Multiple sequence alignment - TraesCS2D01G569600

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 TraesCS2D01G569600 chr2D 100.000 2604 0 0 636 3239 637386470 637383867 0.000000e+00 4809.0
1 TraesCS2D01G569600 chr2D 85.373 1463 135 23 846 2270 637354415 637352994 0.000000e+00 1443.0
2 TraesCS2D01G569600 chr2D 77.987 1540 242 43 1040 2506 636740737 636742252 0.000000e+00 876.0
3 TraesCS2D01G569600 chr2D 77.987 1540 242 43 1040 2506 636887666 636886151 0.000000e+00 876.0
4 TraesCS2D01G569600 chr2D 78.623 1249 202 40 1045 2245 636946928 636945697 0.000000e+00 767.0
5 TraesCS2D01G569600 chr2D 100.000 258 0 0 1 258 637387105 637386848 8.130000e-131 477.0
6 TraesCS2D01G569600 chr2D 96.538 260 7 2 1 258 603695525 603695784 2.310000e-116 429.0
7 TraesCS2D01G569600 chr2D 90.431 209 18 1 636 842 469999063 469999271 1.140000e-69 274.0
8 TraesCS2D01G569600 chr2D 81.783 258 43 3 1817 2071 638314501 638314757 2.530000e-51 213.0
9 TraesCS2D01G569600 chr2D 92.453 106 4 1 2633 2738 75666893 75666994 7.240000e-32 148.0
10 TraesCS2D01G569600 chr2D 93.750 48 2 1 2459 2506 637352913 637352867 1.610000e-08 71.3
11 TraesCS2D01G569600 chrUn 89.467 1481 101 22 940 2386 234389635 234391094 0.000000e+00 1820.0
12 TraesCS2D01G569600 chrUn 95.702 349 11 2 2895 3239 234391528 234391876 2.820000e-155 558.0
13 TraesCS2D01G569600 chrUn 96.479 142 4 1 2735 2876 234391272 234391412 1.940000e-57 233.0
14 TraesCS2D01G569600 chrUn 92.647 68 3 1 2441 2506 234391105 234391172 2.660000e-16 97.1
15 TraesCS2D01G569600 chrUn 94.444 54 3 0 2506 2559 234391211 234391264 2.070000e-12 84.2
16 TraesCS2D01G569600 chr2A 88.551 1380 98 24 901 2248 762659863 762661214 0.000000e+00 1618.0
17 TraesCS2D01G569600 chr2A 89.003 1173 101 19 1349 2506 762744614 762745773 0.000000e+00 1426.0
18 TraesCS2D01G569600 chr2A 79.710 1035 165 23 1043 2055 762720240 762721251 0.000000e+00 706.0
19 TraesCS2D01G569600 chr2A 95.942 345 11 1 2895 3239 762746131 762746472 1.020000e-154 556.0
20 TraesCS2D01G569600 chr2A 88.713 443 24 12 2511 2927 762661583 762662025 4.790000e-143 518.0
21 TraesCS2D01G569600 chr2A 89.189 370 10 5 2874 3239 762662013 762662356 4.960000e-118 435.0
22 TraesCS2D01G569600 chr2A 80.426 516 75 15 1116 1612 762878225 762878733 1.420000e-98 370.0
23 TraesCS2D01G569600 chr2A 78.756 579 95 21 1679 2252 763057417 763056862 2.380000e-96 363.0
24 TraesCS2D01G569600 chr2A 87.308 260 12 7 2253 2506 762661286 762661530 8.850000e-71 278.0
25 TraesCS2D01G569600 chr2A 97.183 142 4 0 2735 2876 762745873 762746014 1.160000e-59 241.0
26 TraesCS2D01G569600 chr2A 94.444 54 3 0 2506 2559 762745812 762745865 2.070000e-12 84.2
27 TraesCS2D01G569600 chr2B 77.725 1046 184 31 1058 2071 797177709 797178737 2.150000e-166 595.0
28 TraesCS2D01G569600 chr2B 83.123 397 59 7 1679 2071 794490822 794491214 3.970000e-94 355.0
29 TraesCS2D01G569600 chr2B 81.586 353 54 7 1839 2191 794767457 794767116 6.840000e-72 281.0
30 TraesCS2D01G569600 chr2B 75.155 644 102 34 1646 2248 797255919 797256545 1.930000e-62 250.0
31 TraesCS2D01G569600 chr2B 74.725 637 114 34 1646 2248 797209524 797210147 1.160000e-59 241.0
32 TraesCS2D01G569600 chr2B 75.529 425 73 25 1675 2089 796165239 796165642 2.570000e-41 180.0
33 TraesCS2D01G569600 chr2B 97.260 73 2 0 2531 2603 794675422 794675350 1.220000e-24 124.0
34 TraesCS2D01G569600 chr2B 97.778 45 1 0 2902 2946 794380966 794381010 9.630000e-11 78.7
35 TraesCS2D01G569600 chr7A 94.961 258 13 0 1 258 211210794 211211051 3.890000e-109 405.0
36 TraesCS2D01G569600 chr7D 94.942 257 12 1 1 256 182601010 182601266 5.030000e-108 401.0
37 TraesCS2D01G569600 chr7D 94.595 259 12 2 1 258 474003242 474002985 1.810000e-107 399.0
38 TraesCS2D01G569600 chr5D 95.618 251 10 1 1 250 543593856 543593606 5.030000e-108 401.0
39 TraesCS2D01G569600 chr5D 94.595 259 12 2 1 258 57215423 57215680 1.810000e-107 399.0
40 TraesCS2D01G569600 chr5D 91.262 206 16 2 636 839 552635915 552636120 2.460000e-71 279.0
41 TraesCS2D01G569600 chr5D 90.541 74 7 0 2530 2603 565751514 565751441 7.400000e-17 99.0
42 TraesCS2D01G569600 chr1D 94.942 257 12 1 1 256 423279556 423279300 5.030000e-108 401.0
43 TraesCS2D01G569600 chr1D 94.595 259 13 1 1 258 9004907 9004649 1.810000e-107 399.0
44 TraesCS2D01G569600 chr1D 91.262 206 16 1 636 839 423279250 423279045 2.460000e-71 279.0
45 TraesCS2D01G569600 chr4D 94.595 259 13 1 1 258 41197630 41197372 1.810000e-107 399.0
46 TraesCS2D01G569600 chr6D 91.121 214 17 1 636 847 420557005 420556792 4.090000e-74 289.0
47 TraesCS2D01G569600 chr6D 90.821 207 17 1 639 843 24575008 24575214 3.180000e-70 276.0
48 TraesCS2D01G569600 chr6D 90.777 206 17 1 636 839 10676372 10676577 1.140000e-69 274.0
49 TraesCS2D01G569600 chr6D 91.045 67 6 0 2545 2611 445175421 445175355 1.240000e-14 91.6
50 TraesCS2D01G569600 chr6D 100.000 38 0 0 2906 2943 436376161 436376198 1.610000e-08 71.3
51 TraesCS2D01G569600 chr1B 91.748 206 15 1 636 839 675985867 675986072 5.290000e-73 285.0
52 TraesCS2D01G569600 chr5B 90.909 209 15 3 636 842 485077365 485077571 8.850000e-71 278.0
53 TraesCS2D01G569600 chr6A 90.431 209 18 1 636 842 286335633 286335425 1.140000e-69 274.0
54 TraesCS2D01G569600 chr7B 98.630 73 1 0 2531 2603 746124946 746124874 2.620000e-26 130.0
55 TraesCS2D01G569600 chr7B 85.556 90 6 4 2911 2993 746124846 746124757 1.600000e-13 87.9
56 TraesCS2D01G569600 chr7B 93.750 48 2 1 2459 2506 746126480 746126434 1.610000e-08 71.3
57 TraesCS2D01G569600 chr4B 90.909 77 7 0 2535 2611 546685170 546685246 1.590000e-18 104.0
58 TraesCS2D01G569600 chr6B 100.000 40 0 0 2904 2943 659608234 659608273 1.250000e-09 75.0
59 TraesCS2D01G569600 chr3A 97.143 35 0 1 1557 1590 9500676 9500710 1.260000e-04 58.4


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 TraesCS2D01G569600 chr2D 637383867 637387105 3238 True 2643.00 4809 100.00000 1 3239 2 chr2D.!!$R4 3238
1 TraesCS2D01G569600 chr2D 636740737 636742252 1515 False 876.00 876 77.98700 1040 2506 1 chr2D.!!$F4 1466
2 TraesCS2D01G569600 chr2D 636886151 636887666 1515 True 876.00 876 77.98700 1040 2506 1 chr2D.!!$R1 1466
3 TraesCS2D01G569600 chr2D 636945697 636946928 1231 True 767.00 767 78.62300 1045 2245 1 chr2D.!!$R2 1200
4 TraesCS2D01G569600 chr2D 637352867 637354415 1548 True 757.15 1443 89.56150 846 2506 2 chr2D.!!$R3 1660
5 TraesCS2D01G569600 chrUn 234389635 234391876 2241 False 558.46 1820 93.74780 940 3239 5 chrUn.!!$F1 2299
6 TraesCS2D01G569600 chr2A 762659863 762662356 2493 False 712.25 1618 88.44025 901 3239 4 chr2A.!!$F3 2338
7 TraesCS2D01G569600 chr2A 762720240 762721251 1011 False 706.00 706 79.71000 1043 2055 1 chr2A.!!$F1 1012
8 TraesCS2D01G569600 chr2A 762744614 762746472 1858 False 576.80 1426 94.14300 1349 3239 4 chr2A.!!$F4 1890
9 TraesCS2D01G569600 chr2A 762878225 762878733 508 False 370.00 370 80.42600 1116 1612 1 chr2A.!!$F2 496
10 TraesCS2D01G569600 chr2A 763056862 763057417 555 True 363.00 363 78.75600 1679 2252 1 chr2A.!!$R1 573
11 TraesCS2D01G569600 chr2B 797177709 797178737 1028 False 595.00 595 77.72500 1058 2071 1 chr2B.!!$F4 1013
12 TraesCS2D01G569600 chr2B 797255919 797256545 626 False 250.00 250 75.15500 1646 2248 1 chr2B.!!$F6 602
13 TraesCS2D01G569600 chr2B 797209524 797210147 623 False 241.00 241 74.72500 1646 2248 1 chr2B.!!$F5 602
14 TraesCS2D01G569600 chr1D 423279045 423279556 511 True 340.00 401 93.10200 1 839 2 chr1D.!!$R2 838

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
684 685 0.026803 GAGCGGACGCAGCAAATAAG 59.973 55.0 19.48 0.0 44.88 1.73 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2660 3155 0.107165 AAATTACCGGCCCAGAGCTC 60.107 55.0 5.27 5.27 43.05 4.09 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
25 26 6.861065 ACGACAAACTCATCTACAATGTTT 57.139 33.333 0.00 0.00 0.00 2.83
92 93 7.611467 TCATGAAGTTTGAGCAATACATACCTT 59.389 33.333 0.00 0.00 0.00 3.50
93 94 7.144722 TGAAGTTTGAGCAATACATACCTTG 57.855 36.000 0.00 0.00 0.00 3.61
94 95 5.567138 AGTTTGAGCAATACATACCTTGC 57.433 39.130 0.00 0.00 46.32 4.01
98 99 2.781945 GCAATACATACCTTGCAGGC 57.218 50.000 2.60 0.00 45.50 4.85
99 100 1.002468 GCAATACATACCTTGCAGGCG 60.002 52.381 2.60 0.00 45.50 5.52
100 101 2.288666 CAATACATACCTTGCAGGCGT 58.711 47.619 2.50 0.00 39.63 5.68
101 102 2.682856 CAATACATACCTTGCAGGCGTT 59.317 45.455 2.50 0.00 39.63 4.84
102 103 2.483014 TACATACCTTGCAGGCGTTT 57.517 45.000 2.50 0.00 39.63 3.60
103 104 1.616159 ACATACCTTGCAGGCGTTTT 58.384 45.000 2.50 0.00 39.63 2.43
104 105 1.269448 ACATACCTTGCAGGCGTTTTG 59.731 47.619 2.50 1.94 39.63 2.44
105 106 1.269448 CATACCTTGCAGGCGTTTTGT 59.731 47.619 2.50 0.00 39.63 2.83
106 107 0.948678 TACCTTGCAGGCGTTTTGTC 59.051 50.000 2.50 0.00 39.63 3.18
107 108 1.370414 CCTTGCAGGCGTTTTGTCG 60.370 57.895 0.00 0.00 0.00 4.35
108 109 1.646540 CTTGCAGGCGTTTTGTCGA 59.353 52.632 0.00 0.00 0.00 4.20
109 110 0.028770 CTTGCAGGCGTTTTGTCGAA 59.971 50.000 0.00 0.00 0.00 3.71
110 111 0.248296 TTGCAGGCGTTTTGTCGAAC 60.248 50.000 0.00 0.00 0.00 3.95
111 112 1.353804 GCAGGCGTTTTGTCGAACA 59.646 52.632 0.00 0.00 0.00 3.18
112 113 0.928451 GCAGGCGTTTTGTCGAACAC 60.928 55.000 0.00 0.00 0.00 3.32
113 114 0.316689 CAGGCGTTTTGTCGAACACC 60.317 55.000 0.00 0.00 33.03 4.16
114 115 0.463116 AGGCGTTTTGTCGAACACCT 60.463 50.000 0.00 0.00 37.27 4.00
115 116 0.379316 GGCGTTTTGTCGAACACCTT 59.621 50.000 0.00 0.00 30.80 3.50
116 117 1.462791 GCGTTTTGTCGAACACCTTG 58.537 50.000 0.00 0.00 0.00 3.61
117 118 1.462791 CGTTTTGTCGAACACCTTGC 58.537 50.000 0.00 0.00 0.00 4.01
118 119 1.462791 GTTTTGTCGAACACCTTGCG 58.537 50.000 0.00 0.00 0.00 4.85
119 120 0.378962 TTTTGTCGAACACCTTGCGG 59.621 50.000 0.00 0.00 0.00 5.69
120 121 1.440938 TTTGTCGAACACCTTGCGGG 61.441 55.000 0.00 0.00 41.89 6.13
121 122 3.723348 GTCGAACACCTTGCGGGC 61.723 66.667 0.00 0.00 39.10 6.13
155 156 4.524318 CGCCCGGGTGCTATTCGT 62.524 66.667 23.59 0.00 0.00 3.85
156 157 2.588034 GCCCGGGTGCTATTCGTC 60.588 66.667 24.63 0.00 0.00 4.20
157 158 2.279252 CCCGGGTGCTATTCGTCG 60.279 66.667 14.18 0.00 0.00 5.12
158 159 2.279252 CCGGGTGCTATTCGTCGG 60.279 66.667 0.00 0.00 0.00 4.79
159 160 2.777972 CCGGGTGCTATTCGTCGGA 61.778 63.158 0.00 0.00 39.83 4.55
160 161 1.299165 CGGGTGCTATTCGTCGGAG 60.299 63.158 0.00 0.00 0.00 4.63
161 162 1.067582 GGGTGCTATTCGTCGGAGG 59.932 63.158 0.00 0.00 0.00 4.30
162 163 1.389609 GGGTGCTATTCGTCGGAGGA 61.390 60.000 0.00 0.00 0.00 3.71
163 164 0.248949 GGTGCTATTCGTCGGAGGAC 60.249 60.000 0.00 0.00 39.89 3.85
194 195 4.208686 GGGCGGCGGTGACTAGAG 62.209 72.222 9.78 0.00 0.00 2.43
195 196 4.208686 GGCGGCGGTGACTAGAGG 62.209 72.222 9.78 0.00 0.00 3.69
196 197 4.208686 GCGGCGGTGACTAGAGGG 62.209 72.222 9.78 0.00 0.00 4.30
197 198 2.439701 CGGCGGTGACTAGAGGGA 60.440 66.667 0.00 0.00 0.00 4.20
198 199 2.482333 CGGCGGTGACTAGAGGGAG 61.482 68.421 0.00 0.00 0.00 4.30
199 200 2.787567 GGCGGTGACTAGAGGGAGC 61.788 68.421 0.00 0.00 0.00 4.70
200 201 3.111939 CGGTGACTAGAGGGAGCG 58.888 66.667 0.00 0.00 0.00 5.03
201 202 2.482333 CGGTGACTAGAGGGAGCGG 61.482 68.421 0.00 0.00 0.00 5.52
202 203 1.076923 GGTGACTAGAGGGAGCGGA 60.077 63.158 0.00 0.00 0.00 5.54
203 204 1.104577 GGTGACTAGAGGGAGCGGAG 61.105 65.000 0.00 0.00 0.00 4.63
204 205 1.104577 GTGACTAGAGGGAGCGGAGG 61.105 65.000 0.00 0.00 0.00 4.30
205 206 1.279749 TGACTAGAGGGAGCGGAGGA 61.280 60.000 0.00 0.00 0.00 3.71
206 207 0.106619 GACTAGAGGGAGCGGAGGAA 60.107 60.000 0.00 0.00 0.00 3.36
207 208 0.106419 ACTAGAGGGAGCGGAGGAAG 60.106 60.000 0.00 0.00 0.00 3.46
208 209 1.455959 TAGAGGGAGCGGAGGAAGC 60.456 63.158 0.00 0.00 0.00 3.86
209 210 2.930777 TAGAGGGAGCGGAGGAAGCC 62.931 65.000 0.00 0.00 34.64 4.35
236 237 3.165685 CGGGAATAGGCCGGGGAA 61.166 66.667 2.18 0.00 0.00 3.97
237 238 2.836888 GGGAATAGGCCGGGGAAG 59.163 66.667 2.18 0.00 0.00 3.46
238 239 2.113351 GGAATAGGCCGGGGAAGC 59.887 66.667 2.18 0.00 0.00 3.86
239 240 2.280865 GAATAGGCCGGGGAAGCG 60.281 66.667 2.18 0.00 0.00 4.68
240 241 4.564110 AATAGGCCGGGGAAGCGC 62.564 66.667 2.18 0.00 0.00 5.92
681 682 3.127533 GGAGCGGACGCAGCAAAT 61.128 61.111 19.48 0.00 44.88 2.32
682 683 1.813753 GGAGCGGACGCAGCAAATA 60.814 57.895 19.48 0.00 44.88 1.40
683 684 1.366111 GGAGCGGACGCAGCAAATAA 61.366 55.000 19.48 0.00 44.88 1.40
684 685 0.026803 GAGCGGACGCAGCAAATAAG 59.973 55.000 19.48 0.00 44.88 1.73
685 686 1.583709 GCGGACGCAGCAAATAAGC 60.584 57.895 12.31 0.00 41.49 3.09
690 691 2.951227 GCAGCAAATAAGCGGCGC 60.951 61.111 26.86 26.86 45.03 6.53
691 692 2.484662 CAGCAAATAAGCGGCGCA 59.515 55.556 35.02 15.48 40.15 6.09
692 693 1.064621 CAGCAAATAAGCGGCGCAT 59.935 52.632 35.02 25.83 40.15 4.73
693 694 1.064621 AGCAAATAAGCGGCGCATG 59.935 52.632 35.02 22.86 40.15 4.06
694 695 1.063972 GCAAATAAGCGGCGCATGA 59.936 52.632 35.02 18.69 0.00 3.07
695 696 0.318107 GCAAATAAGCGGCGCATGAT 60.318 50.000 35.02 20.17 0.00 2.45
696 697 1.865248 GCAAATAAGCGGCGCATGATT 60.865 47.619 35.02 24.53 0.00 2.57
697 698 2.604373 GCAAATAAGCGGCGCATGATTA 60.604 45.455 35.02 22.83 0.00 1.75
698 699 3.626977 CAAATAAGCGGCGCATGATTAA 58.373 40.909 35.02 6.84 0.00 1.40
699 700 3.542712 AATAAGCGGCGCATGATTAAG 57.457 42.857 35.02 0.00 0.00 1.85
700 701 1.948104 TAAGCGGCGCATGATTAAGT 58.052 45.000 35.02 6.66 0.00 2.24
701 702 1.094785 AAGCGGCGCATGATTAAGTT 58.905 45.000 35.02 13.21 0.00 2.66
702 703 1.094785 AGCGGCGCATGATTAAGTTT 58.905 45.000 35.02 5.17 0.00 2.66
703 704 1.064060 AGCGGCGCATGATTAAGTTTC 59.936 47.619 35.02 0.00 0.00 2.78
704 705 1.730176 CGGCGCATGATTAAGTTTCG 58.270 50.000 10.83 0.00 0.00 3.46
705 706 1.594518 CGGCGCATGATTAAGTTTCGG 60.595 52.381 10.83 0.00 0.00 4.30
706 707 1.466855 GCGCATGATTAAGTTTCGGC 58.533 50.000 0.30 0.00 0.00 5.54
707 708 1.859998 GCGCATGATTAAGTTTCGGCC 60.860 52.381 0.30 0.00 0.00 6.13
708 709 1.268539 CGCATGATTAAGTTTCGGCCC 60.269 52.381 0.00 0.00 0.00 5.80
709 710 1.268539 GCATGATTAAGTTTCGGCCCG 60.269 52.381 0.00 0.00 0.00 6.13
710 711 1.021968 ATGATTAAGTTTCGGCCCGC 58.978 50.000 0.00 0.00 0.00 6.13
711 712 0.035820 TGATTAAGTTTCGGCCCGCT 60.036 50.000 0.00 0.00 0.00 5.52
712 713 0.656259 GATTAAGTTTCGGCCCGCTC 59.344 55.000 0.00 0.00 0.00 5.03
713 714 1.087771 ATTAAGTTTCGGCCCGCTCG 61.088 55.000 0.00 0.00 0.00 5.03
721 722 4.143333 GGCCCGCTCGCTGAACTA 62.143 66.667 0.00 0.00 0.00 2.24
722 723 2.583593 GCCCGCTCGCTGAACTAG 60.584 66.667 0.00 0.00 0.00 2.57
723 724 3.064987 GCCCGCTCGCTGAACTAGA 62.065 63.158 0.00 0.00 0.00 2.43
724 725 1.736586 CCCGCTCGCTGAACTAGAT 59.263 57.895 0.00 0.00 0.00 1.98
725 726 0.952280 CCCGCTCGCTGAACTAGATA 59.048 55.000 0.00 0.00 0.00 1.98
726 727 1.542030 CCCGCTCGCTGAACTAGATAT 59.458 52.381 0.00 0.00 0.00 1.63
727 728 2.590073 CCGCTCGCTGAACTAGATATG 58.410 52.381 0.00 0.00 0.00 1.78
728 729 1.982223 CGCTCGCTGAACTAGATATGC 59.018 52.381 0.00 0.00 0.00 3.14
729 730 2.333014 GCTCGCTGAACTAGATATGCC 58.667 52.381 0.00 0.00 0.00 4.40
730 731 2.590073 CTCGCTGAACTAGATATGCCG 58.410 52.381 0.00 0.00 0.00 5.69
731 732 1.063806 CGCTGAACTAGATATGCCGC 58.936 55.000 0.00 0.00 0.00 6.53
732 733 1.063806 GCTGAACTAGATATGCCGCG 58.936 55.000 0.00 0.00 0.00 6.46
733 734 1.063806 CTGAACTAGATATGCCGCGC 58.936 55.000 0.00 0.00 0.00 6.86
734 735 0.673985 TGAACTAGATATGCCGCGCT 59.326 50.000 5.56 0.00 0.00 5.92
735 736 1.335964 TGAACTAGATATGCCGCGCTC 60.336 52.381 5.56 0.00 0.00 5.03
736 737 0.962489 AACTAGATATGCCGCGCTCT 59.038 50.000 5.56 2.35 0.00 4.09
737 738 0.242286 ACTAGATATGCCGCGCTCTG 59.758 55.000 5.56 0.00 0.00 3.35
738 739 0.242286 CTAGATATGCCGCGCTCTGT 59.758 55.000 5.56 0.00 0.00 3.41
739 740 0.673985 TAGATATGCCGCGCTCTGTT 59.326 50.000 5.56 0.00 0.00 3.16
740 741 0.179073 AGATATGCCGCGCTCTGTTT 60.179 50.000 5.56 0.00 0.00 2.83
741 742 0.657840 GATATGCCGCGCTCTGTTTT 59.342 50.000 5.56 0.00 0.00 2.43
742 743 1.064060 GATATGCCGCGCTCTGTTTTT 59.936 47.619 5.56 0.00 0.00 1.94
743 744 0.167908 TATGCCGCGCTCTGTTTTTG 59.832 50.000 5.56 0.00 0.00 2.44
744 745 3.099574 GCCGCGCTCTGTTTTTGC 61.100 61.111 5.56 0.00 0.00 3.68
748 749 3.514546 CGCTCTGTTTTTGCGTGC 58.485 55.556 0.00 0.00 44.00 5.34
749 750 2.010817 CGCTCTGTTTTTGCGTGCC 61.011 57.895 0.00 0.00 44.00 5.01
750 751 1.661509 GCTCTGTTTTTGCGTGCCC 60.662 57.895 0.00 0.00 0.00 5.36
751 752 1.370414 CTCTGTTTTTGCGTGCCCG 60.370 57.895 0.00 0.00 37.07 6.13
762 763 4.643387 GTGCCCGCTGGAACCACT 62.643 66.667 0.00 0.00 33.46 4.00
763 764 2.925706 TGCCCGCTGGAACCACTA 60.926 61.111 0.00 0.00 0.00 2.74
764 765 2.297895 TGCCCGCTGGAACCACTAT 61.298 57.895 0.00 0.00 0.00 2.12
765 766 0.978667 TGCCCGCTGGAACCACTATA 60.979 55.000 0.00 0.00 0.00 1.31
766 767 0.532196 GCCCGCTGGAACCACTATAC 60.532 60.000 0.00 0.00 0.00 1.47
767 768 0.106149 CCCGCTGGAACCACTATACC 59.894 60.000 0.00 0.00 0.00 2.73
768 769 0.249322 CCGCTGGAACCACTATACCG 60.249 60.000 0.00 0.00 0.00 4.02
769 770 0.249322 CGCTGGAACCACTATACCGG 60.249 60.000 0.00 0.00 0.00 5.28
770 771 0.828677 GCTGGAACCACTATACCGGT 59.171 55.000 13.98 13.98 36.98 5.28
772 773 2.901249 CTGGAACCACTATACCGGTTG 58.099 52.381 15.04 4.29 45.54 3.77
773 774 1.660167 GGAACCACTATACCGGTTGC 58.340 55.000 15.04 5.33 45.54 4.17
774 775 1.283736 GAACCACTATACCGGTTGCG 58.716 55.000 15.04 3.45 45.54 4.85
775 776 0.741927 AACCACTATACCGGTTGCGC 60.742 55.000 15.04 0.00 43.88 6.09
776 777 2.235016 CCACTATACCGGTTGCGCG 61.235 63.158 15.04 0.00 0.00 6.86
777 778 1.517694 CACTATACCGGTTGCGCGT 60.518 57.895 15.04 0.01 0.00 6.01
778 779 1.517694 ACTATACCGGTTGCGCGTG 60.518 57.895 15.04 0.00 0.00 5.34
779 780 2.867091 CTATACCGGTTGCGCGTGC 61.867 63.158 15.04 15.48 43.20 5.34
790 791 2.277247 CGCGTGCGCTAAAATGGG 60.277 61.111 9.73 0.00 39.32 4.00
791 792 2.579518 GCGTGCGCTAAAATGGGC 60.580 61.111 9.73 0.00 44.63 5.36
799 800 4.514545 GCGCTAAAATGGGCAATTTTAC 57.485 40.909 14.42 10.94 44.84 2.01
800 801 3.000177 GCGCTAAAATGGGCAATTTTACG 60.000 43.478 23.14 23.14 44.84 3.18
801 802 3.549873 CGCTAAAATGGGCAATTTTACGG 59.450 43.478 21.45 13.73 44.84 4.02
802 803 3.308595 GCTAAAATGGGCAATTTTACGGC 59.691 43.478 14.42 13.49 44.84 5.68
803 804 2.003196 AAATGGGCAATTTTACGGCG 57.997 45.000 4.80 4.80 34.72 6.46
804 805 0.459411 AATGGGCAATTTTACGGCGC 60.459 50.000 6.90 0.00 40.46 6.53
805 806 2.578445 GGGCAATTTTACGGCGCG 60.578 61.111 6.90 0.00 0.00 6.86
806 807 2.578445 GGCAATTTTACGGCGCGG 60.578 61.111 14.03 14.03 0.00 6.46
807 808 3.244603 GCAATTTTACGGCGCGGC 61.245 61.111 24.49 24.49 0.00 6.53
808 809 2.942022 CAATTTTACGGCGCGGCG 60.942 61.111 46.57 46.57 0.00 6.46
824 825 4.012895 CGCTTGTTTGACGCGGCT 62.013 61.111 15.80 0.00 42.88 5.52
825 826 2.427410 GCTTGTTTGACGCGGCTG 60.427 61.111 15.80 0.00 0.00 4.85
826 827 3.022287 CTTGTTTGACGCGGCTGT 58.978 55.556 15.80 0.00 0.00 4.40
827 828 1.355210 CTTGTTTGACGCGGCTGTT 59.645 52.632 15.80 0.00 0.00 3.16
828 829 0.929824 CTTGTTTGACGCGGCTGTTG 60.930 55.000 15.80 0.00 0.00 3.33
829 830 2.051345 GTTTGACGCGGCTGTTGG 60.051 61.111 15.80 0.00 0.00 3.77
830 831 2.203084 TTTGACGCGGCTGTTGGA 60.203 55.556 15.80 0.00 0.00 3.53
831 832 2.250939 TTTGACGCGGCTGTTGGAG 61.251 57.895 15.80 0.00 0.00 3.86
832 833 2.652382 TTTGACGCGGCTGTTGGAGA 62.652 55.000 15.80 0.00 0.00 3.71
833 834 2.125512 GACGCGGCTGTTGGAGAT 60.126 61.111 12.47 0.00 0.00 2.75
834 835 2.434884 ACGCGGCTGTTGGAGATG 60.435 61.111 12.47 0.00 0.00 2.90
835 836 3.869272 CGCGGCTGTTGGAGATGC 61.869 66.667 0.00 0.00 0.00 3.91
836 837 2.437359 GCGGCTGTTGGAGATGCT 60.437 61.111 0.00 0.00 0.00 3.79
837 838 2.467826 GCGGCTGTTGGAGATGCTC 61.468 63.158 0.00 0.00 0.00 4.26
838 839 1.220206 CGGCTGTTGGAGATGCTCT 59.780 57.895 0.00 0.00 0.00 4.09
839 840 0.392193 CGGCTGTTGGAGATGCTCTT 60.392 55.000 0.00 0.00 0.00 2.85
840 841 1.134699 CGGCTGTTGGAGATGCTCTTA 60.135 52.381 0.00 0.00 0.00 2.10
841 842 2.559440 GGCTGTTGGAGATGCTCTTAG 58.441 52.381 0.00 0.00 0.00 2.18
842 843 2.559440 GCTGTTGGAGATGCTCTTAGG 58.441 52.381 0.00 0.00 0.00 2.69
843 844 2.559440 CTGTTGGAGATGCTCTTAGGC 58.441 52.381 0.00 0.00 0.00 3.93
844 845 1.210478 TGTTGGAGATGCTCTTAGGCC 59.790 52.381 0.00 0.00 0.00 5.19
848 849 1.383248 AGATGCTCTTAGGCCGGGT 60.383 57.895 2.18 0.00 0.00 5.28
875 876 2.158623 TGGGCTCGGATTTTCATAGCAT 60.159 45.455 0.00 0.00 34.85 3.79
880 881 4.781071 CTCGGATTTTCATAGCATGCTTC 58.219 43.478 28.02 15.05 0.00 3.86
884 885 5.343249 GGATTTTCATAGCATGCTTCGTTT 58.657 37.500 28.02 2.18 0.00 3.60
885 886 5.230726 GGATTTTCATAGCATGCTTCGTTTG 59.769 40.000 28.02 15.32 0.00 2.93
888 889 1.402968 CATAGCATGCTTCGTTTGGCT 59.597 47.619 28.02 0.00 35.50 4.75
915 922 2.907482 TATCCGACATGGCCTGGGGT 62.907 60.000 3.32 0.00 37.80 4.95
916 923 2.907482 ATCCGACATGGCCTGGGGTA 62.907 60.000 3.32 0.00 37.80 3.69
917 924 2.189521 CGACATGGCCTGGGGTAC 59.810 66.667 3.32 0.00 0.00 3.34
918 925 2.189521 GACATGGCCTGGGGTACG 59.810 66.667 3.32 0.00 0.00 3.67
920 927 1.306312 ACATGGCCTGGGGTACGTA 60.306 57.895 3.32 0.00 0.00 3.57
921 928 0.693092 ACATGGCCTGGGGTACGTAT 60.693 55.000 3.32 0.00 0.00 3.06
922 929 0.250295 CATGGCCTGGGGTACGTATG 60.250 60.000 3.32 0.00 0.00 2.39
923 930 0.399376 ATGGCCTGGGGTACGTATGA 60.399 55.000 3.32 0.00 0.00 2.15
924 931 0.399376 TGGCCTGGGGTACGTATGAT 60.399 55.000 3.32 0.00 0.00 2.45
925 932 0.034896 GGCCTGGGGTACGTATGATG 59.965 60.000 0.00 0.00 0.00 3.07
927 934 1.270147 GCCTGGGGTACGTATGATGTC 60.270 57.143 0.00 0.00 0.00 3.06
928 935 2.317040 CCTGGGGTACGTATGATGTCT 58.683 52.381 0.00 0.00 0.00 3.41
930 937 3.492656 CCTGGGGTACGTATGATGTCTTG 60.493 52.174 0.00 0.00 0.00 3.02
931 938 3.101437 TGGGGTACGTATGATGTCTTGT 58.899 45.455 0.00 0.00 0.00 3.16
932 939 3.131577 TGGGGTACGTATGATGTCTTGTC 59.868 47.826 0.00 0.00 0.00 3.18
933 940 3.492137 GGGGTACGTATGATGTCTTGTCC 60.492 52.174 0.00 0.00 0.00 4.02
934 941 3.131577 GGGTACGTATGATGTCTTGTCCA 59.868 47.826 0.00 0.00 0.00 4.02
935 942 4.360563 GGTACGTATGATGTCTTGTCCAG 58.639 47.826 0.00 0.00 0.00 3.86
984 992 1.594293 CCCCAAATCGGTCCGATCG 60.594 63.158 26.54 19.47 46.30 3.69
987 995 0.102481 CCAAATCGGTCCGATCGTCT 59.898 55.000 26.54 8.81 46.30 4.18
988 996 1.478137 CAAATCGGTCCGATCGTCTC 58.522 55.000 26.54 3.73 46.30 3.36
989 997 1.065701 CAAATCGGTCCGATCGTCTCT 59.934 52.381 26.54 7.65 46.30 3.10
1023 1031 4.792125 CGAAAGCGACACCGAAAC 57.208 55.556 0.00 0.00 40.82 2.78
1095 1109 0.538057 CCGTGGATATGCTGGCCAAT 60.538 55.000 7.01 0.00 32.68 3.16
1196 1210 2.284921 CCCCTGTCTCCTCCTGCA 60.285 66.667 0.00 0.00 0.00 4.41
1199 1233 2.575993 CTGTCTCCTCCTGCACGG 59.424 66.667 0.00 0.00 0.00 4.94
1204 1238 3.535629 CTCCTCCTGCACGGCACAA 62.536 63.158 0.00 0.00 33.79 3.33
1376 1421 4.838152 CCCGGCCATCGACACCAG 62.838 72.222 2.24 0.00 42.43 4.00
1729 1779 0.457851 CGAGGGCAGGTTCTACTCAG 59.542 60.000 0.00 0.00 0.00 3.35
2127 2278 2.394912 GACGACGACGACGAGGAG 59.605 66.667 25.15 4.59 42.66 3.69
2171 2334 0.318762 AAGGACCGCAGAACAGAGAC 59.681 55.000 0.00 0.00 0.00 3.36
2191 2354 3.023116 TGGAGGGCCTTGGATGGG 61.023 66.667 7.89 0.00 34.31 4.00
2346 2751 3.054878 CAGTTTGGTTTGCAGCATCTTC 58.945 45.455 0.00 0.00 0.00 2.87
2358 2763 3.431233 GCAGCATCTTCTTTTTGCCTTTC 59.569 43.478 0.00 0.00 37.07 2.62
2400 2805 2.316108 AGGTGGCCCTTTTAGTTGTTG 58.684 47.619 0.00 0.00 38.13 3.33
2401 2806 1.343142 GGTGGCCCTTTTAGTTGTTGG 59.657 52.381 0.00 0.00 0.00 3.77
2402 2807 2.312390 GTGGCCCTTTTAGTTGTTGGA 58.688 47.619 0.00 0.00 0.00 3.53
2403 2808 2.035449 GTGGCCCTTTTAGTTGTTGGAC 59.965 50.000 0.00 0.00 0.00 4.02
2404 2809 1.268625 GGCCCTTTTAGTTGTTGGACG 59.731 52.381 0.00 0.00 0.00 4.79
2405 2810 1.268625 GCCCTTTTAGTTGTTGGACGG 59.731 52.381 0.00 0.00 0.00 4.79
2406 2811 1.883926 CCCTTTTAGTTGTTGGACGGG 59.116 52.381 0.00 0.00 0.00 5.28
2407 2812 2.487625 CCCTTTTAGTTGTTGGACGGGA 60.488 50.000 0.00 0.00 0.00 5.14
2408 2813 2.812011 CCTTTTAGTTGTTGGACGGGAG 59.188 50.000 0.00 0.00 0.00 4.30
2409 2814 2.554370 TTTAGTTGTTGGACGGGAGG 57.446 50.000 0.00 0.00 0.00 4.30
2410 2815 1.719529 TTAGTTGTTGGACGGGAGGA 58.280 50.000 0.00 0.00 0.00 3.71
2411 2816 1.946984 TAGTTGTTGGACGGGAGGAT 58.053 50.000 0.00 0.00 0.00 3.24
2412 2817 1.946984 AGTTGTTGGACGGGAGGATA 58.053 50.000 0.00 0.00 0.00 2.59
2413 2818 2.478292 AGTTGTTGGACGGGAGGATAT 58.522 47.619 0.00 0.00 0.00 1.63
2414 2819 2.170607 AGTTGTTGGACGGGAGGATATG 59.829 50.000 0.00 0.00 0.00 1.78
2415 2820 1.128200 TGTTGGACGGGAGGATATGG 58.872 55.000 0.00 0.00 0.00 2.74
2416 2821 1.129058 GTTGGACGGGAGGATATGGT 58.871 55.000 0.00 0.00 0.00 3.55
2417 2822 1.070289 GTTGGACGGGAGGATATGGTC 59.930 57.143 0.00 0.00 0.00 4.02
2418 2823 0.561184 TGGACGGGAGGATATGGTCT 59.439 55.000 0.00 0.00 0.00 3.85
2419 2824 1.784593 TGGACGGGAGGATATGGTCTA 59.215 52.381 0.00 0.00 0.00 2.59
2420 2825 2.178325 TGGACGGGAGGATATGGTCTAA 59.822 50.000 0.00 0.00 0.00 2.10
2421 2826 3.181410 TGGACGGGAGGATATGGTCTAAT 60.181 47.826 0.00 0.00 0.00 1.73
2422 2827 4.044952 TGGACGGGAGGATATGGTCTAATA 59.955 45.833 0.00 0.00 0.00 0.98
2458 2863 8.743085 TCTTGCTCAGATTTTATTCTATGCTT 57.257 30.769 0.00 0.00 0.00 3.91
2506 2917 1.539388 CTATTGCCTTGTGCGGTTTCA 59.461 47.619 0.00 0.00 45.60 2.69
2643 3138 4.177783 GTGTTTGGAATGTCGTTTTGGTT 58.822 39.130 0.00 0.00 0.00 3.67
2663 3158 0.608640 TCCGGTTGGAAAGAGAGAGC 59.391 55.000 0.00 0.00 42.85 4.09
2664 3159 0.610687 CCGGTTGGAAAGAGAGAGCT 59.389 55.000 0.00 0.00 37.49 4.09
2665 3160 1.404851 CCGGTTGGAAAGAGAGAGCTC 60.405 57.143 5.27 5.27 38.38 4.09
2666 3161 3.731097 CCGGTTGGAAAGAGAGAGCTCT 61.731 54.545 18.28 18.28 45.89 4.09
2667 3162 5.778398 CCGGTTGGAAAGAGAGAGCTCTG 62.778 56.522 23.91 1.01 44.19 3.35
2675 3170 2.442272 GAGAGCTCTGGGCCGGTA 60.442 66.667 23.91 0.00 43.05 4.02
2696 3191 9.034544 CCGGTAATTTACACCTGTAAGTTATAC 57.965 37.037 13.26 10.01 41.44 1.47
3098 3691 2.373169 TGAGCAGAGTCAGTTGGGATTT 59.627 45.455 0.00 0.00 0.00 2.17
3124 3717 9.258826 TGTTTGAACAATTAGGAACAATGAATG 57.741 29.630 0.00 0.00 35.67 2.67
3125 3718 9.260002 GTTTGAACAATTAGGAACAATGAATGT 57.740 29.630 0.00 0.00 46.82 2.71
3159 3756 3.261643 TCTCTAAGACATGTGGCATGTGT 59.738 43.478 17.98 12.03 31.52 3.72
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
92 93 1.353804 GTTCGACAAAACGCCTGCA 59.646 52.632 0.00 0.00 0.00 4.41
93 94 0.928451 GTGTTCGACAAAACGCCTGC 60.928 55.000 0.00 0.00 34.35 4.85
94 95 3.142796 GTGTTCGACAAAACGCCTG 57.857 52.632 0.00 0.00 34.35 4.85
97 98 1.462791 CAAGGTGTTCGACAAAACGC 58.537 50.000 0.00 0.00 38.60 4.84
98 99 1.462791 GCAAGGTGTTCGACAAAACG 58.537 50.000 0.00 0.00 31.58 3.60
99 100 1.462791 CGCAAGGTGTTCGACAAAAC 58.537 50.000 0.00 0.00 0.00 2.43
100 101 3.907927 CGCAAGGTGTTCGACAAAA 57.092 47.368 0.00 0.00 0.00 2.44
135 136 4.547367 AATAGCACCCGGGCGCTC 62.547 66.667 38.29 16.16 39.70 5.03
136 137 4.547367 GAATAGCACCCGGGCGCT 62.547 66.667 36.53 36.53 42.34 5.92
138 139 4.524318 ACGAATAGCACCCGGGCG 62.524 66.667 24.08 13.88 39.27 6.13
139 140 2.588034 GACGAATAGCACCCGGGC 60.588 66.667 24.08 7.69 0.00 6.13
140 141 2.279252 CGACGAATAGCACCCGGG 60.279 66.667 22.25 22.25 0.00 5.73
141 142 2.279252 CCGACGAATAGCACCCGG 60.279 66.667 0.00 0.00 0.00 5.73
142 143 1.299165 CTCCGACGAATAGCACCCG 60.299 63.158 0.00 0.00 0.00 5.28
143 144 1.067582 CCTCCGACGAATAGCACCC 59.932 63.158 0.00 0.00 0.00 4.61
144 145 0.248949 GTCCTCCGACGAATAGCACC 60.249 60.000 0.00 0.00 0.00 5.01
145 146 3.253416 GTCCTCCGACGAATAGCAC 57.747 57.895 0.00 0.00 0.00 4.40
177 178 4.208686 CTCTAGTCACCGCCGCCC 62.209 72.222 0.00 0.00 0.00 6.13
178 179 4.208686 CCTCTAGTCACCGCCGCC 62.209 72.222 0.00 0.00 0.00 6.13
179 180 4.208686 CCCTCTAGTCACCGCCGC 62.209 72.222 0.00 0.00 0.00 6.53
180 181 2.439701 TCCCTCTAGTCACCGCCG 60.440 66.667 0.00 0.00 0.00 6.46
181 182 2.787567 GCTCCCTCTAGTCACCGCC 61.788 68.421 0.00 0.00 0.00 6.13
182 183 2.809010 GCTCCCTCTAGTCACCGC 59.191 66.667 0.00 0.00 0.00 5.68
183 184 2.482333 CCGCTCCCTCTAGTCACCG 61.482 68.421 0.00 0.00 0.00 4.94
184 185 1.076923 TCCGCTCCCTCTAGTCACC 60.077 63.158 0.00 0.00 0.00 4.02
185 186 1.104577 CCTCCGCTCCCTCTAGTCAC 61.105 65.000 0.00 0.00 0.00 3.67
186 187 1.227664 CCTCCGCTCCCTCTAGTCA 59.772 63.158 0.00 0.00 0.00 3.41
187 188 0.106619 TTCCTCCGCTCCCTCTAGTC 60.107 60.000 0.00 0.00 0.00 2.59
188 189 0.106419 CTTCCTCCGCTCCCTCTAGT 60.106 60.000 0.00 0.00 0.00 2.57
189 190 1.460273 GCTTCCTCCGCTCCCTCTAG 61.460 65.000 0.00 0.00 0.00 2.43
190 191 1.455959 GCTTCCTCCGCTCCCTCTA 60.456 63.158 0.00 0.00 0.00 2.43
191 192 2.762043 GCTTCCTCCGCTCCCTCT 60.762 66.667 0.00 0.00 0.00 3.69
192 193 3.855853 GGCTTCCTCCGCTCCCTC 61.856 72.222 0.00 0.00 0.00 4.30
219 220 3.165685 TTCCCCGGCCTATTCCCG 61.166 66.667 0.00 0.00 45.17 5.14
220 221 2.836888 CTTCCCCGGCCTATTCCC 59.163 66.667 0.00 0.00 0.00 3.97
221 222 2.113351 GCTTCCCCGGCCTATTCC 59.887 66.667 0.00 0.00 0.00 3.01
222 223 2.280865 CGCTTCCCCGGCCTATTC 60.281 66.667 0.00 0.00 0.00 1.75
223 224 4.564110 GCGCTTCCCCGGCCTATT 62.564 66.667 0.00 0.00 0.00 1.73
664 665 1.366111 TTATTTGCTGCGTCCGCTCC 61.366 55.000 13.31 4.42 42.51 4.70
665 666 0.026803 CTTATTTGCTGCGTCCGCTC 59.973 55.000 13.31 5.51 42.51 5.03
666 667 1.982073 GCTTATTTGCTGCGTCCGCT 61.982 55.000 13.31 0.00 42.51 5.52
667 668 1.583709 GCTTATTTGCTGCGTCCGC 60.584 57.895 4.42 4.42 42.35 5.54
668 669 1.296867 CGCTTATTTGCTGCGTCCG 60.297 57.895 0.00 0.00 44.00 4.79
669 670 4.670606 CGCTTATTTGCTGCGTCC 57.329 55.556 0.00 0.00 44.00 4.79
673 674 2.941964 ATGCGCCGCTTATTTGCTGC 62.942 55.000 11.67 0.00 39.28 5.25
674 675 1.064621 ATGCGCCGCTTATTTGCTG 59.935 52.632 11.67 0.00 0.00 4.41
675 676 1.064621 CATGCGCCGCTTATTTGCT 59.935 52.632 11.67 0.00 0.00 3.91
676 677 0.318107 ATCATGCGCCGCTTATTTGC 60.318 50.000 11.67 0.00 0.00 3.68
677 678 2.124011 AATCATGCGCCGCTTATTTG 57.876 45.000 11.67 0.42 0.00 2.32
678 679 3.315191 ACTTAATCATGCGCCGCTTATTT 59.685 39.130 11.67 3.86 0.00 1.40
679 680 2.878406 ACTTAATCATGCGCCGCTTATT 59.122 40.909 11.67 9.76 0.00 1.40
680 681 2.494059 ACTTAATCATGCGCCGCTTAT 58.506 42.857 11.67 0.00 0.00 1.73
681 682 1.948104 ACTTAATCATGCGCCGCTTA 58.052 45.000 11.67 0.00 0.00 3.09
682 683 1.094785 AACTTAATCATGCGCCGCTT 58.905 45.000 11.67 0.00 0.00 4.68
683 684 1.064060 GAAACTTAATCATGCGCCGCT 59.936 47.619 11.67 0.00 0.00 5.52
684 685 1.466855 GAAACTTAATCATGCGCCGC 58.533 50.000 4.18 0.00 0.00 6.53
685 686 1.594518 CCGAAACTTAATCATGCGCCG 60.595 52.381 4.18 0.00 0.00 6.46
686 687 1.859998 GCCGAAACTTAATCATGCGCC 60.860 52.381 4.18 0.00 0.00 6.53
687 688 1.466855 GCCGAAACTTAATCATGCGC 58.533 50.000 0.00 0.00 0.00 6.09
688 689 1.268539 GGGCCGAAACTTAATCATGCG 60.269 52.381 0.00 0.00 0.00 4.73
689 690 1.268539 CGGGCCGAAACTTAATCATGC 60.269 52.381 24.41 0.00 0.00 4.06
690 691 1.268539 GCGGGCCGAAACTTAATCATG 60.269 52.381 33.44 0.00 0.00 3.07
691 692 1.021968 GCGGGCCGAAACTTAATCAT 58.978 50.000 33.44 0.00 0.00 2.45
692 693 0.035820 AGCGGGCCGAAACTTAATCA 60.036 50.000 33.44 0.00 0.00 2.57
693 694 0.656259 GAGCGGGCCGAAACTTAATC 59.344 55.000 33.44 8.38 0.00 1.75
694 695 1.087771 CGAGCGGGCCGAAACTTAAT 61.088 55.000 33.44 3.42 0.00 1.40
695 696 1.738830 CGAGCGGGCCGAAACTTAA 60.739 57.895 33.44 0.00 0.00 1.85
696 697 2.125832 CGAGCGGGCCGAAACTTA 60.126 61.111 33.44 0.00 0.00 2.24
704 705 4.143333 TAGTTCAGCGAGCGGGCC 62.143 66.667 0.00 0.00 0.00 5.80
705 706 2.356818 ATCTAGTTCAGCGAGCGGGC 62.357 60.000 0.00 0.00 0.00 6.13
706 707 0.952280 TATCTAGTTCAGCGAGCGGG 59.048 55.000 0.00 0.00 0.00 6.13
707 708 2.590073 CATATCTAGTTCAGCGAGCGG 58.410 52.381 0.00 0.00 0.00 5.52
708 709 1.982223 GCATATCTAGTTCAGCGAGCG 59.018 52.381 0.00 0.00 0.00 5.03
709 710 2.333014 GGCATATCTAGTTCAGCGAGC 58.667 52.381 0.00 0.00 0.00 5.03
710 711 2.590073 CGGCATATCTAGTTCAGCGAG 58.410 52.381 0.00 0.00 0.00 5.03
711 712 1.335964 GCGGCATATCTAGTTCAGCGA 60.336 52.381 0.00 0.00 0.00 4.93
712 713 1.063806 GCGGCATATCTAGTTCAGCG 58.936 55.000 0.00 0.00 0.00 5.18
713 714 1.063806 CGCGGCATATCTAGTTCAGC 58.936 55.000 0.00 0.00 0.00 4.26
714 715 1.063806 GCGCGGCATATCTAGTTCAG 58.936 55.000 8.83 0.00 0.00 3.02
715 716 0.673985 AGCGCGGCATATCTAGTTCA 59.326 50.000 8.83 0.00 0.00 3.18
716 717 1.068194 AGAGCGCGGCATATCTAGTTC 60.068 52.381 8.83 0.00 0.00 3.01
717 718 0.962489 AGAGCGCGGCATATCTAGTT 59.038 50.000 8.83 0.00 0.00 2.24
718 719 0.242286 CAGAGCGCGGCATATCTAGT 59.758 55.000 8.83 0.00 0.00 2.57
719 720 0.242286 ACAGAGCGCGGCATATCTAG 59.758 55.000 8.83 0.00 0.00 2.43
720 721 0.673985 AACAGAGCGCGGCATATCTA 59.326 50.000 8.83 0.00 0.00 1.98
721 722 0.179073 AAACAGAGCGCGGCATATCT 60.179 50.000 8.83 0.00 0.00 1.98
722 723 0.657840 AAAACAGAGCGCGGCATATC 59.342 50.000 8.83 0.00 0.00 1.63
723 724 1.094785 AAAAACAGAGCGCGGCATAT 58.905 45.000 8.83 0.00 0.00 1.78
724 725 0.167908 CAAAAACAGAGCGCGGCATA 59.832 50.000 8.83 0.00 0.00 3.14
725 726 1.081242 CAAAAACAGAGCGCGGCAT 60.081 52.632 8.83 0.00 0.00 4.40
726 727 2.331098 CAAAAACAGAGCGCGGCA 59.669 55.556 8.83 0.00 0.00 5.69
727 728 3.099574 GCAAAAACAGAGCGCGGC 61.100 61.111 8.83 0.00 0.00 6.53
728 729 2.796617 CGCAAAAACAGAGCGCGG 60.797 61.111 8.83 0.00 45.14 6.46
732 733 1.661509 GGGCACGCAAAAACAGAGC 60.662 57.895 0.00 0.00 0.00 4.09
733 734 1.370414 CGGGCACGCAAAAACAGAG 60.370 57.895 0.00 0.00 0.00 3.35
734 735 2.718731 CGGGCACGCAAAAACAGA 59.281 55.556 0.00 0.00 0.00 3.41
745 746 2.536997 ATAGTGGTTCCAGCGGGCAC 62.537 60.000 0.00 0.00 0.00 5.01
746 747 0.978667 TATAGTGGTTCCAGCGGGCA 60.979 55.000 0.00 0.00 0.00 5.36
747 748 0.532196 GTATAGTGGTTCCAGCGGGC 60.532 60.000 0.00 0.00 0.00 6.13
748 749 0.106149 GGTATAGTGGTTCCAGCGGG 59.894 60.000 0.00 0.00 0.00 6.13
749 750 0.249322 CGGTATAGTGGTTCCAGCGG 60.249 60.000 0.00 0.00 0.00 5.52
750 751 0.249322 CCGGTATAGTGGTTCCAGCG 60.249 60.000 0.00 0.00 0.00 5.18
751 752 0.828677 ACCGGTATAGTGGTTCCAGC 59.171 55.000 4.49 0.00 33.81 4.85
752 753 2.901249 CAACCGGTATAGTGGTTCCAG 58.099 52.381 8.00 0.00 45.10 3.86
753 754 1.065998 GCAACCGGTATAGTGGTTCCA 60.066 52.381 8.00 0.00 45.10 3.53
754 755 1.660167 GCAACCGGTATAGTGGTTCC 58.340 55.000 8.00 0.00 45.10 3.62
755 756 1.283736 CGCAACCGGTATAGTGGTTC 58.716 55.000 8.00 0.00 45.10 3.62
757 758 1.153509 GCGCAACCGGTATAGTGGT 60.154 57.895 8.00 0.00 41.20 4.16
758 759 2.235016 CGCGCAACCGGTATAGTGG 61.235 63.158 8.00 0.00 34.32 4.00
759 760 1.517694 ACGCGCAACCGGTATAGTG 60.518 57.895 8.00 11.35 34.32 2.74
760 761 1.517694 CACGCGCAACCGGTATAGT 60.518 57.895 8.00 0.83 34.32 2.12
761 762 2.867091 GCACGCGCAACCGGTATAG 61.867 63.158 8.00 2.65 38.36 1.31
762 763 2.886604 GCACGCGCAACCGGTATA 60.887 61.111 8.00 0.00 38.36 1.47
774 775 2.579518 GCCCATTTTAGCGCACGC 60.580 61.111 11.47 6.99 42.33 5.34
775 776 0.179140 ATTGCCCATTTTAGCGCACG 60.179 50.000 11.47 0.00 0.00 5.34
776 777 2.008752 AATTGCCCATTTTAGCGCAC 57.991 45.000 11.47 0.00 0.00 5.34
777 778 2.758736 AAATTGCCCATTTTAGCGCA 57.241 40.000 11.47 0.00 30.09 6.09
778 779 3.000177 CGTAAAATTGCCCATTTTAGCGC 60.000 43.478 0.00 0.00 44.54 5.92
779 780 3.549873 CCGTAAAATTGCCCATTTTAGCG 59.450 43.478 9.94 13.67 44.54 4.26
780 781 3.308595 GCCGTAAAATTGCCCATTTTAGC 59.691 43.478 9.94 8.15 44.54 3.09
781 782 3.549873 CGCCGTAAAATTGCCCATTTTAG 59.450 43.478 9.94 3.54 44.54 1.85
782 783 3.512680 CGCCGTAAAATTGCCCATTTTA 58.487 40.909 6.76 6.76 42.35 1.52
783 784 2.342179 CGCCGTAAAATTGCCCATTTT 58.658 42.857 8.35 8.35 45.45 1.82
784 785 2.003196 CGCCGTAAAATTGCCCATTT 57.997 45.000 0.00 0.00 36.57 2.32
785 786 0.459411 GCGCCGTAAAATTGCCCATT 60.459 50.000 0.00 0.00 0.00 3.16
786 787 1.140804 GCGCCGTAAAATTGCCCAT 59.859 52.632 0.00 0.00 0.00 4.00
787 788 2.569134 GCGCCGTAAAATTGCCCA 59.431 55.556 0.00 0.00 0.00 5.36
788 789 2.578445 CGCGCCGTAAAATTGCCC 60.578 61.111 0.00 0.00 0.00 5.36
789 790 2.578445 CCGCGCCGTAAAATTGCC 60.578 61.111 0.00 0.00 0.00 4.52
790 791 3.244603 GCCGCGCCGTAAAATTGC 61.245 61.111 0.00 0.00 0.00 3.56
791 792 2.942022 CGCCGCGCCGTAAAATTG 60.942 61.111 0.00 0.00 0.00 2.32
808 809 2.427410 CAGCCGCGTCAAACAAGC 60.427 61.111 4.92 0.00 0.00 4.01
809 810 0.929824 CAACAGCCGCGTCAAACAAG 60.930 55.000 4.92 0.00 0.00 3.16
810 811 1.063327 CAACAGCCGCGTCAAACAA 59.937 52.632 4.92 0.00 0.00 2.83
811 812 2.712539 CAACAGCCGCGTCAAACA 59.287 55.556 4.92 0.00 0.00 2.83
812 813 2.051345 CCAACAGCCGCGTCAAAC 60.051 61.111 4.92 0.00 0.00 2.93
813 814 2.203084 TCCAACAGCCGCGTCAAA 60.203 55.556 4.92 0.00 0.00 2.69
814 815 2.449031 ATCTCCAACAGCCGCGTCAA 62.449 55.000 4.92 0.00 0.00 3.18
815 816 2.942796 ATCTCCAACAGCCGCGTCA 61.943 57.895 4.92 0.00 0.00 4.35
816 817 2.125512 ATCTCCAACAGCCGCGTC 60.126 61.111 4.92 0.00 0.00 5.19
817 818 2.434884 CATCTCCAACAGCCGCGT 60.435 61.111 4.92 0.00 0.00 6.01
818 819 3.869272 GCATCTCCAACAGCCGCG 61.869 66.667 0.00 0.00 0.00 6.46
819 820 2.437359 AGCATCTCCAACAGCCGC 60.437 61.111 0.00 0.00 0.00 6.53
820 821 3.805267 GAGCATCTCCAACAGCCG 58.195 61.111 0.00 0.00 0.00 5.52
831 832 0.318762 CTACCCGGCCTAAGAGCATC 59.681 60.000 0.00 0.00 0.00 3.91
832 833 1.122019 CCTACCCGGCCTAAGAGCAT 61.122 60.000 0.00 0.00 0.00 3.79
833 834 1.760875 CCTACCCGGCCTAAGAGCA 60.761 63.158 0.00 0.00 0.00 4.26
834 835 2.508751 CCCTACCCGGCCTAAGAGC 61.509 68.421 0.00 0.00 0.00 4.09
835 836 1.837499 CCCCTACCCGGCCTAAGAG 60.837 68.421 0.00 0.00 0.00 2.85
836 837 2.284493 CCCCTACCCGGCCTAAGA 59.716 66.667 0.00 0.00 0.00 2.10
837 838 2.041197 ACCCCTACCCGGCCTAAG 60.041 66.667 0.00 0.00 0.00 2.18
838 839 2.365901 CACCCCTACCCGGCCTAA 60.366 66.667 0.00 0.00 0.00 2.69
839 840 4.485530 CCACCCCTACCCGGCCTA 62.486 72.222 0.00 0.00 0.00 3.93
848 849 0.917333 AAAATCCGAGCCCACCCCTA 60.917 55.000 0.00 0.00 0.00 3.53
875 876 3.353836 GCCGAGCCAAACGAAGCA 61.354 61.111 0.00 0.00 0.00 3.91
896 897 2.146724 CCCCAGGCCATGTCGGATA 61.147 63.158 5.01 0.00 36.56 2.59
915 922 4.097437 GGACTGGACAAGACATCATACGTA 59.903 45.833 0.00 0.00 0.00 3.57
916 923 3.119101 GGACTGGACAAGACATCATACGT 60.119 47.826 0.00 0.00 0.00 3.57
917 924 3.119137 TGGACTGGACAAGACATCATACG 60.119 47.826 0.00 0.00 0.00 3.06
918 925 4.437239 CTGGACTGGACAAGACATCATAC 58.563 47.826 0.00 0.00 0.00 2.39
920 927 2.238144 CCTGGACTGGACAAGACATCAT 59.762 50.000 0.00 0.00 0.00 2.45
921 928 1.625315 CCTGGACTGGACAAGACATCA 59.375 52.381 0.00 0.00 0.00 3.07
922 929 1.065854 CCCTGGACTGGACAAGACATC 60.066 57.143 0.00 0.00 0.00 3.06
923 930 0.987294 CCCTGGACTGGACAAGACAT 59.013 55.000 0.00 0.00 0.00 3.06
924 931 1.768684 GCCCTGGACTGGACAAGACA 61.769 60.000 0.00 0.00 0.00 3.41
925 932 1.003233 GCCCTGGACTGGACAAGAC 60.003 63.158 0.00 0.00 0.00 3.01
927 934 0.111253 AAAGCCCTGGACTGGACAAG 59.889 55.000 0.00 0.00 0.00 3.16
928 935 1.440618 TAAAGCCCTGGACTGGACAA 58.559 50.000 0.00 0.00 0.00 3.18
930 937 3.926058 TTATAAAGCCCTGGACTGGAC 57.074 47.619 0.00 0.00 0.00 4.02
931 938 4.938575 TTTTATAAAGCCCTGGACTGGA 57.061 40.909 0.00 0.00 0.00 3.86
932 939 5.016831 AGTTTTTATAAAGCCCTGGACTGG 58.983 41.667 0.00 0.00 0.00 4.00
933 940 6.015434 ACAAGTTTTTATAAAGCCCTGGACTG 60.015 38.462 0.00 0.00 0.00 3.51
934 941 6.075315 ACAAGTTTTTATAAAGCCCTGGACT 58.925 36.000 0.00 0.00 0.00 3.85
935 942 6.340962 ACAAGTTTTTATAAAGCCCTGGAC 57.659 37.500 0.00 0.00 0.00 4.02
984 992 3.129462 GCCCCATTGCTTAAAGAAGAGAC 59.871 47.826 0.00 0.00 34.25 3.36
987 995 2.091541 CGCCCCATTGCTTAAAGAAGA 58.908 47.619 0.00 0.00 34.25 2.87
988 996 2.091541 TCGCCCCATTGCTTAAAGAAG 58.908 47.619 0.00 0.00 35.60 2.85
989 997 2.208132 TCGCCCCATTGCTTAAAGAA 57.792 45.000 0.00 0.00 0.00 2.52
1095 1109 3.536917 CTGAGGCGGGCGTGGATA 61.537 66.667 0.00 0.00 0.00 2.59
1114 1128 3.379445 GGTGAGGCGGTCGAGGAA 61.379 66.667 0.00 0.00 0.00 3.36
1179 1193 2.284921 TGCAGGAGGAGACAGGGG 60.285 66.667 0.00 0.00 0.00 4.79
1196 1210 0.250513 GAGGGAGAAGATTGTGCCGT 59.749 55.000 0.00 0.00 37.03 5.68
1199 1233 1.092345 GGCGAGGGAGAAGATTGTGC 61.092 60.000 0.00 0.00 0.00 4.57
1204 1238 1.817209 GTTCGGCGAGGGAGAAGAT 59.183 57.895 10.46 0.00 0.00 2.40
1266 1300 4.787280 CGGGAGGAGGAGCCCAGT 62.787 72.222 0.00 0.00 44.94 4.00
1639 1685 3.534941 GGCCTCCGACGTAGGAAT 58.465 61.111 18.49 0.00 40.25 3.01
1729 1779 1.513586 CTTCGCCGGAGTACGTGAC 60.514 63.158 5.05 0.00 42.24 3.67
1954 2071 2.660064 CCGTCTCCTTCCACCCCTG 61.660 68.421 0.00 0.00 0.00 4.45
2126 2277 1.202879 TGAAAACCCTGACGCCATTCT 60.203 47.619 0.00 0.00 0.00 2.40
2127 2278 1.200020 CTGAAAACCCTGACGCCATTC 59.800 52.381 0.00 0.00 0.00 2.67
2171 2334 3.411517 ATCCAAGGCCCTCCACCG 61.412 66.667 0.00 0.00 33.74 4.94
2346 2751 4.571580 TGTTGCAATCTGAAAGGCAAAAAG 59.428 37.500 0.59 0.00 46.50 2.27
2358 2763 5.446206 CCTTTGTTTGTTGTGTTGCAATCTG 60.446 40.000 0.59 0.00 39.55 2.90
2397 2802 1.070289 GACCATATCCTCCCGTCCAAC 59.930 57.143 0.00 0.00 0.00 3.77
2400 2805 2.599408 TAGACCATATCCTCCCGTCC 57.401 55.000 0.00 0.00 0.00 4.79
2401 2806 5.715753 ACTTATTAGACCATATCCTCCCGTC 59.284 44.000 0.00 0.00 0.00 4.79
2402 2807 5.652324 ACTTATTAGACCATATCCTCCCGT 58.348 41.667 0.00 0.00 0.00 5.28
2403 2808 5.952947 AGACTTATTAGACCATATCCTCCCG 59.047 44.000 0.00 0.00 0.00 5.14
2404 2809 6.351456 GCAGACTTATTAGACCATATCCTCCC 60.351 46.154 0.00 0.00 0.00 4.30
2405 2810 6.211584 TGCAGACTTATTAGACCATATCCTCC 59.788 42.308 0.00 0.00 0.00 4.30
2406 2811 7.039363 AGTGCAGACTTATTAGACCATATCCTC 60.039 40.741 0.00 0.00 0.00 3.71
2407 2812 6.784969 AGTGCAGACTTATTAGACCATATCCT 59.215 38.462 0.00 0.00 0.00 3.24
2408 2813 6.998802 AGTGCAGACTTATTAGACCATATCC 58.001 40.000 0.00 0.00 0.00 2.59
2409 2814 8.364142 AGAAGTGCAGACTTATTAGACCATATC 58.636 37.037 0.00 0.00 42.80 1.63
2410 2815 8.256356 AGAAGTGCAGACTTATTAGACCATAT 57.744 34.615 0.00 0.00 42.80 1.78
2411 2816 7.661536 AGAAGTGCAGACTTATTAGACCATA 57.338 36.000 0.00 0.00 42.80 2.74
2412 2817 6.552445 AGAAGTGCAGACTTATTAGACCAT 57.448 37.500 0.00 0.00 42.80 3.55
2413 2818 6.166279 CAAGAAGTGCAGACTTATTAGACCA 58.834 40.000 0.00 0.00 40.81 4.02
2414 2819 6.654793 CAAGAAGTGCAGACTTATTAGACC 57.345 41.667 0.00 0.00 40.81 3.85
2453 2858 6.594788 AATCTTGGTTACACATCAAAGCAT 57.405 33.333 0.00 0.00 33.52 3.79
2458 2863 8.729756 CAAGTGATAATCTTGGTTACACATCAA 58.270 33.333 0.00 0.00 38.70 2.57
2466 2873 9.109393 GCAATAGTCAAGTGATAATCTTGGTTA 57.891 33.333 5.95 1.12 41.52 2.85
2578 3043 5.229423 GCACACTGCAATAAATTCCTTTGA 58.771 37.500 0.00 0.00 44.26 2.69
2656 3151 2.912987 TACCGGCCCAGAGCTCTCTC 62.913 65.000 14.96 5.55 43.05 3.20
2659 3154 0.983378 AATTACCGGCCCAGAGCTCT 60.983 55.000 11.45 11.45 43.05 4.09
2660 3155 0.107165 AAATTACCGGCCCAGAGCTC 60.107 55.000 5.27 5.27 43.05 4.09
2661 3156 1.134189 GTAAATTACCGGCCCAGAGCT 60.134 52.381 0.00 0.00 43.05 4.09
2662 3157 1.306148 GTAAATTACCGGCCCAGAGC 58.694 55.000 0.00 0.00 42.60 4.09
2663 3158 2.285977 GTGTAAATTACCGGCCCAGAG 58.714 52.381 0.00 0.00 0.00 3.35
2664 3159 1.065272 GGTGTAAATTACCGGCCCAGA 60.065 52.381 0.00 0.00 0.00 3.86
2665 3160 1.064979 AGGTGTAAATTACCGGCCCAG 60.065 52.381 0.00 0.00 43.06 4.45
2666 3161 0.993470 AGGTGTAAATTACCGGCCCA 59.007 50.000 0.00 0.00 43.06 5.36
2667 3162 1.340308 ACAGGTGTAAATTACCGGCCC 60.340 52.381 0.00 0.00 43.06 5.80
2668 3163 2.118313 ACAGGTGTAAATTACCGGCC 57.882 50.000 0.00 0.00 43.06 6.13
2669 3164 4.256110 ACTTACAGGTGTAAATTACCGGC 58.744 43.478 0.00 0.00 43.06 6.13
2670 3165 9.034544 GTATAACTTACAGGTGTAAATTACCGG 57.965 37.037 0.00 0.00 43.06 5.28
2671 3166 9.585099 TGTATAACTTACAGGTGTAAATTACCG 57.415 33.333 6.05 0.00 43.06 4.02
2675 3170 9.223099 GGTGTGTATAACTTACAGGTGTAAATT 57.777 33.333 4.22 3.33 39.70 1.82
2696 3191 9.424319 GTATGGATGTAATCTTATACAGGTGTG 57.576 37.037 0.00 0.00 44.71 3.82
3098 3691 9.258826 CATTCATTGTTCCTAATTGTTCAAACA 57.741 29.630 0.00 0.00 37.08 2.83
3124 3717 1.903877 TTAGAGAGGCTGGGCTGCAC 61.904 60.000 0.50 0.00 34.04 4.57
3125 3718 1.613332 TTAGAGAGGCTGGGCTGCA 60.613 57.895 0.50 0.00 34.04 4.41
3159 3756 4.591929 TGAAAGACTGATGATGGATGCAA 58.408 39.130 0.00 0.00 0.00 4.08


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

AutoCloner maintained by Alex Coulton.