 0.0 0.00 4.26 R
2811 3071 0.796312 GCCATGAATTCACACGACGT 59.204 50.000 11.07 0.0 0.00 4.34 R
3407 3679 0.951558 CAAAAGCCTTACACCACGCT 59.048 50.000 0.00 0.0 0.00 5.07 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
17 18 3.662153 CCGCATGCAGCACACACA 61.662 61.111 19.57 0.00 46.13 3.72
18 19 2.564458 CGCATGCAGCACACACAT 59.436 55.556 19.57 0.00 46.13 3.21
19 20 1.799916 CGCATGCAGCACACACATG 60.800 57.895 19.57 0.00 46.13 3.21
20 21 1.287815 GCATGCAGCACACACATGT 59.712 52.632 14.21 0.00 42.50 3.21
21 22 0.319211 GCATGCAGCACACACATGTT 60.319 50.000 14.21 0.00 42.50 2.71
22 23 1.870580 GCATGCAGCACACACATGTTT 60.871 47.619 14.21 0.00 42.50 2.83
23 24 2.607526 GCATGCAGCACACACATGTTTA 60.608 45.455 14.21 0.00 42.50 2.01
24 25 3.640592 CATGCAGCACACACATGTTTAA 58.359 40.909 0.00 0.00 36.72 1.52
25 26 4.239304 CATGCAGCACACACATGTTTAAT 58.761 39.130 0.00 0.00 36.72 1.40
26 27 5.400703 CATGCAGCACACACATGTTTAATA 58.599 37.500 0.00 0.00 36.72 0.98
27 28 5.444663 TGCAGCACACACATGTTTAATAA 57.555 34.783 0.00 0.00 36.72 1.40
28 29 6.023357 TGCAGCACACACATGTTTAATAAT 57.977 33.333 0.00 0.00 36.72 1.28
29 30 7.150783 TGCAGCACACACATGTTTAATAATA 57.849 32.000 0.00 0.00 36.72 0.98
30 31 7.597386 TGCAGCACACACATGTTTAATAATAA 58.403 30.769 0.00 0.00 36.72 1.40
31 32 8.249638 TGCAGCACACACATGTTTAATAATAAT 58.750 29.630 0.00 0.00 36.72 1.28
32 33 9.729023 GCAGCACACACATGTTTAATAATAATA 57.271 29.630 0.00 0.00 36.72 0.98
53 54 7.817418 AATAATACAACTTCACTTGGTGTGT 57.183 32.000 0.00 0.00 46.27 3.72
54 55 7.817418 ATAATACAACTTCACTTGGTGTGTT 57.183 32.000 0.00 0.00 46.27 3.32
55 56 3.848272 ACAACTTCACTTGGTGTGTTG 57.152 42.857 22.60 22.60 46.27 3.33
56 57 2.094752 ACAACTTCACTTGGTGTGTTGC 60.095 45.455 23.34 0.00 43.98 4.17
57 58 0.732571 ACTTCACTTGGTGTGTTGCG 59.267 50.000 0.00 0.00 46.27 4.85
58 59 1.013596 CTTCACTTGGTGTGTTGCGA 58.986 50.000 0.00 0.00 46.27 5.10
59 60 1.400142 CTTCACTTGGTGTGTTGCGAA 59.600 47.619 0.00 0.00 46.27 4.70
60 61 1.674359 TCACTTGGTGTGTTGCGAAT 58.326 45.000 0.00 0.00 46.27 3.34
61 62 2.020720 TCACTTGGTGTGTTGCGAATT 58.979 42.857 0.00 0.00 46.27 2.17
62 63 2.425312 TCACTTGGTGTGTTGCGAATTT 59.575 40.909 0.00 0.00 46.27 1.82
63 64 2.788786 CACTTGGTGTGTTGCGAATTTC 59.211 45.455 0.00 0.00 41.53 2.17
64 65 2.043411 CTTGGTGTGTTGCGAATTTCG 58.957 47.619 14.33 14.33 43.89 3.46
65 66 1.018148 TGGTGTGTTGCGAATTTCGT 58.982 45.000 19.10 0.00 42.81 3.85
66 67 1.003331 TGGTGTGTTGCGAATTTCGTC 60.003 47.619 19.10 12.19 42.81 4.20
67 68 1.662026 GGTGTGTTGCGAATTTCGTCC 60.662 52.381 19.10 8.64 42.81 4.79
68 69 1.003331 GTGTGTTGCGAATTTCGTCCA 60.003 47.619 19.10 10.85 42.81 4.02
69 70 1.262950 TGTGTTGCGAATTTCGTCCAG 59.737 47.619 19.10 0.00 42.81 3.86
70 71 0.237235 TGTTGCGAATTTCGTCCAGC 59.763 50.000 19.10 12.07 42.81 4.85
71 72 0.517316 GTTGCGAATTTCGTCCAGCT 59.483 50.000 19.10 0.00 42.81 4.24
72 73 1.069227 GTTGCGAATTTCGTCCAGCTT 60.069 47.619 19.10 0.00 42.81 3.74
73 74 0.516877 TGCGAATTTCGTCCAGCTTG 59.483 50.000 19.10 0.00 42.81 4.01
74 75 0.179189 GCGAATTTCGTCCAGCTTGG 60.179 55.000 19.10 0.00 42.81 3.61
75 76 1.156736 CGAATTTCGTCCAGCTTGGT 58.843 50.000 10.61 0.00 39.03 3.67
76 77 1.135972 CGAATTTCGTCCAGCTTGGTG 60.136 52.381 10.61 0.00 39.03 4.17
77 78 0.598065 AATTTCGTCCAGCTTGGTGC 59.402 50.000 0.00 0.00 39.03 5.01
78 79 1.244019 ATTTCGTCCAGCTTGGTGCC 61.244 55.000 0.00 0.00 44.23 5.01
79 80 2.337879 TTTCGTCCAGCTTGGTGCCT 62.338 55.000 0.00 0.00 44.23 4.75
80 81 2.281761 CGTCCAGCTTGGTGCCTT 60.282 61.111 0.00 0.00 44.23 4.35
81 82 2.328099 CGTCCAGCTTGGTGCCTTC 61.328 63.158 0.00 0.00 44.23 3.46
82 83 1.228245 GTCCAGCTTGGTGCCTTCA 60.228 57.895 0.00 0.00 44.23 3.02
83 84 0.610232 GTCCAGCTTGGTGCCTTCAT 60.610 55.000 0.00 0.00 44.23 2.57
84 85 0.991146 TCCAGCTTGGTGCCTTCATA 59.009 50.000 0.00 0.00 44.23 2.15
85 86 1.065199 TCCAGCTTGGTGCCTTCATAG 60.065 52.381 0.00 0.00 44.23 2.23
86 87 1.340405 CCAGCTTGGTGCCTTCATAGT 60.340 52.381 0.00 0.00 44.23 2.12
87 88 2.440409 CAGCTTGGTGCCTTCATAGTT 58.560 47.619 0.00 0.00 44.23 2.24
88 89 2.421424 CAGCTTGGTGCCTTCATAGTTC 59.579 50.000 0.00 0.00 44.23 3.01
89 90 2.307098 AGCTTGGTGCCTTCATAGTTCT 59.693 45.455 0.00 0.00 44.23 3.01
90 91 3.084786 GCTTGGTGCCTTCATAGTTCTT 58.915 45.455 0.00 0.00 35.15 2.52
91 92 4.019321 AGCTTGGTGCCTTCATAGTTCTTA 60.019 41.667 0.00 0.00 44.23 2.10
92 93 4.095036 GCTTGGTGCCTTCATAGTTCTTAC 59.905 45.833 0.00 0.00 35.15 2.34
93 94 5.491982 CTTGGTGCCTTCATAGTTCTTACT 58.508 41.667 0.00 0.00 38.44 2.24
94 95 5.086104 TGGTGCCTTCATAGTTCTTACTC 57.914 43.478 0.00 0.00 35.78 2.59
95 96 4.081087 TGGTGCCTTCATAGTTCTTACTCC 60.081 45.833 0.00 0.00 35.78 3.85
96 97 4.113354 GTGCCTTCATAGTTCTTACTCCG 58.887 47.826 0.00 0.00 35.78 4.63
97 98 4.021229 TGCCTTCATAGTTCTTACTCCGA 58.979 43.478 0.00 0.00 35.78 4.55
98 99 4.464951 TGCCTTCATAGTTCTTACTCCGAA 59.535 41.667 0.00 0.00 35.78 4.30
99 100 5.128827 TGCCTTCATAGTTCTTACTCCGAAT 59.871 40.000 0.00 0.00 35.78 3.34
100 101 6.049790 GCCTTCATAGTTCTTACTCCGAATT 58.950 40.000 0.00 0.00 35.78 2.17
101 102 6.539103 GCCTTCATAGTTCTTACTCCGAATTT 59.461 38.462 0.00 0.00 35.78 1.82
102 103 7.065923 GCCTTCATAGTTCTTACTCCGAATTTT 59.934 37.037 0.00 0.00 35.78 1.82
103 104 9.595823 CCTTCATAGTTCTTACTCCGAATTTTA 57.404 33.333 0.00 0.00 35.78 1.52
150 151 8.768957 TCTTATCTAAGCAGCAGCATAAATAG 57.231 34.615 3.17 0.00 45.49 1.73
151 152 8.588472 TCTTATCTAAGCAGCAGCATAAATAGA 58.412 33.333 3.17 3.81 45.49 1.98
152 153 9.381033 CTTATCTAAGCAGCAGCATAAATAGAT 57.619 33.333 3.17 10.26 45.49 1.98
178 193 8.528917 TTATATGACAATCATACTACAACCGC 57.471 34.615 0.69 0.00 41.62 5.68
196 211 1.501169 GCATCAAACAACCAAGCACC 58.499 50.000 0.00 0.00 0.00 5.01
215 230 4.116961 CACCAAATGCATCATGATTCACC 58.883 43.478 10.32 0.00 0.00 4.02
227 242 2.573609 GATTCACCGTCGACCTGGGG 62.574 65.000 10.58 7.76 0.00 4.96
228 243 3.813606 TTCACCGTCGACCTGGGGA 62.814 63.158 10.07 10.07 35.37 4.81
261 276 2.039746 ACCAATCCACGAACCTGATCAA 59.960 45.455 0.00 0.00 0.00 2.57
270 285 4.917415 CACGAACCTGATCAACCAATTTTC 59.083 41.667 0.00 0.00 0.00 2.29
280 295 4.187694 TCAACCAATTTTCAACAGCAACC 58.812 39.130 0.00 0.00 0.00 3.77
282 297 4.058721 ACCAATTTTCAACAGCAACCTC 57.941 40.909 0.00 0.00 0.00 3.85
284 299 4.892934 ACCAATTTTCAACAGCAACCTCTA 59.107 37.500 0.00 0.00 0.00 2.43
285 300 5.362430 ACCAATTTTCAACAGCAACCTCTAA 59.638 36.000 0.00 0.00 0.00 2.10
289 304 2.846193 TCAACAGCAACCTCTAACCAC 58.154 47.619 0.00 0.00 0.00 4.16
290 305 2.438021 TCAACAGCAACCTCTAACCACT 59.562 45.455 0.00 0.00 0.00 4.00
292 307 1.072331 ACAGCAACCTCTAACCACTGG 59.928 52.381 0.00 0.00 0.00 4.00
294 309 2.054799 AGCAACCTCTAACCACTGGAA 58.945 47.619 0.71 0.00 0.00 3.53
296 311 2.038557 GCAACCTCTAACCACTGGAAGA 59.961 50.000 0.71 3.60 37.43 2.87
301 316 5.953571 ACCTCTAACCACTGGAAGAAAAAT 58.046 37.500 0.71 0.00 37.43 1.82
303 318 5.122396 CCTCTAACCACTGGAAGAAAAATCG 59.878 44.000 0.71 0.00 37.43 3.34
311 326 4.340950 ACTGGAAGAAAAATCGGAAAGCAA 59.659 37.500 0.00 0.00 37.43 3.91
315 330 5.332280 GGAAGAAAAATCGGAAAGCAAAACG 60.332 40.000 0.00 0.00 0.00 3.60
316 331 3.489416 AGAAAAATCGGAAAGCAAAACGC 59.511 39.130 0.00 0.00 42.91 4.84
335 350 3.056107 ACGCCTTGATTCAGCAAGTACTA 60.056 43.478 0.00 0.00 42.84 1.82
336 351 3.553511 CGCCTTGATTCAGCAAGTACTAG 59.446 47.826 0.00 0.00 42.84 2.57
337 352 4.508662 GCCTTGATTCAGCAAGTACTAGT 58.491 43.478 0.00 0.00 42.84 2.57
338 353 4.331168 GCCTTGATTCAGCAAGTACTAGTG 59.669 45.833 5.39 0.00 42.84 2.74
339 354 4.331168 CCTTGATTCAGCAAGTACTAGTGC 59.669 45.833 10.95 10.95 42.84 4.40
663 691 2.045926 GCCGATCCAACCACTGCT 60.046 61.111 0.00 0.00 0.00 4.24
664 692 1.675641 GCCGATCCAACCACTGCTT 60.676 57.895 0.00 0.00 0.00 3.91
665 693 1.244019 GCCGATCCAACCACTGCTTT 61.244 55.000 0.00 0.00 0.00 3.51
666 694 0.804989 CCGATCCAACCACTGCTTTC 59.195 55.000 0.00 0.00 0.00 2.62
667 695 1.611673 CCGATCCAACCACTGCTTTCT 60.612 52.381 0.00 0.00 0.00 2.52
668 696 1.734465 CGATCCAACCACTGCTTTCTC 59.266 52.381 0.00 0.00 0.00 2.87
669 697 2.087646 GATCCAACCACTGCTTTCTCC 58.912 52.381 0.00 0.00 0.00 3.71
670 698 0.110486 TCCAACCACTGCTTTCTCCC 59.890 55.000 0.00 0.00 0.00 4.30
671 699 0.111253 CCAACCACTGCTTTCTCCCT 59.889 55.000 0.00 0.00 0.00 4.20
672 700 1.528129 CAACCACTGCTTTCTCCCTC 58.472 55.000 0.00 0.00 0.00 4.30
673 701 0.402121 AACCACTGCTTTCTCCCTCC 59.598 55.000 0.00 0.00 0.00 4.30
674 702 1.301293 CCACTGCTTTCTCCCTCCC 59.699 63.158 0.00 0.00 0.00 4.30
675 703 1.301293 CACTGCTTTCTCCCTCCCC 59.699 63.158 0.00 0.00 0.00 4.81
676 704 1.925972 ACTGCTTTCTCCCTCCCCC 60.926 63.158 0.00 0.00 0.00 5.40
677 705 3.009115 TGCTTTCTCCCTCCCCCG 61.009 66.667 0.00 0.00 0.00 5.73
678 706 2.687566 GCTTTCTCCCTCCCCCGA 60.688 66.667 0.00 0.00 0.00 5.14
679 707 2.073101 GCTTTCTCCCTCCCCCGAT 61.073 63.158 0.00 0.00 0.00 4.18
680 708 2.046009 GCTTTCTCCCTCCCCCGATC 62.046 65.000 0.00 0.00 0.00 3.69
693 721 1.211969 CCGATCGGTCAACTCGTGT 59.788 57.895 26.35 0.00 0.00 4.49
737 779 1.065782 ACTCTCTCACTGAGCGAGCTA 60.066 52.381 21.19 0.00 43.00 3.32
763 805 2.350522 CCGGTCCAGAGAAATGTCTTG 58.649 52.381 0.00 0.00 32.80 3.02
824 867 1.737008 GAAGCCTCCAACGGTCGAC 60.737 63.158 7.13 7.13 0.00 4.20
922 973 3.646715 CACGCCTTCCTCCCCCAA 61.647 66.667 0.00 0.00 0.00 4.12
926 977 2.548547 GCCTTCCTCCCCCAACCTT 61.549 63.158 0.00 0.00 0.00 3.50
972 1028 3.432588 CACCTGCTGCTGCTGCTC 61.433 66.667 27.67 8.99 40.48 4.26
1171 1253 3.144193 CCTCGCCGCCTTCTCTCT 61.144 66.667 0.00 0.00 0.00 3.10
1172 1254 2.716017 CCTCGCCGCCTTCTCTCTT 61.716 63.158 0.00 0.00 0.00 2.85
1173 1255 1.226831 CTCGCCGCCTTCTCTCTTC 60.227 63.158 0.00 0.00 0.00 2.87
1174 1256 2.202810 CGCCGCCTTCTCTCTTCC 60.203 66.667 0.00 0.00 0.00 3.46
1175 1257 2.716017 CGCCGCCTTCTCTCTTCCT 61.716 63.158 0.00 0.00 0.00 3.36
1176 1258 1.153469 GCCGCCTTCTCTCTTCCTG 60.153 63.158 0.00 0.00 0.00 3.86
1177 1259 1.153469 CCGCCTTCTCTCTTCCTGC 60.153 63.158 0.00 0.00 0.00 4.85
1180 1262 0.177836 GCCTTCTCTCTTCCTGCCTC 59.822 60.000 0.00 0.00 0.00 4.70
1181 1263 1.864669 CCTTCTCTCTTCCTGCCTCT 58.135 55.000 0.00 0.00 0.00 3.69
1182 1264 1.481772 CCTTCTCTCTTCCTGCCTCTG 59.518 57.143 0.00 0.00 0.00 3.35
1183 1265 0.901124 TTCTCTCTTCCTGCCTCTGC 59.099 55.000 0.00 0.00 38.26 4.26
1184 1266 0.975040 TCTCTCTTCCTGCCTCTGCC 60.975 60.000 0.00 0.00 36.33 4.85
1185 1267 2.186384 CTCTTCCTGCCTCTGCCG 59.814 66.667 0.00 0.00 36.33 5.69
1186 1268 4.087892 TCTTCCTGCCTCTGCCGC 62.088 66.667 0.00 0.00 36.33 6.53
1234 1320 1.348594 GTCGCTCGCTGCCATTAAC 59.651 57.895 0.00 0.00 38.78 2.01
1240 1326 1.134487 CGCTGCCATTAACCGTGTG 59.866 57.895 0.00 0.00 0.00 3.82
1254 1342 4.091453 ACCGTGTGTTTTCTTTCTTGTG 57.909 40.909 0.00 0.00 0.00 3.33
1257 1345 4.920927 CCGTGTGTTTTCTTTCTTGTGTTT 59.079 37.500 0.00 0.00 0.00 2.83
1258 1346 5.164100 CCGTGTGTTTTCTTTCTTGTGTTTG 60.164 40.000 0.00 0.00 0.00 2.93
1259 1347 5.608146 GTGTGTTTTCTTTCTTGTGTTTGC 58.392 37.500 0.00 0.00 0.00 3.68
1260 1348 4.384247 TGTGTTTTCTTTCTTGTGTTTGCG 59.616 37.500 0.00 0.00 0.00 4.85
1409 1505 3.117738 GGTATCCATCCATCCATCCATCC 60.118 52.174 0.00 0.00 0.00 3.51
1410 1506 2.136974 TCCATCCATCCATCCATCCA 57.863 50.000 0.00 0.00 0.00 3.41
1412 1508 2.579400 TCCATCCATCCATCCATCCATC 59.421 50.000 0.00 0.00 0.00 3.51
1413 1509 2.310647 CCATCCATCCATCCATCCATCA 59.689 50.000 0.00 0.00 0.00 3.07
1414 1510 3.245479 CCATCCATCCATCCATCCATCAA 60.245 47.826 0.00 0.00 0.00 2.57
1461 1558 4.693283 GCTTTTGGGGGAAATGCTTATAC 58.307 43.478 0.00 0.00 40.13 1.47
1463 1560 5.596772 GCTTTTGGGGGAAATGCTTATACTA 59.403 40.000 0.00 0.00 40.13 1.82
1470 1567 9.362151 TGGGGGAAATGCTTATACTAAATAAAG 57.638 33.333 0.00 0.00 0.00 1.85
1482 1579 5.977489 ACTAAATAAAGGCACCTGTTTCC 57.023 39.130 0.00 0.00 0.00 3.13
1497 1594 4.687483 CCTGTTTCCTGTGATTTTTGCATC 59.313 41.667 0.00 0.00 0.00 3.91
1506 1603 4.142491 TGTGATTTTTGCATCCATACGGTC 60.142 41.667 0.00 0.00 0.00 4.79
1512 1609 1.136891 TGCATCCATACGGTCTCTGTG 59.863 52.381 0.00 0.00 0.00 3.66
1534 1631 0.733150 GTCCCTTGCGTGGCTAATTC 59.267 55.000 0.00 0.00 0.00 2.17
1612 1709 1.814394 TGATTTTGCATTCTGCTCGCT 59.186 42.857 0.34 0.00 45.31 4.93
1613 1710 2.159476 TGATTTTGCATTCTGCTCGCTC 60.159 45.455 0.34 0.00 45.31 5.03
1616 1715 1.081892 TTGCATTCTGCTCGCTCTTC 58.918 50.000 0.34 0.00 45.31 2.87
1656 1756 6.823182 TGCTCATACTGTAACTGCAAATACAT 59.177 34.615 10.66 5.66 32.02 2.29
1657 1757 7.011389 TGCTCATACTGTAACTGCAAATACATC 59.989 37.037 10.66 0.00 32.02 3.06
1658 1758 7.519008 GCTCATACTGTAACTGCAAATACATCC 60.519 40.741 10.66 0.00 32.02 3.51
1660 1760 7.495606 TCATACTGTAACTGCAAATACATCCTG 59.504 37.037 10.66 8.75 32.02 3.86
1661 1761 5.560724 ACTGTAACTGCAAATACATCCTGT 58.439 37.500 10.66 4.33 32.02 4.00
1664 1764 3.855689 ACTGCAAATACATCCTGTTGC 57.144 42.857 0.40 0.40 45.19 4.17
1669 1769 3.366883 GCAAATACATCCTGTTGCGGAAA 60.367 43.478 0.00 0.00 37.25 3.13
1688 1789 7.029563 GCGGAAATGAAGATGATGTTTACTTT 58.970 34.615 0.00 0.00 0.00 2.66
1713 1825 6.299141 ACATTTGTATCTGTTGAACTGTCCT 58.701 36.000 0.00 0.00 0.00 3.85
1715 1827 7.387948 ACATTTGTATCTGTTGAACTGTCCTAC 59.612 37.037 0.00 2.14 0.00 3.18
1729 1841 9.295825 TGAACTGTCCTACATTATGTCAATTTT 57.704 29.630 0.00 0.00 0.00 1.82
1778 1913 3.746492 ACTAATTTGACCGTTCTCACTGC 59.254 43.478 0.00 0.00 0.00 4.40
1780 1915 1.865865 TTTGACCGTTCTCACTGCTC 58.134 50.000 0.00 0.00 0.00 4.26
1787 1922 1.989165 CGTTCTCACTGCTCTTACTGC 59.011 52.381 0.00 0.00 0.00 4.40
1800 1935 0.950555 TTACTGCCTTGTGCTGCTCG 60.951 55.000 0.00 0.00 42.24 5.03
1804 1939 2.730672 GCCTTGTGCTGCTCGTACG 61.731 63.158 9.53 9.53 36.87 3.67
1808 1946 0.387622 TTGTGCTGCTCGTACGGTAC 60.388 55.000 16.52 8.25 32.70 3.34
1837 1975 1.881973 TGTTGCTCAACTGAAGATGCC 59.118 47.619 13.16 0.00 41.67 4.40
1885 2027 8.956426 GTTGAACTGTCCCAGATTATTTGAATA 58.044 33.333 0.00 0.00 35.18 1.75
1886 2028 9.527157 TTGAACTGTCCCAGATTATTTGAATAA 57.473 29.630 0.00 0.00 35.18 1.40
1887 2029 9.699410 TGAACTGTCCCAGATTATTTGAATAAT 57.301 29.630 8.34 8.34 42.61 1.28
1989 2143 5.356470 AGAGGCATCTTGTATTCTTTTCTGC 59.644 40.000 0.00 0.00 28.57 4.26
2077 2232 5.122396 ACGTTTTCTATCTTGTCCTTGCATC 59.878 40.000 0.00 0.00 0.00 3.91
2081 2236 2.119801 ATCTTGTCCTTGCATCGCTT 57.880 45.000 0.00 0.00 0.00 4.68
2094 2249 3.056962 TGCATCGCTTATTTGCCTTTTGA 60.057 39.130 0.00 0.00 35.51 2.69
2265 2454 2.057922 ACTGTGGAACTGTCCCAGATT 58.942 47.619 14.40 0.00 46.64 2.40
2266 2455 3.248024 ACTGTGGAACTGTCCCAGATTA 58.752 45.455 14.40 0.00 46.64 1.75
2267 2456 3.846588 ACTGTGGAACTGTCCCAGATTAT 59.153 43.478 14.40 0.00 46.64 1.28
2268 2457 4.194640 CTGTGGAACTGTCCCAGATTATG 58.805 47.826 0.00 0.00 44.23 1.90
2269 2458 2.945668 GTGGAACTGTCCCAGATTATGC 59.054 50.000 0.00 0.00 44.23 3.14
2320 2552 8.715191 AAAAACAAGTGCATGTCATTCTAAAA 57.285 26.923 0.00 0.00 31.81 1.52
2324 2569 8.891671 ACAAGTGCATGTCATTCTAAAATTTT 57.108 26.923 8.75 8.75 0.00 1.82
2326 2571 7.801547 AGTGCATGTCATTCTAAAATTTTCG 57.198 32.000 6.72 0.90 0.00 3.46
2364 2609 5.178797 GTTCAGAGGCAGCTTGTATTCTTA 58.821 41.667 0.00 0.00 0.00 2.10
2385 2630 9.967346 TTCTTATCTGTAAAATCTCGTATCCTG 57.033 33.333 0.00 0.00 0.00 3.86
2386 2631 9.132923 TCTTATCTGTAAAATCTCGTATCCTGT 57.867 33.333 0.00 0.00 0.00 4.00
2405 2650 1.803555 GTGAGAAAGAGCTTCAGGCAC 59.196 52.381 0.00 0.00 44.79 5.01
2542 2802 3.557595 GGTTTGTGAATCATAGGAGCTCG 59.442 47.826 7.83 0.00 0.00 5.03
2553 2813 2.445682 AGGAGCTCGAGACCTGTAAT 57.554 50.000 24.04 6.44 32.39 1.89
2809 3069 6.037172 GGTTGGTGAGTATTGCACTACTATTG 59.963 42.308 15.93 0.00 37.72 1.90
2816 3076 1.624487 TGCACTACTATTGCACGTCG 58.376 50.000 0.00 0.00 45.06 5.12
2978 3243 4.448537 AGATGAAGAGTTCGAGTCCAAG 57.551 45.455 0.00 0.00 0.00 3.61
3152 3417 0.322975 AGCTGCGAACTCAAGATGGT 59.677 50.000 0.00 0.00 0.00 3.55
3291 3558 6.261826 TGCTAAGAACTAACCTATCGGTAGAC 59.738 42.308 3.68 0.00 44.73 2.59
3407 3679 4.263905 ACAAGATGGCAAGTAGGATTTGGA 60.264 41.667 0.00 0.00 0.00 3.53
3417 3689 0.981183 AGGATTTGGAGCGTGGTGTA 59.019 50.000 0.00 0.00 0.00 2.90
3542 3863 6.377146 TGTGTCTGTCTGCTACTACATATTGA 59.623 38.462 0.00 0.00 30.69 2.57
3623 4059 7.333323 CAGGAAATGATTCTTTGGCCTAAAAT 58.667 34.615 3.32 5.73 35.79 1.82
3808 4359 9.823098 GTATCTCTTGTATACATAAGTGTACCG 57.177 37.037 6.36 0.00 43.21 4.02
3880 4431 1.421646 AGTTTGTTCCCCTCAGTCCTG 59.578 52.381 0.00 0.00 0.00 3.86
3913 4464 9.135843 GTTATTCATGCAAACCATATCATCATG 57.864 33.333 0.00 0.00 31.47 3.07
3916 4467 7.533289 TCATGCAAACCATATCATCATGATT 57.467 32.000 5.19 0.00 38.26 2.57
3917 4468 7.599171 TCATGCAAACCATATCATCATGATTC 58.401 34.615 5.19 0.00 38.26 2.52
4046 4603 0.817634 TGTTGTTCAGGAACCTGCCG 60.818 55.000 15.20 0.00 43.31 5.69
4061 4618 1.658409 GCCGTTGTGCAGAGCAAAC 60.658 57.895 0.00 0.85 41.47 2.93
4094 4651 1.535896 GAAAGCCGGTGAAAGAACCTC 59.464 52.381 1.90 0.00 38.14 3.85
4113 4670 2.230025 CTCGAGAAGGAGAAACTGAGCA 59.770 50.000 6.58 0.00 36.08 4.26
4162 4719 2.885644 CAGCGACGGGTTGATCGG 60.886 66.667 0.00 0.00 38.78 4.18
4175 4732 1.519455 GATCGGTCCGCTGAACTGG 60.519 63.158 6.34 0.00 33.10 4.00
4181 4738 3.726517 CCGCTGAACTGGTTGCCG 61.727 66.667 0.00 0.00 0.00 5.69
4197 4754 1.000385 TGCCGTCAAGATGCCTTTTTG 60.000 47.619 0.00 0.00 0.00 2.44
4215 4772 6.147656 CCTTTTTGGAAATGTGGAATGTTAGC 59.852 38.462 0.00 0.00 38.35 3.09
4219 4776 5.015515 TGGAAATGTGGAATGTTAGCATGA 58.984 37.500 0.00 0.00 35.15 3.07
4234 4791 9.866655 ATGTTAGCATGAAGGAAAATAATCCTA 57.133 29.630 0.00 0.00 40.37 2.94
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 2.985117 ATGTGTGTGCTGCATGCGG 61.985 57.895 22.66 22.66 46.63 5.69
1 2 1.799916 CATGTGTGTGCTGCATGCG 60.800 57.895 14.09 9.16 46.63 4.73
2 3 0.319211 AACATGTGTGTGCTGCATGC 60.319 50.000 11.82 11.82 42.50 4.06
3 4 2.143008 AAACATGTGTGTGCTGCATG 57.857 45.000 5.27 0.78 43.84 4.06
4 5 4.524316 ATTAAACATGTGTGTGCTGCAT 57.476 36.364 5.27 0.00 38.92 3.96
5 6 5.444663 TTATTAAACATGTGTGTGCTGCA 57.555 34.783 0.00 0.00 38.92 4.41
6 7 8.633075 ATTATTATTAAACATGTGTGTGCTGC 57.367 30.769 0.00 0.00 38.92 5.25
41 42 6.770378 CGAAATTCGCAACACACCAAGTGA 62.770 45.833 1.35 0.00 41.24 3.41
42 43 4.622978 CGAAATTCGCAACACACCAAGTG 61.623 47.826 1.35 0.00 43.09 3.16
43 44 2.540769 CGAAATTCGCAACACACCAAGT 60.541 45.455 1.35 0.00 31.14 3.16
44 45 2.043411 CGAAATTCGCAACACACCAAG 58.957 47.619 1.35 0.00 31.14 3.61
45 46 1.402259 ACGAAATTCGCAACACACCAA 59.598 42.857 15.90 0.00 45.12 3.67
46 47 1.003331 GACGAAATTCGCAACACACCA 60.003 47.619 15.90 0.00 45.12 4.17
47 48 1.662026 GGACGAAATTCGCAACACACC 60.662 52.381 15.90 4.40 45.12 4.16
48 49 1.003331 TGGACGAAATTCGCAACACAC 60.003 47.619 15.90 0.00 45.12 3.82
49 50 1.262950 CTGGACGAAATTCGCAACACA 59.737 47.619 15.90 6.60 45.12 3.72
50 51 1.950472 CTGGACGAAATTCGCAACAC 58.050 50.000 15.90 2.20 45.12 3.32
51 52 0.237235 GCTGGACGAAATTCGCAACA 59.763 50.000 15.90 10.67 45.12 3.33
52 53 0.517316 AGCTGGACGAAATTCGCAAC 59.483 50.000 15.90 6.46 45.12 4.17
53 54 1.069296 CAAGCTGGACGAAATTCGCAA 60.069 47.619 15.90 1.17 45.12 4.85
54 55 0.516877 CAAGCTGGACGAAATTCGCA 59.483 50.000 15.90 5.45 45.12 5.10
55 56 0.179189 CCAAGCTGGACGAAATTCGC 60.179 55.000 15.90 8.17 45.12 4.70
56 57 1.135972 CACCAAGCTGGACGAAATTCG 60.136 52.381 14.35 14.35 40.96 3.34
57 58 1.401539 GCACCAAGCTGGACGAAATTC 60.402 52.381 8.91 0.00 40.96 2.17
58 59 0.598065 GCACCAAGCTGGACGAAATT 59.402 50.000 8.91 0.00 40.96 1.82
59 60 1.244019 GGCACCAAGCTGGACGAAAT 61.244 55.000 8.91 0.00 40.96 2.17
60 61 1.896660 GGCACCAAGCTGGACGAAA 60.897 57.895 8.91 0.00 40.96 3.46
61 62 2.281484 GGCACCAAGCTGGACGAA 60.281 61.111 8.91 0.00 40.96 3.85
62 63 2.731691 GAAGGCACCAAGCTGGACGA 62.732 60.000 8.91 0.00 40.96 4.20
63 64 2.281761 AAGGCACCAAGCTGGACG 60.282 61.111 8.91 1.88 40.96 4.79
64 65 0.610232 ATGAAGGCACCAAGCTGGAC 60.610 55.000 8.91 1.62 40.96 4.02
65 66 0.991146 TATGAAGGCACCAAGCTGGA 59.009 50.000 8.91 0.00 40.96 3.86
66 67 1.340405 ACTATGAAGGCACCAAGCTGG 60.340 52.381 0.00 0.00 45.02 4.85
67 68 2.119801 ACTATGAAGGCACCAAGCTG 57.880 50.000 0.00 0.00 44.79 4.24
68 69 2.307098 AGAACTATGAAGGCACCAAGCT 59.693 45.455 0.00 0.00 44.79 3.74
69 70 2.716217 AGAACTATGAAGGCACCAAGC 58.284 47.619 0.00 0.00 44.65 4.01
70 71 5.491982 AGTAAGAACTATGAAGGCACCAAG 58.508 41.667 0.00 0.00 32.84 3.61
71 72 5.488341 GAGTAAGAACTATGAAGGCACCAA 58.512 41.667 0.00 0.00 35.56 3.67
72 73 4.081087 GGAGTAAGAACTATGAAGGCACCA 60.081 45.833 0.00 0.00 35.56 4.17
73 74 4.443621 GGAGTAAGAACTATGAAGGCACC 58.556 47.826 0.00 0.00 35.56 5.01
74 75 4.113354 CGGAGTAAGAACTATGAAGGCAC 58.887 47.826 0.00 0.00 35.56 5.01
75 76 4.021229 TCGGAGTAAGAACTATGAAGGCA 58.979 43.478 0.00 0.00 35.56 4.75
76 77 4.650754 TCGGAGTAAGAACTATGAAGGC 57.349 45.455 0.00 0.00 35.56 4.35
77 78 8.494016 AAAATTCGGAGTAAGAACTATGAAGG 57.506 34.615 0.00 0.00 35.56 3.46
117 118 6.873076 GCTGCTGCTTAGATAAGAACTATGAT 59.127 38.462 8.53 0.00 35.33 2.45
152 153 8.984764 GCGGTTGTAGTATGATTGTCATATAAA 58.015 33.333 3.26 0.00 40.97 1.40
162 177 5.645929 TGTTTGATGCGGTTGTAGTATGATT 59.354 36.000 0.00 0.00 0.00 2.57
163 178 5.182487 TGTTTGATGCGGTTGTAGTATGAT 58.818 37.500 0.00 0.00 0.00 2.45
168 183 2.292292 GGTTGTTTGATGCGGTTGTAGT 59.708 45.455 0.00 0.00 0.00 2.73
176 191 1.130955 GTGCTTGGTTGTTTGATGCG 58.869 50.000 0.00 0.00 0.00 4.73
178 193 2.886862 TGGTGCTTGGTTGTTTGATG 57.113 45.000 0.00 0.00 0.00 3.07
196 211 4.036567 ACGGTGAATCATGATGCATTTG 57.963 40.909 19.55 13.91 0.00 2.32
207 222 1.589630 CCAGGTCGACGGTGAATCA 59.410 57.895 16.02 0.00 0.00 2.57
235 250 2.028476 CAGGTTCGTGGATTGGTAGTGA 60.028 50.000 0.00 0.00 0.00 3.41
261 276 3.706086 AGAGGTTGCTGTTGAAAATTGGT 59.294 39.130 0.00 0.00 0.00 3.67
270 285 2.549754 CAGTGGTTAGAGGTTGCTGTTG 59.450 50.000 0.00 0.00 0.00 3.33
280 295 5.122396 CCGATTTTTCTTCCAGTGGTTAGAG 59.878 44.000 9.54 3.87 0.00 2.43
282 297 5.001232 TCCGATTTTTCTTCCAGTGGTTAG 58.999 41.667 9.54 8.30 0.00 2.34
284 299 3.827722 TCCGATTTTTCTTCCAGTGGTT 58.172 40.909 9.54 0.00 0.00 3.67
285 300 3.502123 TCCGATTTTTCTTCCAGTGGT 57.498 42.857 9.54 0.00 0.00 4.16
289 304 4.503741 TGCTTTCCGATTTTTCTTCCAG 57.496 40.909 0.00 0.00 0.00 3.86
290 305 4.927978 TTGCTTTCCGATTTTTCTTCCA 57.072 36.364 0.00 0.00 0.00 3.53
292 307 5.656537 CGTTTTGCTTTCCGATTTTTCTTC 58.343 37.500 0.00 0.00 0.00 2.87
294 309 3.489416 GCGTTTTGCTTTCCGATTTTTCT 59.511 39.130 0.00 0.00 41.73 2.52
296 311 2.542178 GGCGTTTTGCTTTCCGATTTTT 59.458 40.909 0.00 0.00 45.43 1.94
301 316 0.030101 CAAGGCGTTTTGCTTTCCGA 59.970 50.000 0.00 0.00 41.57 4.55
303 318 2.438868 ATCAAGGCGTTTTGCTTTCC 57.561 45.000 0.00 0.00 41.57 3.13
311 326 1.956477 ACTTGCTGAATCAAGGCGTTT 59.044 42.857 8.17 0.00 45.72 3.60
315 330 4.331168 CACTAGTACTTGCTGAATCAAGGC 59.669 45.833 0.00 0.00 45.72 4.35
316 331 4.331168 GCACTAGTACTTGCTGAATCAAGG 59.669 45.833 11.53 0.00 45.72 3.61
353 375 2.572284 GACCCCTCCGTCTTCACG 59.428 66.667 0.00 0.00 46.29 4.35
663 691 1.760875 CGATCGGGGGAGGGAGAAA 60.761 63.158 7.38 0.00 0.00 2.52
664 692 2.123425 CGATCGGGGGAGGGAGAA 60.123 66.667 7.38 0.00 0.00 2.87
665 693 4.220163 CCGATCGGGGGAGGGAGA 62.220 72.222 26.95 0.00 0.00 3.71
666 694 4.541648 ACCGATCGGGGGAGGGAG 62.542 72.222 35.87 9.78 41.60 4.30
667 695 4.534824 GACCGATCGGGGGAGGGA 62.535 72.222 35.87 0.00 41.60 4.20
668 696 4.853142 TGACCGATCGGGGGAGGG 62.853 72.222 35.87 11.28 41.60 4.30
669 697 2.762459 TTGACCGATCGGGGGAGG 60.762 66.667 35.87 12.03 41.60 4.30
670 698 2.017559 GAGTTGACCGATCGGGGGAG 62.018 65.000 35.87 12.79 41.60 4.30
671 699 2.038329 AGTTGACCGATCGGGGGA 59.962 61.111 35.87 18.90 41.60 4.81
672 700 2.499685 GAGTTGACCGATCGGGGG 59.500 66.667 35.87 13.56 41.60 5.40
673 701 2.104331 CGAGTTGACCGATCGGGG 59.896 66.667 35.87 14.32 41.60 5.73
674 702 1.516386 CACGAGTTGACCGATCGGG 60.516 63.158 35.87 19.44 40.67 5.14
675 703 1.071019 CACACGAGTTGACCGATCGG 61.071 60.000 32.20 32.20 40.67 4.18
676 704 0.109919 TCACACGAGTTGACCGATCG 60.110 55.000 8.51 8.51 42.04 3.69
677 705 1.719780 GTTCACACGAGTTGACCGATC 59.280 52.381 0.00 0.00 0.00 3.69
678 706 1.604693 GGTTCACACGAGTTGACCGAT 60.605 52.381 0.00 0.00 0.00 4.18
679 707 0.249155 GGTTCACACGAGTTGACCGA 60.249 55.000 0.00 0.00 0.00 4.69
680 708 0.528901 TGGTTCACACGAGTTGACCG 60.529 55.000 9.09 0.00 34.43 4.79
693 721 1.762858 TGGACTCGTGGGTGGTTCA 60.763 57.895 0.00 0.00 0.00 3.18
737 779 3.846405 TTCTCTGGACCGGCCCACT 62.846 63.158 4.87 0.00 34.97 4.00
921 972 2.754664 CTTGGAGGCAGGCGAAGGTT 62.755 60.000 0.00 0.00 0.00 3.50
922 973 3.249189 TTGGAGGCAGGCGAAGGT 61.249 61.111 0.00 0.00 0.00 3.50
926 977 1.302511 GTTTCTTGGAGGCAGGCGA 60.303 57.895 0.00 0.00 0.00 5.54
972 1028 3.610669 CCTCGATCCCGGAGCAGG 61.611 72.222 0.73 5.26 36.24 4.85
1234 1320 4.091453 ACACAAGAAAGAAAACACACGG 57.909 40.909 0.00 0.00 0.00 4.94
1240 1326 3.366422 TGCGCAAACACAAGAAAGAAAAC 59.634 39.130 8.16 0.00 0.00 2.43
1254 1342 2.505557 GCTCAGGCATGCGCAAAC 60.506 61.111 17.11 9.72 41.24 2.93
1352 1440 1.673808 GCGTACTTGACCTCGGGGAT 61.674 60.000 9.33 0.00 36.25 3.85
1409 1505 2.723322 TCAGGCAAGGGAGATTGATG 57.277 50.000 0.00 0.00 31.55 3.07
1410 1506 3.054576 AGATCAGGCAAGGGAGATTGAT 58.945 45.455 0.00 0.00 31.55 2.57
1412 1508 2.092538 ACAGATCAGGCAAGGGAGATTG 60.093 50.000 0.00 0.00 0.00 2.67
1413 1509 2.203584 ACAGATCAGGCAAGGGAGATT 58.796 47.619 0.00 0.00 0.00 2.40
1414 1510 1.890552 ACAGATCAGGCAAGGGAGAT 58.109 50.000 0.00 0.00 0.00 2.75
1461 1558 5.476945 ACAGGAAACAGGTGCCTTTATTTAG 59.523 40.000 0.00 0.00 0.00 1.85
1463 1560 4.039124 CACAGGAAACAGGTGCCTTTATTT 59.961 41.667 0.00 0.00 32.41 1.40
1470 1567 1.620822 AATCACAGGAAACAGGTGCC 58.379 50.000 0.00 0.00 37.68 5.01
1482 1579 4.142403 ACCGTATGGATGCAAAAATCACAG 60.142 41.667 8.33 0.00 39.21 3.66
1497 1594 0.809385 ACGACACAGAGACCGTATGG 59.191 55.000 0.00 0.00 42.84 2.74
1506 1603 1.734477 CGCAAGGGACGACACAGAG 60.734 63.158 0.00 0.00 0.00 3.35
1601 1698 3.779759 CAGTAAGAAGAGCGAGCAGAAT 58.220 45.455 0.00 0.00 0.00 2.40
1603 1700 1.135257 GCAGTAAGAAGAGCGAGCAGA 60.135 52.381 0.00 0.00 0.00 4.26
1656 1756 2.559698 TCTTCATTTCCGCAACAGGA 57.440 45.000 0.00 0.00 38.79 3.86
1657 1757 2.749076 TCATCTTCATTTCCGCAACAGG 59.251 45.455 0.00 0.00 0.00 4.00
1658 1758 4.142534 ACATCATCTTCATTTCCGCAACAG 60.143 41.667 0.00 0.00 0.00 3.16
1660 1760 4.361451 ACATCATCTTCATTTCCGCAAC 57.639 40.909 0.00 0.00 0.00 4.17
1661 1761 5.389859 AAACATCATCTTCATTTCCGCAA 57.610 34.783 0.00 0.00 0.00 4.85
1664 1764 9.490663 GTAAAGTAAACATCATCTTCATTTCCG 57.509 33.333 0.00 0.00 0.00 4.30
1688 1789 7.450074 AGGACAGTTCAACAGATACAAATGTA 58.550 34.615 0.00 0.00 34.67 2.29
1695 1796 9.035607 CATAATGTAGGACAGTTCAACAGATAC 57.964 37.037 0.00 0.00 0.00 2.24
1743 1855 6.921307 CGGTCAAATTAGTTGCCTTTACTTTT 59.079 34.615 4.90 0.00 37.13 2.27
1744 1856 6.040054 ACGGTCAAATTAGTTGCCTTTACTTT 59.960 34.615 4.90 0.00 37.13 2.66
1752 1886 3.500680 TGAGAACGGTCAAATTAGTTGCC 59.499 43.478 1.87 0.00 37.13 4.52
1760 1894 2.037772 AGAGCAGTGAGAACGGTCAAAT 59.962 45.455 1.87 0.00 0.00 2.32
1768 1902 2.028567 AGGCAGTAAGAGCAGTGAGAAC 60.029 50.000 0.00 0.00 0.00 3.01
1787 1922 2.094659 CCGTACGAGCAGCACAAGG 61.095 63.158 18.76 0.00 0.00 3.61
1804 1939 2.452767 GCAACAGGCTGTACGTACC 58.547 57.895 22.37 7.92 40.25 3.34
1989 2143 9.860898 CCTTTTGTTTTAGGATAGGAGATTTTG 57.139 33.333 0.00 0.00 33.13 2.44
2064 2218 4.100529 CAAATAAGCGATGCAAGGACAAG 58.899 43.478 0.00 0.00 0.00 3.16
2077 2232 4.484236 TCACATCAAAAGGCAAATAAGCG 58.516 39.130 0.00 0.00 34.64 4.68
2081 2236 5.394443 GCCATCTCACATCAAAAGGCAAATA 60.394 40.000 0.00 0.00 40.50 1.40
2094 2249 5.533903 GGATAAATCAGTTGCCATCTCACAT 59.466 40.000 0.00 0.00 0.00 3.21
2144 2332 6.713792 AAAAACAGCGAGTAAAAAGCAAAA 57.286 29.167 0.00 0.00 0.00 2.44
2306 2538 6.585702 TGGCACGAAAATTTTAGAATGACATG 59.414 34.615 16.66 4.99 0.00 3.21
2311 2543 6.616260 GCAGTTGGCACGAAAATTTTAGAATG 60.616 38.462 16.66 7.47 43.97 2.67
2326 2571 3.323258 TCTGAACAGAAGCAGTTGGCAC 61.323 50.000 1.79 0.00 37.49 5.01
2364 2609 7.285629 TCTCACAGGATACGAGATTTTACAGAT 59.714 37.037 0.00 0.00 46.39 2.90
2385 2630 1.803555 GTGCCTGAAGCTCTTTCTCAC 59.196 52.381 0.00 0.00 44.23 3.51
2386 2631 1.696336 AGTGCCTGAAGCTCTTTCTCA 59.304 47.619 0.00 0.00 42.62 3.27
2405 2650 4.130118 GGGACAATACTACAATGGCTCAG 58.870 47.826 0.00 0.00 0.00 3.35
2542 2802 4.339814 ACGATGGAAGAGATTACAGGTCTC 59.660 45.833 0.00 0.00 41.89 3.36
2553 2813 6.037786 AGTTATTTCACACGATGGAAGAGA 57.962 37.500 0.00 0.00 0.00 3.10
2809 3069 1.464023 CCATGAATTCACACGACGTGC 60.464 52.381 27.11 10.69 45.92 5.34
2811 3071 0.796312 GCCATGAATTCACACGACGT 59.204 50.000 11.07 0.00 0.00 4.34
2812 3072 1.061131 GAGCCATGAATTCACACGACG 59.939 52.381 11.07 0.00 0.00 5.12
2816 3076 2.938451 TCGATGAGCCATGAATTCACAC 59.062 45.455 11.07 3.15 0.00 3.82
2820 3084 4.514441 ACAAGATCGATGAGCCATGAATTC 59.486 41.667 0.54 0.00 0.00 2.17
2828 3092 4.021544 AGGAGAATACAAGATCGATGAGCC 60.022 45.833 0.54 0.00 0.00 4.70
3096 3361 7.435488 CAGATATTAGTGTCCAGTAGGTTTTCG 59.565 40.741 0.00 0.00 35.89 3.46
3291 3558 3.359950 ACCCAACTCCTAACTAGTACCG 58.640 50.000 0.00 0.00 0.00 4.02
3379 3651 3.263170 TCCTACTTGCCATCTTGTAAGCA 59.737 43.478 0.00 0.00 0.00 3.91
3407 3679 0.951558 CAAAAGCCTTACACCACGCT 59.048 50.000 0.00 0.00 0.00 5.07
3417 3689 5.652452 GGTAATCCTGATACACAAAAGCCTT 59.348 40.000 0.00 0.00 0.00 4.35
3451 3723 4.093850 GGTGGACACGGAAACATATTACAC 59.906 45.833 0.00 0.00 0.00 2.90
3542 3863 8.602472 ACACTAGAGACTTCATTTAGGAAGAT 57.398 34.615 10.74 0.00 45.66 2.40
3623 4059 9.182214 CTAGTGTAGGACTTTAGGTACATACAA 57.818 37.037 0.00 0.00 35.96 2.41
3644 4186 3.866651 CCATTGTGTCCTTCTCCTAGTG 58.133 50.000 0.00 0.00 0.00 2.74
3880 4431 6.012658 TGGTTTGCATGAATAACTTCTGAC 57.987 37.500 0.00 0.00 32.29 3.51
3913 4464 8.424731 CCGCTTACATTGTTTACTTTTTGAATC 58.575 33.333 0.00 0.00 0.00 2.52
3916 4467 7.028926 TCCGCTTACATTGTTTACTTTTTGA 57.971 32.000 0.00 0.00 0.00 2.69
3917 4468 6.129194 GCTCCGCTTACATTGTTTACTTTTTG 60.129 38.462 0.00 0.00 0.00 2.44
3931 4485 0.108992 AACGAATCGCTCCGCTTACA 60.109 50.000 1.15 0.00 0.00 2.41
4046 4603 2.223144 TGATACGTTTGCTCTGCACAAC 59.777 45.455 0.00 0.64 38.71 3.32
4061 4618 1.806623 CGGCTTTCTTCCCCTGATACG 60.807 57.143 0.00 0.00 0.00 3.06
4094 4651 2.029470 AGTGCTCAGTTTCTCCTTCTCG 60.029 50.000 0.00 0.00 0.00 4.04
4162 4719 2.617274 GGCAACCAGTTCAGCGGAC 61.617 63.158 0.00 0.00 0.00 4.79
4175 4732 0.598065 AAAGGCATCTTGACGGCAAC 59.402 50.000 0.00 0.00 32.75 4.17
4181 4738 5.178067 CACATTTCCAAAAAGGCATCTTGAC 59.822 40.000 0.00 0.00 37.29 3.18
4197 4754 5.581126 TCATGCTAACATTCCACATTTCC 57.419 39.130 0.00 0.00 32.87 3.13
4215 4772 9.578576 TTCATCCTAGGATTATTTTCCTTCATG 57.421 33.333 22.29 7.20 43.88 3.07


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

AutoCloner maintained by Alex Coulton.