Multiple sequence alignment - TraesCS3A01G506700

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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 TraesCS3A01G506700 chr3A 100.000 5713 0 0 2338 8050 728096295 728102007 0.000000e+00 10551.0
1 TraesCS3A01G506700 chr3A 93.129 3624 222 6 4131 7750 728236544 728240144 0.000000e+00 5288.0
2 TraesCS3A01G506700 chr3A 100.000 2252 0 0 1 2252 728093958 728096209 0.000000e+00 4159.0
3 TraesCS3A01G506700 chr3A 94.894 1841 52 11 2339 4139 728226825 728228663 0.000000e+00 2841.0
4 TraesCS3A01G506700 chr3A 92.035 1808 87 23 471 2252 728224504 728226280 0.000000e+00 2488.0
5 TraesCS3A01G506700 chr3A 85.614 994 142 1 6072 7065 728321894 728322886 0.000000e+00 1042.0
6 TraesCS3A01G506700 chr3A 95.726 234 9 1 7808 8040 728245186 728245419 7.630000e-100 375.0
7 TraesCS3A01G506700 chr3A 84.868 304 46 0 1 304 728076191 728076494 2.820000e-79 307.0
8 TraesCS3A01G506700 chr3A 74.350 577 131 16 4963 5531 700627724 700628291 6.280000e-56 230.0
9 TraesCS3A01G506700 chr3A 91.275 149 10 2 586 731 728085557 728085705 4.930000e-47 200.0
10 TraesCS3A01G506700 chr3A 83.200 125 20 1 4465 4588 546703132 546703008 6.600000e-21 113.0
11 TraesCS3A01G506700 chr3A 97.297 37 1 0 7745 7781 728245148 728245184 6.740000e-06 63.9
12 TraesCS3A01G506700 chr3B 89.215 4775 383 53 2387 7093 805095315 805100025 0.000000e+00 5843.0
13 TraesCS3A01G506700 chr3B 89.818 1974 174 17 5285 7255 805126766 805128715 0.000000e+00 2507.0
14 TraesCS3A01G506700 chr3B 91.568 1767 102 18 382 2141 805093300 805095026 0.000000e+00 2394.0
15 TraesCS3A01G506700 chr3B 87.390 2046 160 39 2339 4319 805122727 805124739 0.000000e+00 2259.0
16 TraesCS3A01G506700 chr3B 94.202 1121 51 6 596 1707 805117774 805118889 0.000000e+00 1698.0
17 TraesCS3A01G506700 chr3B 94.202 1121 51 6 596 1707 805121038 805122153 0.000000e+00 1698.0
18 TraesCS3A01G506700 chr3B 84.940 996 146 2 6070 7065 805256859 805257850 0.000000e+00 1005.0
19 TraesCS3A01G506700 chr3B 84.326 957 112 17 4311 5256 805125840 805126769 0.000000e+00 904.0
20 TraesCS3A01G506700 chr3B 88.593 526 52 6 7202 7726 805100130 805100648 4.100000e-177 632.0
21 TraesCS3A01G506700 chr3B 89.286 168 16 2 7443 7609 805129185 805129351 8.190000e-50 209.0
22 TraesCS3A01G506700 chr3B 95.745 47 2 0 382 428 805115389 805115435 8.660000e-10 76.8
23 TraesCS3A01G506700 chr3D 92.003 2376 162 13 5351 7720 598079132 598081485 0.000000e+00 3310.0
24 TraesCS3A01G506700 chr3D 89.612 2628 199 39 2343 4918 598074880 598077485 0.000000e+00 3273.0
25 TraesCS3A01G506700 chr3D 93.854 1497 84 5 588 2082 598072335 598073825 0.000000e+00 2248.0
26 TraesCS3A01G506700 chr3D 85.456 997 139 5 6072 7065 598162064 598163057 0.000000e+00 1033.0
27 TraesCS3A01G506700 chr3D 84.845 1003 148 4 6050 7051 597917203 597916204 0.000000e+00 1007.0
28 TraesCS3A01G506700 chr3D 82.376 505 77 6 21 525 598071765 598072257 5.770000e-116 429.0
29 TraesCS3A01G506700 chr3D 90.432 324 22 2 7717 8040 598081770 598082084 1.250000e-112 418.0
30 TraesCS3A01G506700 chr3D 82.094 363 60 4 23 383 522296642 522297001 1.010000e-78 305.0
31 TraesCS3A01G506700 chr3D 89.785 186 11 1 2075 2252 598074247 598074432 1.750000e-56 231.0
32 TraesCS3A01G506700 chr3D 92.857 70 4 1 3313 3382 598075837 598075905 5.140000e-17 100.0
33 TraesCS3A01G506700 chrUn 89.853 1971 173 18 5288 7255 291745893 291743947 0.000000e+00 2507.0
34 TraesCS3A01G506700 chrUn 80.702 570 82 15 4688 5256 291746435 291745893 1.250000e-112 418.0
35 TraesCS3A01G506700 chrUn 79.396 364 69 5 21 381 79966161 79965801 1.340000e-62 252.0
36 TraesCS3A01G506700 chrUn 89.286 168 16 2 7443 7609 291743477 291743311 8.190000e-50 209.0
37 TraesCS3A01G506700 chrUn 97.727 44 1 0 385 428 341958575 341958532 8.660000e-10 76.8
38 TraesCS3A01G506700 chrUn 97.727 44 1 0 385 428 341993521 341993478 8.660000e-10 76.8
39 TraesCS3A01G506700 chrUn 100.000 28 0 0 1979 2006 300566157 300566130 1.500000e-02 52.8
40 TraesCS3A01G506700 chrUn 100.000 28 0 0 1979 2006 353964759 353964786 1.500000e-02 52.8
41 TraesCS3A01G506700 chr7B 80.978 1309 210 21 4477 5774 460586437 460587717 0.000000e+00 1002.0
42 TraesCS3A01G506700 chr7B 78.335 937 174 24 4465 5384 138035236 138034312 5.420000e-161 579.0
43 TraesCS3A01G506700 chr7B 71.532 555 140 16 5013 5559 192523583 192524127 5.070000e-27 134.0
44 TraesCS3A01G506700 chr2D 83.175 737 106 11 4492 5224 337846999 337847721 0.000000e+00 658.0
45 TraesCS3A01G506700 chr2D 80.501 359 59 11 31 383 600439806 600440159 1.720000e-66 265.0
46 TraesCS3A01G506700 chr2D 81.600 125 15 4 7870 7989 632316886 632316765 6.650000e-16 97.1
47 TraesCS3A01G506700 chr5D 83.155 653 95 10 4542 5183 477306640 477305992 4.190000e-162 582.0
48 TraesCS3A01G506700 chr5D 80.165 363 69 2 21 381 470050399 470050038 1.330000e-67 268.0
49 TraesCS3A01G506700 chr5D 79.945 364 67 5 21 383 172256713 172257071 6.200000e-66 263.0
50 TraesCS3A01G506700 chr5B 82.879 660 91 7 4531 5183 584869459 584868815 2.520000e-159 573.0
51 TraesCS3A01G506700 chr5B 74.828 580 122 21 4963 5532 144242719 144243284 2.900000e-59 241.0
52 TraesCS3A01G506700 chr5B 74.035 570 134 12 4987 5550 243414091 243413530 3.780000e-53 220.0
53 TraesCS3A01G506700 chr6B 82.744 481 73 6 4462 4935 4519194 4519671 3.470000e-113 420.0
54 TraesCS3A01G506700 chr6B 79.670 364 68 5 21 381 12971673 12971313 2.880000e-64 257.0
55 TraesCS3A01G506700 chr7D 78.188 596 97 20 4478 5060 171640553 171639978 4.620000e-92 350.0
56 TraesCS3A01G506700 chr7D 83.486 109 18 0 1040 1148 579570468 579570576 1.430000e-17 102.0
57 TraesCS3A01G506700 chr6D 81.044 364 67 2 23 385 391567560 391567922 1.020000e-73 289.0
58 TraesCS3A01G506700 chr6D 80.769 364 63 6 21 381 394889478 394889837 2.210000e-70 278.0
59 TraesCS3A01G506700 chr1A 76.759 469 96 10 5044 5506 21082560 21082099 4.820000e-62 250.0
60 TraesCS3A01G506700 chr6A 75.524 429 90 15 4963 5384 613703714 613704134 6.370000e-46 196.0
61 TraesCS3A01G506700 chr4B 86.290 124 17 0 1061 1184 64775097 64774974 1.410000e-27 135.0
62 TraesCS3A01G506700 chr4A 83.448 145 24 0 1040 1184 554853374 554853518 1.410000e-27 135.0
63 TraesCS3A01G506700 chr4D 83.688 141 23 0 1042 1182 44756593 44756453 5.070000e-27 134.0
64 TraesCS3A01G506700 chr7A 100.000 29 0 0 1978 2006 182566928 182566956 4.000000e-03 54.7
65 TraesCS3A01G506700 chr5A 100.000 29 0 0 1978 2006 640739797 640739769 4.000000e-03 54.7


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 TraesCS3A01G506700 chr3A 728093958 728102007 8049 False 7355.000000 10551 100.000000 1 8050 2 chr3A.!!$F6 8049
1 TraesCS3A01G506700 chr3A 728236544 728240144 3600 False 5288.000000 5288 93.129000 4131 7750 1 chr3A.!!$F4 3619
2 TraesCS3A01G506700 chr3A 728224504 728228663 4159 False 2664.500000 2841 93.464500 471 4139 2 chr3A.!!$F7 3668
3 TraesCS3A01G506700 chr3A 728321894 728322886 992 False 1042.000000 1042 85.614000 6072 7065 1 chr3A.!!$F5 993
4 TraesCS3A01G506700 chr3A 700627724 700628291 567 False 230.000000 230 74.350000 4963 5531 1 chr3A.!!$F1 568
5 TraesCS3A01G506700 chr3B 805093300 805100648 7348 False 2956.333333 5843 89.792000 382 7726 3 chr3B.!!$F2 7344
6 TraesCS3A01G506700 chr3B 805115389 805129351 13962 False 1335.971429 2507 90.709857 382 7609 7 chr3B.!!$F3 7227
7 TraesCS3A01G506700 chr3B 805256859 805257850 991 False 1005.000000 1005 84.940000 6070 7065 1 chr3B.!!$F1 995
8 TraesCS3A01G506700 chr3D 598071765 598082084 10319 False 1429.857143 3310 90.131286 21 8040 7 chr3D.!!$F3 8019
9 TraesCS3A01G506700 chr3D 598162064 598163057 993 False 1033.000000 1033 85.456000 6072 7065 1 chr3D.!!$F2 993
10 TraesCS3A01G506700 chr3D 597916204 597917203 999 True 1007.000000 1007 84.845000 6050 7051 1 chr3D.!!$R1 1001
11 TraesCS3A01G506700 chrUn 291743311 291746435 3124 True 1044.666667 2507 86.613667 4688 7609 3 chrUn.!!$R5 2921
12 TraesCS3A01G506700 chr7B 460586437 460587717 1280 False 1002.000000 1002 80.978000 4477 5774 1 chr7B.!!$F2 1297
13 TraesCS3A01G506700 chr7B 138034312 138035236 924 True 579.000000 579 78.335000 4465 5384 1 chr7B.!!$R1 919
14 TraesCS3A01G506700 chr2D 337846999 337847721 722 False 658.000000 658 83.175000 4492 5224 1 chr2D.!!$F1 732
15 TraesCS3A01G506700 chr5D 477305992 477306640 648 True 582.000000 582 83.155000 4542 5183 1 chr5D.!!$R2 641
16 TraesCS3A01G506700 chr5B 584868815 584869459 644 True 573.000000 573 82.879000 4531 5183 1 chr5B.!!$R2 652
17 TraesCS3A01G506700 chr5B 144242719 144243284 565 False 241.000000 241 74.828000 4963 5532 1 chr5B.!!$F1 569
18 TraesCS3A01G506700 chr5B 243413530 243414091 561 True 220.000000 220 74.035000 4987 5550 1 chr5B.!!$R1 563
19 TraesCS3A01G506700 chr7D 171639978 171640553 575 True 350.000000 350 78.188000 4478 5060 1 chr7D.!!$R1 582

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
354 355 0.317479 CCCGGACGTTTGAGAAGAGT 59.683 55.000 0.73 0.00 0.00 3.24 F
370 371 0.606604 GAGTTTGAGACACCCGGCTA 59.393 55.000 0.00 0.00 0.00 3.93 F
858 3041 0.686441 CGGACCCCTGGTGTCTATCA 60.686 60.000 9.20 0.00 35.25 2.15 F
2115 4863 0.750850 ATCAGCTTGATGCCCATTGC 59.249 50.000 0.00 0.00 44.23 3.56 F
2120 4868 0.899720 CTTGATGCCCATTGCCACTT 59.100 50.000 0.00 0.00 40.16 3.16 F
3548 9457 1.064463 CCTGCCCCTACAACATGACAT 60.064 52.381 0.00 0.00 0.00 3.06 F
4129 10050 1.349688 AGTACAAATGGTTGCGGGAGA 59.650 47.619 0.00 0.00 38.39 3.71 F
5799 14210 0.037882 CGCTATCCCATGACTGCGAT 60.038 55.000 11.08 0.48 43.65 4.58 F
6652 15065 1.273606 CTTTGAGGAAGAGGCACGAGA 59.726 52.381 0.00 0.00 37.57 4.04 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1962 4273 3.751518 AGTACTTGGTAAACTTGGCAGG 58.248 45.455 0.0 0.0 0.00 4.85 R
2198 4946 4.535526 ATGCATGTTACCTTGTTTTCCC 57.464 40.909 0.0 0.0 0.00 3.97 R
2879 8741 4.002906 ACACCTCGTATGCTTCTTTCAA 57.997 40.909 0.0 0.0 0.00 2.69 R
4046 9965 1.000896 CTTTCATTCGGCCCCACCT 60.001 57.895 0.0 0.0 35.61 4.00 R
4129 10050 7.224297 ACTTCAGTGGTATGTGTACTTCAAAT 58.776 34.615 0.0 0.0 0.00 2.32 R
4684 11741 1.001974 CTGCTACACAGGTTGGTGCTA 59.998 52.381 0.0 0.0 43.19 3.49 R
5877 14288 0.037160 GTTTTAACCCTCCTCCCGCA 59.963 55.000 0.0 0.0 0.00 5.69 R
6915 15328 0.179089 CGCCTCATCTCTCCACCTTG 60.179 60.000 0.0 0.0 0.00 3.61 R
7803 16805 0.327924 TTGGTGATTCATCCGCCAGT 59.672 50.000 0.0 0.0 34.14 4.00 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 4.131376 CCTGCACGGGATGACATC 57.869 61.111 6.91 6.91 0.00 3.06
43 44 0.841961 AGATCTGCTGCCTGCCATAA 59.158 50.000 0.00 0.00 42.00 1.90
44 45 1.424302 AGATCTGCTGCCTGCCATAAT 59.576 47.619 0.00 0.00 42.00 1.28
50 51 1.602311 CTGCCTGCCATAATGGAGAC 58.398 55.000 0.00 0.00 40.96 3.36
88 89 2.202987 GAGCTCAGGTGGCGGATG 60.203 66.667 9.40 0.00 34.52 3.51
89 90 2.685017 AGCTCAGGTGGCGGATGA 60.685 61.111 0.00 0.00 34.52 2.92
95 96 1.305297 AGGTGGCGGATGAGAGTGA 60.305 57.895 0.00 0.00 0.00 3.41
105 106 1.484240 GATGAGAGTGAAGGGGAGTGG 59.516 57.143 0.00 0.00 0.00 4.00
113 114 1.132849 TGAAGGGGAGTGGAGTGAAGA 60.133 52.381 0.00 0.00 0.00 2.87
115 116 0.787084 AGGGGAGTGGAGTGAAGAGA 59.213 55.000 0.00 0.00 0.00 3.10
116 117 0.899019 GGGGAGTGGAGTGAAGAGAC 59.101 60.000 0.00 0.00 0.00 3.36
117 118 0.899019 GGGAGTGGAGTGAAGAGACC 59.101 60.000 0.00 0.00 0.00 3.85
136 137 3.680786 GGGTTTGGTCCGGCAAGC 61.681 66.667 0.00 0.00 0.00 4.01
138 139 2.975799 GTTTGGTCCGGCAAGCGA 60.976 61.111 0.00 0.00 0.00 4.93
140 141 1.602323 TTTGGTCCGGCAAGCGAAT 60.602 52.632 0.00 0.00 0.00 3.34
142 143 3.508840 GGTCCGGCAAGCGAATGG 61.509 66.667 0.00 0.00 0.00 3.16
160 161 5.627735 CGAATGGAGAGGAATATATGTGGGG 60.628 48.000 0.00 0.00 0.00 4.96
206 207 4.966005 ACGTGACGGACATGTCTG 57.034 55.556 29.25 29.25 44.30 3.51
213 214 4.101448 GGACATGTCTGGGCGCCT 62.101 66.667 28.56 2.49 0.00 5.52
214 215 2.512515 GACATGTCTGGGCGCCTC 60.513 66.667 28.56 17.27 0.00 4.70
216 217 4.100084 CATGTCTGGGCGCCTCCA 62.100 66.667 28.56 16.20 36.21 3.86
222 223 3.596066 CTGGGCGCCTCCATATCCG 62.596 68.421 28.56 0.00 36.05 4.18
226 227 3.314331 CGCCTCCATATCCGCCCT 61.314 66.667 0.00 0.00 0.00 5.19
232 233 3.495100 GCCTCCATATCCGCCCTATATTG 60.495 52.174 0.00 0.00 0.00 1.90
249 250 5.786121 ATATTGGGACTGAATATGAGGGG 57.214 43.478 0.00 0.00 0.00 4.79
258 259 0.986019 AATATGAGGGGTGCCGGTCA 60.986 55.000 1.90 0.00 0.00 4.02
282 283 1.007387 GGCGTTTGAGGCCTGTTTG 60.007 57.895 12.00 0.00 45.16 2.93
295 296 1.336517 CCTGTTTGAGGCGTTCGTCTA 60.337 52.381 0.00 0.00 34.01 2.59
297 298 1.610038 TGTTTGAGGCGTTCGTCTAGA 59.390 47.619 0.00 0.00 0.00 2.43
302 303 2.490509 TGAGGCGTTCGTCTAGATCAAA 59.509 45.455 0.00 0.00 0.00 2.69
325 326 0.455815 TCATGACCGATCAGTGACCG 59.544 55.000 0.00 0.00 38.57 4.79
327 328 1.676678 ATGACCGATCAGTGACCGGG 61.677 60.000 29.42 16.32 46.83 5.73
329 330 4.873129 CCGATCAGTGACCGGGCG 62.873 72.222 19.04 6.16 39.59 6.13
330 331 3.822192 CGATCAGTGACCGGGCGA 61.822 66.667 6.32 0.00 0.00 5.54
350 351 2.356553 CGCCCGGACGTTTGAGAA 60.357 61.111 0.73 0.00 0.00 2.87
352 353 1.005394 GCCCGGACGTTTGAGAAGA 60.005 57.895 0.73 0.00 0.00 2.87
353 354 1.014564 GCCCGGACGTTTGAGAAGAG 61.015 60.000 0.73 0.00 0.00 2.85
354 355 0.317479 CCCGGACGTTTGAGAAGAGT 59.683 55.000 0.73 0.00 0.00 3.24
355 356 1.270147 CCCGGACGTTTGAGAAGAGTT 60.270 52.381 0.73 0.00 0.00 3.01
356 357 2.480845 CCGGACGTTTGAGAAGAGTTT 58.519 47.619 0.00 0.00 0.00 2.66
357 358 2.221055 CCGGACGTTTGAGAAGAGTTTG 59.779 50.000 0.00 0.00 0.00 2.93
358 359 3.120792 CGGACGTTTGAGAAGAGTTTGA 58.879 45.455 0.00 0.00 0.00 2.69
359 360 3.182572 CGGACGTTTGAGAAGAGTTTGAG 59.817 47.826 0.00 0.00 0.00 3.02
360 361 4.369182 GGACGTTTGAGAAGAGTTTGAGA 58.631 43.478 0.00 0.00 0.00 3.27
361 362 4.209495 GGACGTTTGAGAAGAGTTTGAGAC 59.791 45.833 0.00 0.00 0.00 3.36
362 363 4.755411 ACGTTTGAGAAGAGTTTGAGACA 58.245 39.130 0.00 0.00 0.00 3.41
370 371 0.606604 GAGTTTGAGACACCCGGCTA 59.393 55.000 0.00 0.00 0.00 3.93
376 377 2.239400 TGAGACACCCGGCTATAGATG 58.761 52.381 3.21 0.00 0.00 2.90
379 380 0.969894 ACACCCGGCTATAGATGCTC 59.030 55.000 3.21 0.00 0.00 4.26
383 384 3.258372 CACCCGGCTATAGATGCTCTAAA 59.742 47.826 3.21 0.00 31.96 1.85
385 386 3.502920 CCGGCTATAGATGCTCTAAACG 58.497 50.000 3.21 0.00 31.96 3.60
386 387 2.917971 CGGCTATAGATGCTCTAAACGC 59.082 50.000 3.21 0.00 31.96 4.84
461 462 2.304761 TGTAAGTGGAAGGACCCATGAC 59.695 50.000 0.00 0.00 38.66 3.06
464 465 2.915869 AGTGGAAGGACCCATGACTTA 58.084 47.619 0.00 0.00 38.66 2.24
644 2816 2.241281 TCGTAACCTCTTGGATGGGA 57.759 50.000 0.00 0.00 37.04 4.37
784 2967 5.758296 GTGGATGTACATCGGTATGAATTGT 59.242 40.000 25.65 0.00 38.69 2.71
798 2981 7.465989 GGTATGAATTGTAAACCGATCGAAAA 58.534 34.615 18.66 0.00 0.00 2.29
854 3037 1.229529 ATTCGGACCCCTGGTGTCT 60.230 57.895 9.20 0.00 35.25 3.41
858 3041 0.686441 CGGACCCCTGGTGTCTATCA 60.686 60.000 9.20 0.00 35.25 2.15
871 3054 0.959553 TCTATCAATCGTCTCCCGCC 59.040 55.000 0.00 0.00 36.19 6.13
936 3119 6.909550 TTCCTGTATAAAAACCAACAGCAT 57.090 33.333 0.00 0.00 38.39 3.79
938 3121 8.410673 TTCCTGTATAAAAACCAACAGCATAA 57.589 30.769 0.00 0.00 38.39 1.90
940 3123 7.668052 TCCTGTATAAAAACCAACAGCATAAGT 59.332 33.333 0.00 0.00 38.39 2.24
960 3143 6.928348 AAGTATCCATATGTCCATCGGTAA 57.072 37.500 1.24 0.00 0.00 2.85
961 3144 7.496346 AAGTATCCATATGTCCATCGGTAAT 57.504 36.000 1.24 0.00 0.00 1.89
962 3145 7.113658 AGTATCCATATGTCCATCGGTAATC 57.886 40.000 1.24 0.00 0.00 1.75
981 3164 0.817654 CATCAGGCACGTACTCCTCA 59.182 55.000 0.00 0.00 0.00 3.86
1071 3254 1.065109 GTTGTTTCCGCTGCCGTTT 59.935 52.632 0.00 0.00 0.00 3.60
1234 3417 3.068064 TGCCGATCGCAGACCTCA 61.068 61.111 10.32 0.00 44.64 3.86
1327 3510 2.281761 ACAGCCTCCGCAAGTTGG 60.282 61.111 4.75 0.00 37.52 3.77
1336 3519 1.006102 CGCAAGTTGGTCCTCGAGT 60.006 57.895 12.31 0.00 0.00 4.18
1578 3765 2.224161 CGGGACATTCCTCTTGGAGATC 60.224 54.545 0.00 0.00 44.24 2.75
1713 3900 4.408921 CACACTATTCTATTCACCCTCCCA 59.591 45.833 0.00 0.00 0.00 4.37
1715 3902 6.270000 CACACTATTCTATTCACCCTCCCATA 59.730 42.308 0.00 0.00 0.00 2.74
1725 4032 4.855340 TCACCCTCCCATACTTTTTCATC 58.145 43.478 0.00 0.00 0.00 2.92
1727 4034 3.596046 ACCCTCCCATACTTTTTCATCCA 59.404 43.478 0.00 0.00 0.00 3.41
1735 4042 8.654997 TCCCATACTTTTTCATCCAATTTTCAA 58.345 29.630 0.00 0.00 0.00 2.69
1882 4191 7.111247 TCTGAAACATGGTGAAAGAAAATGT 57.889 32.000 0.00 0.00 32.99 2.71
1904 4214 6.291377 TGTTGCACTCTAGAACTTGAAAGAT 58.709 36.000 0.00 0.00 0.00 2.40
1906 4216 7.600375 TGTTGCACTCTAGAACTTGAAAGATAG 59.400 37.037 0.00 0.00 0.00 2.08
2019 4330 8.197439 CCATGATATAAGACGCTATTACATCCA 58.803 37.037 0.00 0.00 0.00 3.41
2115 4863 0.750850 ATCAGCTTGATGCCCATTGC 59.249 50.000 0.00 0.00 44.23 3.56
2120 4868 0.899720 CTTGATGCCCATTGCCACTT 59.100 50.000 0.00 0.00 40.16 3.16
2129 4877 3.068165 GCCCATTGCCACTTAATCTAACC 59.932 47.826 0.00 0.00 0.00 2.85
2198 4946 3.064958 TGAGACCGTATGAAACTAGCGAG 59.935 47.826 0.00 0.00 0.00 5.03
2879 8741 6.487828 TCTTCATTGATGGTTCTCTGGAAAT 58.512 36.000 0.23 0.00 32.81 2.17
2893 8755 7.383102 TCTCTGGAAATTGAAAGAAGCATAC 57.617 36.000 0.00 0.00 0.00 2.39
2937 8806 3.285484 AGCCATTGACAAGCAGATAAGG 58.715 45.455 2.66 0.00 0.00 2.69
2939 8808 3.696051 GCCATTGACAAGCAGATAAGGAA 59.304 43.478 0.00 0.00 0.00 3.36
3275 9155 5.058490 GGCCACAACTGTACACTTTTACTA 58.942 41.667 0.00 0.00 0.00 1.82
3328 9208 9.205719 GGATAGAACGAAAATCTTAGGGATTAC 57.794 37.037 0.00 0.00 43.17 1.89
3382 9262 4.849883 ACTTCGTCGAATGTCATAGCTAG 58.150 43.478 8.36 0.00 0.00 3.42
3383 9263 3.269486 TCGTCGAATGTCATAGCTAGC 57.731 47.619 6.62 6.62 0.00 3.42
3469 9378 4.363991 AGCAGAGGTTCTTGTTGAGAAT 57.636 40.909 0.00 0.00 45.66 2.40
3470 9379 4.070716 AGCAGAGGTTCTTGTTGAGAATG 58.929 43.478 0.00 0.00 45.66 2.67
3531 9440 4.637483 ATATGCGTCACCATTTTTCCTG 57.363 40.909 0.00 0.00 0.00 3.86
3548 9457 1.064463 CCTGCCCCTACAACATGACAT 60.064 52.381 0.00 0.00 0.00 3.06
3643 9552 9.218440 ACCCAAAATATTTCTGCATACAAAAAG 57.782 29.630 0.10 0.00 0.00 2.27
3647 9556 8.483307 AAATATTTCTGCATACAAAAAGGCTG 57.517 30.769 0.00 0.00 0.00 4.85
3867 9778 5.047377 GGATTTGGAAGGTGCAAATTAGACA 60.047 40.000 8.79 0.00 46.12 3.41
3869 9780 4.846779 TGGAAGGTGCAAATTAGACAAC 57.153 40.909 0.00 0.00 0.00 3.32
3912 9823 6.624352 TTGCTCATCTAGGATACATTTTGC 57.376 37.500 0.00 0.00 41.41 3.68
3927 9838 5.387279 ACATTTTGCGGTGAAAAGTATACG 58.613 37.500 0.00 0.00 0.00 3.06
4027 9946 1.355720 ACTAAGCCCAGAAAGCCATGT 59.644 47.619 0.00 0.00 0.00 3.21
4028 9947 1.747355 CTAAGCCCAGAAAGCCATGTG 59.253 52.381 0.00 0.00 0.00 3.21
4066 9986 2.052104 GTGGGGCCGAATGAAAGGG 61.052 63.158 0.00 0.00 0.00 3.95
4067 9987 2.442087 GGGGCCGAATGAAAGGGG 60.442 66.667 0.00 0.00 0.00 4.79
4129 10050 1.349688 AGTACAAATGGTTGCGGGAGA 59.650 47.619 0.00 0.00 38.39 3.71
4212 10133 7.891183 AGCATACCATAAGATCGATGTAAAC 57.109 36.000 0.54 0.00 0.00 2.01
4213 10134 7.671302 AGCATACCATAAGATCGATGTAAACT 58.329 34.615 0.54 0.00 0.00 2.66
4276 10215 3.677156 AATCCATAAGAAGCAAGGCCT 57.323 42.857 0.00 0.00 0.00 5.19
4293 10232 1.955208 GCCTGGGAACGGATCACAAAT 60.955 52.381 0.00 0.00 42.11 2.32
4377 11426 8.408601 GCATTATCACAACTGATATTTTGGAGT 58.591 33.333 0.00 0.00 38.85 3.85
4385 11434 7.119846 ACAACTGATATTTTGGAGTACTCAAGC 59.880 37.037 23.91 7.86 0.00 4.01
4399 11448 5.888724 AGTACTCAAGCTAAGAGCATACTGA 59.111 40.000 14.22 0.00 45.56 3.41
4444 11493 5.728637 AGCAAGGAAATCCAAGTAAAAGG 57.271 39.130 1.67 0.00 38.89 3.11
4659 11710 1.672881 GCACACCATCTAATCCAGTGC 59.327 52.381 0.00 0.00 43.08 4.40
4729 11797 3.740397 CCACACACCCATGCGCAG 61.740 66.667 18.32 4.62 0.00 5.18
4736 11804 1.028330 CACCCATGCGCAGACTGAAT 61.028 55.000 18.32 0.00 0.00 2.57
4737 11805 0.322816 ACCCATGCGCAGACTGAATT 60.323 50.000 18.32 0.00 0.00 2.17
4748 11816 3.430929 GCAGACTGAATTATCCGACACCT 60.431 47.826 6.65 0.00 0.00 4.00
4790 11859 5.851720 TCTTCAGGAGAGATCAATGCATAC 58.148 41.667 0.00 0.00 0.00 2.39
4795 11864 2.992543 GAGAGATCAATGCATACGGCTC 59.007 50.000 0.00 5.57 45.15 4.70
4814 11883 2.912025 CCAAGCCCAACTGCCGTT 60.912 61.111 0.00 0.00 0.00 4.44
4853 11922 1.626356 ATAGCACCACCATCCTGCGT 61.626 55.000 0.00 0.00 35.98 5.24
4880 11951 2.431942 AACACGCGACCATCGTCC 60.432 61.111 15.93 0.00 42.81 4.79
4956 12027 1.550976 GGCTGCTCCACTACTGTAGTT 59.449 52.381 17.46 1.32 36.76 2.24
4985 12059 1.364171 CCTCTAGCCGATGAACCCG 59.636 63.158 0.00 0.00 0.00 5.28
5041 12142 1.078497 AACGCCGCCATCATCTGAA 60.078 52.632 0.00 0.00 0.00 3.02
5061 12162 5.634118 TGAATGACTGATCAAGGGTTTTCT 58.366 37.500 0.00 0.00 38.69 2.52
5232 12337 3.635191 TGCATCGGCCAGACCACA 61.635 61.111 2.24 0.00 40.13 4.17
5246 12351 1.478105 GACCACATTCAAAGCCCCATC 59.522 52.381 0.00 0.00 0.00 3.51
5343 12450 2.592993 GCACCACCACTGGAGCCTA 61.593 63.158 0.71 0.00 45.78 3.93
5395 13804 2.609825 CGAGAGCATCCGGGAAATG 58.390 57.895 0.00 0.00 33.66 2.32
5435 13844 3.282021 CCGTCACTGATCCAATCCAATT 58.718 45.455 0.00 0.00 0.00 2.32
5455 13865 1.308069 CGGAGCCAAACCACCAGATG 61.308 60.000 0.00 0.00 0.00 2.90
5636 14047 1.348008 ATCTCCACCCGCATCACCAT 61.348 55.000 0.00 0.00 0.00 3.55
5649 14060 1.746239 CACCATGAGCATCGCCACA 60.746 57.895 0.00 0.00 38.61 4.17
5748 14159 0.545548 AAGGAGGAGAAGCCCTTCGT 60.546 55.000 2.63 0.00 43.97 3.85
5776 14187 4.675510 CCATCAAATGCACGAGCTTTAAT 58.324 39.130 6.36 1.59 42.74 1.40
5789 14200 2.364324 AGCTTTAATCGTCGCTATCCCA 59.636 45.455 0.00 0.00 0.00 4.37
5799 14210 0.037882 CGCTATCCCATGACTGCGAT 60.038 55.000 11.08 0.48 43.65 4.58
5820 14231 1.954994 AGGGGGAGGAGGGGAGAAT 60.955 63.158 0.00 0.00 0.00 2.40
5823 14234 1.346151 GGGGGAGGAGGGGAGAATAAA 60.346 57.143 0.00 0.00 0.00 1.40
5827 14238 3.375430 GGGAGGAGGGGAGAATAAAGAGA 60.375 52.174 0.00 0.00 0.00 3.10
6144 14557 4.665212 CCACTCGATGGTTGATCATTTTG 58.335 43.478 0.00 0.00 44.46 2.44
6277 14690 4.394920 CACCTTAATAGAACGCATTGTGGT 59.605 41.667 1.77 0.00 0.00 4.16
6652 15065 1.273606 CTTTGAGGAAGAGGCACGAGA 59.726 52.381 0.00 0.00 37.57 4.04
6849 15262 3.370633 GGAGGTGTGGAAGATAGGGTTTC 60.371 52.174 0.00 0.00 0.00 2.78
6850 15263 2.236395 AGGTGTGGAAGATAGGGTTTCG 59.764 50.000 0.00 0.00 0.00 3.46
6914 15327 5.118817 TGTTAAAAAGTTGTTTTGCCACGAC 59.881 36.000 0.00 0.00 35.96 4.34
6915 15328 2.287393 AAAGTTGTTTTGCCACGACC 57.713 45.000 0.00 0.00 32.02 4.79
7029 15442 7.384477 TGATTTGTTGGTGAATTGCATAATGA 58.616 30.769 0.00 0.00 0.00 2.57
7088 15501 4.350368 TGCATATATGTTCCCGTGTGAT 57.650 40.909 14.14 0.00 0.00 3.06
7090 15503 5.859495 TGCATATATGTTCCCGTGTGATAA 58.141 37.500 14.14 0.00 0.00 1.75
7091 15504 6.292150 TGCATATATGTTCCCGTGTGATAAA 58.708 36.000 14.14 0.00 0.00 1.40
7092 15505 6.939730 TGCATATATGTTCCCGTGTGATAAAT 59.060 34.615 14.14 0.00 0.00 1.40
7093 15506 7.094848 TGCATATATGTTCCCGTGTGATAAATG 60.095 37.037 14.14 0.00 0.00 2.32
7094 15507 7.094805 GCATATATGTTCCCGTGTGATAAATGT 60.095 37.037 14.14 0.00 0.00 2.71
7095 15508 9.430623 CATATATGTTCCCGTGTGATAAATGTA 57.569 33.333 4.43 0.00 0.00 2.29
7097 15510 6.618287 ATGTTCCCGTGTGATAAATGTATG 57.382 37.500 0.00 0.00 0.00 2.39
7098 15511 5.735766 TGTTCCCGTGTGATAAATGTATGA 58.264 37.500 0.00 0.00 0.00 2.15
7099 15512 5.583061 TGTTCCCGTGTGATAAATGTATGAC 59.417 40.000 0.00 0.00 0.00 3.06
7100 15513 4.699637 TCCCGTGTGATAAATGTATGACC 58.300 43.478 0.00 0.00 0.00 4.02
7101 15514 3.493129 CCCGTGTGATAAATGTATGACCG 59.507 47.826 0.00 0.00 0.00 4.79
7102 15515 3.059868 CCGTGTGATAAATGTATGACCGC 60.060 47.826 0.00 0.00 0.00 5.68
7103 15516 3.553917 CGTGTGATAAATGTATGACCGCA 59.446 43.478 0.00 0.00 0.00 5.69
7104 15517 4.211164 CGTGTGATAAATGTATGACCGCAT 59.789 41.667 0.00 0.00 38.54 4.73
7106 15519 6.090763 CGTGTGATAAATGTATGACCGCATAT 59.909 38.462 0.00 0.00 39.09 1.78
7237 15661 6.721208 AGCATCCGATGTTTTATAATTGGGAT 59.279 34.615 10.10 0.00 0.00 3.85
7329 15869 5.880332 TGGTTCTTAAGCTACTGCCTTTATG 59.120 40.000 0.00 0.00 40.80 1.90
7340 15880 8.515414 AGCTACTGCCTTTATGAAAGTAAAAAG 58.485 33.333 0.00 0.00 40.80 2.27
7362 15906 8.431910 AAAGAAATCTCACTACAACCCTAGTA 57.568 34.615 0.00 0.00 0.00 1.82
7418 15963 3.402628 ACTCTGGTATGCTTTTCACGT 57.597 42.857 0.00 0.00 0.00 4.49
7435 15980 3.190327 TCACGTGCCCAAATAACAATCTG 59.810 43.478 11.67 0.00 0.00 2.90
7504 16215 7.445900 TTCTTTTGTATAGCTTGTCGATACG 57.554 36.000 0.00 0.00 36.45 3.06
7576 16289 5.587844 TGGAATGAGAAAATCTAGAGCTTGC 59.412 40.000 0.00 0.00 0.00 4.01
7595 16308 1.747355 GCCGAGGCAACACTAGTACTA 59.253 52.381 9.58 1.89 41.49 1.82
7692 16406 1.691482 GGGAGGAGGCTACACATACCA 60.691 57.143 0.00 0.00 0.00 3.25
7713 16427 3.006323 CACTGAAGTCACAGGCTAAGAGT 59.994 47.826 0.00 0.00 41.59 3.24
7726 16728 2.401063 GCTAAGAGTATTTAGCGCGTCG 59.599 50.000 8.43 0.00 44.12 5.12
7729 16731 1.002684 AGAGTATTTAGCGCGTCGAGG 60.003 52.381 8.43 0.00 0.00 4.63
7764 16766 2.201022 ACGCGACACTGGGAGAGTT 61.201 57.895 15.93 0.00 29.75 3.01
7765 16767 0.892358 ACGCGACACTGGGAGAGTTA 60.892 55.000 15.93 0.00 29.75 2.24
7766 16768 0.242825 CGCGACACTGGGAGAGTTAA 59.757 55.000 0.00 0.00 29.75 2.01
7767 16769 1.135083 CGCGACACTGGGAGAGTTAAT 60.135 52.381 0.00 0.00 29.75 1.40
7768 16770 2.674177 CGCGACACTGGGAGAGTTAATT 60.674 50.000 0.00 0.00 29.75 1.40
7769 16771 2.673368 GCGACACTGGGAGAGTTAATTG 59.327 50.000 0.00 0.00 29.75 2.32
7921 16923 2.092646 TGCGAACTTGGTATAATGGGCT 60.093 45.455 0.00 0.00 0.00 5.19
7927 16929 4.894784 ACTTGGTATAATGGGCTCATACG 58.105 43.478 0.00 0.00 32.44 3.06
7936 16938 5.683876 AATGGGCTCATACGCTATAAGAT 57.316 39.130 0.00 0.00 32.44 2.40
7939 16941 4.106197 GGGCTCATACGCTATAAGATTCG 58.894 47.826 0.00 0.00 0.00 3.34
7943 16945 5.118664 GCTCATACGCTATAAGATTCGCAAA 59.881 40.000 0.00 0.00 0.00 3.68
7964 16966 7.253288 CGCAAAGAATTTACCGTAATGACATTG 60.253 37.037 11.05 0.00 35.03 2.82
7971 16973 7.916128 TTTACCGTAATGACATTGTTTTGTG 57.084 32.000 11.05 0.00 0.00 3.33
7978 16980 9.313323 CGTAATGACATTGTTTTGTGTAACTAG 57.687 33.333 11.05 0.00 38.04 2.57
7989 16991 8.402472 TGTTTTGTGTAACTAGGTTTTCATCAG 58.598 33.333 0.00 0.00 38.04 2.90
7990 16992 8.617809 GTTTTGTGTAACTAGGTTTTCATCAGA 58.382 33.333 0.00 0.00 38.04 3.27
7991 16993 7.724305 TTGTGTAACTAGGTTTTCATCAGAC 57.276 36.000 0.00 0.00 38.04 3.51
7999 17001 3.327757 AGGTTTTCATCAGACTAGCCACA 59.672 43.478 0.00 0.00 0.00 4.17
8010 17012 1.115467 CTAGCCACAGTGGGGAGTAG 58.885 60.000 18.10 11.24 38.19 2.57
8036 17038 4.222145 TCAGTAGTAACATGGGTCCAACTC 59.778 45.833 0.00 0.00 0.00 3.01
8040 17042 0.251341 AACATGGGTCCAACTCAGCC 60.251 55.000 0.00 0.00 28.45 4.85
8041 17043 1.379916 CATGGGTCCAACTCAGCCA 59.620 57.895 0.00 0.00 45.35 4.75
8042 17044 0.962356 CATGGGTCCAACTCAGCCAC 60.962 60.000 0.00 0.00 44.11 5.01
8043 17045 1.426251 ATGGGTCCAACTCAGCCACA 61.426 55.000 0.00 0.00 44.11 4.17
8044 17046 1.302832 GGGTCCAACTCAGCCACAG 60.303 63.158 0.00 0.00 0.00 3.66
8045 17047 1.451936 GGTCCAACTCAGCCACAGT 59.548 57.895 0.00 0.00 0.00 3.55
8046 17048 0.886490 GGTCCAACTCAGCCACAGTG 60.886 60.000 0.00 0.00 0.00 3.66
8047 17049 1.227943 TCCAACTCAGCCACAGTGC 60.228 57.895 0.00 0.00 0.00 4.40
8048 17050 1.526686 CCAACTCAGCCACAGTGCA 60.527 57.895 0.00 0.00 0.00 4.57
8049 17051 1.102809 CCAACTCAGCCACAGTGCAA 61.103 55.000 0.00 0.00 0.00 4.08
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 1.524621 GGATGTCATCCCGTGCAGG 60.525 63.158 19.82 0.00 43.88 4.85
1 2 4.131376 GGATGTCATCCCGTGCAG 57.869 61.111 19.82 0.00 43.88 4.41
9 10 3.803021 GCAGATCTGACTGGGATGTCATC 60.803 52.174 27.04 4.06 44.66 2.92
10 11 2.104451 GCAGATCTGACTGGGATGTCAT 59.896 50.000 27.04 0.00 44.66 3.06
11 12 1.483827 GCAGATCTGACTGGGATGTCA 59.516 52.381 27.04 0.00 43.72 3.58
12 13 1.761784 AGCAGATCTGACTGGGATGTC 59.238 52.381 27.04 4.27 38.22 3.06
13 14 1.485480 CAGCAGATCTGACTGGGATGT 59.515 52.381 27.04 0.00 45.72 3.06
14 15 1.810794 GCAGCAGATCTGACTGGGATG 60.811 57.143 30.88 15.71 45.72 3.51
15 16 0.469070 GCAGCAGATCTGACTGGGAT 59.531 55.000 30.88 5.16 45.72 3.85
16 17 1.903294 GCAGCAGATCTGACTGGGA 59.097 57.895 30.88 0.00 45.72 4.37
17 18 4.536316 GCAGCAGATCTGACTGGG 57.464 61.111 30.88 17.74 45.72 4.45
43 44 2.267961 GTTTCCGGCCGTCTCCAT 59.732 61.111 26.12 0.00 0.00 3.41
44 45 4.011517 GGTTTCCGGCCGTCTCCA 62.012 66.667 26.12 0.00 0.00 3.86
88 89 1.190643 CTCCACTCCCCTTCACTCTC 58.809 60.000 0.00 0.00 0.00 3.20
89 90 0.489567 ACTCCACTCCCCTTCACTCT 59.510 55.000 0.00 0.00 0.00 3.24
95 96 1.150135 TCTCTTCACTCCACTCCCCTT 59.850 52.381 0.00 0.00 0.00 3.95
105 106 2.551071 CCAAACCCTGGTCTCTTCACTC 60.551 54.545 0.00 0.00 40.78 3.51
117 118 2.203422 TTGCCGGACCAAACCCTG 60.203 61.111 5.05 0.00 0.00 4.45
131 132 1.673168 ATTCCTCTCCATTCGCTTGC 58.327 50.000 0.00 0.00 0.00 4.01
136 137 5.423015 CCCACATATATTCCTCTCCATTCG 58.577 45.833 0.00 0.00 0.00 3.34
138 139 5.173246 ACCCCACATATATTCCTCTCCATT 58.827 41.667 0.00 0.00 0.00 3.16
140 141 4.168101 GACCCCACATATATTCCTCTCCA 58.832 47.826 0.00 0.00 0.00 3.86
142 143 3.195825 CCGACCCCACATATATTCCTCTC 59.804 52.174 0.00 0.00 0.00 3.20
198 199 4.101448 GGAGGCGCCCAGACATGT 62.101 66.667 26.15 0.00 0.00 3.21
200 201 1.130054 ATATGGAGGCGCCCAGACAT 61.130 55.000 26.15 23.03 39.97 3.06
203 204 2.217038 GGATATGGAGGCGCCCAGA 61.217 63.158 26.15 13.25 39.97 3.86
205 206 3.625897 CGGATATGGAGGCGCCCA 61.626 66.667 26.15 16.30 41.05 5.36
213 214 3.045634 CCCAATATAGGGCGGATATGGA 58.954 50.000 0.00 0.00 43.10 3.41
214 215 3.492102 CCCAATATAGGGCGGATATGG 57.508 52.381 0.00 0.00 43.10 2.74
225 226 6.445139 ACCCCTCATATTCAGTCCCAATATAG 59.555 42.308 0.00 0.00 0.00 1.31
226 227 6.215431 CACCCCTCATATTCAGTCCCAATATA 59.785 42.308 0.00 0.00 0.00 0.86
232 233 1.202818 GCACCCCTCATATTCAGTCCC 60.203 57.143 0.00 0.00 0.00 4.46
234 235 1.541233 CGGCACCCCTCATATTCAGTC 60.541 57.143 0.00 0.00 0.00 3.51
235 236 0.469917 CGGCACCCCTCATATTCAGT 59.530 55.000 0.00 0.00 0.00 3.41
239 240 0.986019 TGACCGGCACCCCTCATATT 60.986 55.000 0.00 0.00 0.00 1.28
282 283 2.846039 TTGATCTAGACGAACGCCTC 57.154 50.000 0.00 0.00 0.00 4.70
302 303 3.941483 GGTCACTGATCGGTCATGATTTT 59.059 43.478 3.54 0.00 32.98 1.82
307 308 2.963499 CGGTCACTGATCGGTCATG 58.037 57.895 3.54 0.05 31.96 3.07
313 314 3.758088 CTCGCCCGGTCACTGATCG 62.758 68.421 4.60 4.60 35.77 3.69
315 316 4.148825 GCTCGCCCGGTCACTGAT 62.149 66.667 0.00 0.00 0.00 2.90
339 340 4.804139 TGTCTCAAACTCTTCTCAAACGTC 59.196 41.667 0.00 0.00 0.00 4.34
340 341 4.567159 GTGTCTCAAACTCTTCTCAAACGT 59.433 41.667 0.00 0.00 0.00 3.99
341 342 4.025647 GGTGTCTCAAACTCTTCTCAAACG 60.026 45.833 0.00 0.00 0.00 3.60
348 349 1.797025 CCGGGTGTCTCAAACTCTTC 58.203 55.000 0.00 0.00 0.00 2.87
350 351 1.122019 AGCCGGGTGTCTCAAACTCT 61.122 55.000 4.72 0.00 0.00 3.24
352 353 1.276622 ATAGCCGGGTGTCTCAAACT 58.723 50.000 18.40 0.00 0.00 2.66
353 354 2.429610 TCTATAGCCGGGTGTCTCAAAC 59.570 50.000 18.40 0.00 0.00 2.93
354 355 2.742348 TCTATAGCCGGGTGTCTCAAA 58.258 47.619 18.40 0.00 0.00 2.69
355 356 2.447408 TCTATAGCCGGGTGTCTCAA 57.553 50.000 18.40 0.00 0.00 3.02
356 357 2.239400 CATCTATAGCCGGGTGTCTCA 58.761 52.381 18.40 0.00 0.00 3.27
357 358 1.067495 GCATCTATAGCCGGGTGTCTC 60.067 57.143 18.40 0.00 0.00 3.36
358 359 0.969894 GCATCTATAGCCGGGTGTCT 59.030 55.000 18.40 0.00 0.00 3.41
359 360 0.969894 AGCATCTATAGCCGGGTGTC 59.030 55.000 18.40 0.00 0.00 3.67
360 361 0.969894 GAGCATCTATAGCCGGGTGT 59.030 55.000 18.40 13.19 0.00 4.16
361 362 3.822607 GAGCATCTATAGCCGGGTG 57.177 57.895 18.40 0.00 0.00 4.61
376 377 1.790387 CTGGTGCTGCGTTTAGAGC 59.210 57.895 0.00 0.00 35.65 4.09
379 380 0.950555 TCTGCTGGTGCTGCGTTTAG 60.951 55.000 0.00 0.00 40.48 1.85
386 387 4.340246 TGGGCTCTGCTGGTGCTG 62.340 66.667 8.69 0.00 40.48 4.41
449 450 4.352893 CCCAATTTAAGTCATGGGTCCTT 58.647 43.478 1.45 0.00 46.13 3.36
461 462 6.391227 ACTATTTCATCGCCCCAATTTAAG 57.609 37.500 0.00 0.00 0.00 1.85
464 465 4.141959 CCAACTATTTCATCGCCCCAATTT 60.142 41.667 0.00 0.00 0.00 1.82
529 672 1.475280 CCGGTTCTCTGTTGGACGATA 59.525 52.381 0.00 0.00 0.00 2.92
590 2762 5.121105 GCCATCGTTAGTTTATTAGGGTGT 58.879 41.667 0.00 0.00 0.00 4.16
644 2816 4.578928 CGATCCCGTTATTGGAAAAATCCT 59.421 41.667 0.00 0.00 35.03 3.24
784 2967 3.655486 TGCTGAGTTTTCGATCGGTTTA 58.345 40.909 16.41 0.00 0.00 2.01
798 2981 5.126067 AGGAAATGCGTTATTATGCTGAGT 58.874 37.500 0.00 0.00 37.19 3.41
871 3054 2.823829 GCGCGCTGAATGGGTTAGG 61.824 63.158 26.67 0.00 0.00 2.69
936 3119 8.603898 ATTACCGATGGACATATGGATACTTA 57.396 34.615 7.80 0.00 37.61 2.24
938 3121 6.667848 TGATTACCGATGGACATATGGATACT 59.332 38.462 7.80 0.00 37.61 2.12
940 3123 7.344352 TGATGATTACCGATGGACATATGGATA 59.656 37.037 7.80 0.00 0.00 2.59
960 3143 1.683917 GAGGAGTACGTGCCTGATGAT 59.316 52.381 10.63 0.00 33.84 2.45
961 3144 1.103803 GAGGAGTACGTGCCTGATGA 58.896 55.000 10.63 0.00 33.84 2.92
962 3145 0.817654 TGAGGAGTACGTGCCTGATG 59.182 55.000 10.63 0.00 33.84 3.07
981 3164 0.754217 TGGCCTCCGTTAGCGAGTAT 60.754 55.000 3.32 0.00 41.33 2.12
1013 3196 1.004560 CTCGCTGGAGCCTTGTTCA 60.005 57.895 0.00 0.00 37.91 3.18
1071 3254 2.763215 GGGTTGATGTGGCCCTGA 59.237 61.111 0.00 0.00 39.31 3.86
1750 4058 9.595357 CCGAATTAGACTTTCAGTTTAAAAGAC 57.405 33.333 2.84 0.00 37.22 3.01
1882 4191 7.671302 ACTATCTTTCAAGTTCTAGAGTGCAA 58.329 34.615 0.00 0.00 0.00 4.08
1962 4273 3.751518 AGTACTTGGTAAACTTGGCAGG 58.248 45.455 0.00 0.00 0.00 4.85
2019 4330 9.060347 CAACATGCTCTTATAGGTTCACATATT 57.940 33.333 0.00 0.00 0.00 1.28
2198 4946 4.535526 ATGCATGTTACCTTGTTTTCCC 57.464 40.909 0.00 0.00 0.00 3.97
2879 8741 4.002906 ACACCTCGTATGCTTCTTTCAA 57.997 40.909 0.00 0.00 0.00 2.69
2980 8849 5.531122 AGAAGTTATGCGCCTATAGTTCA 57.469 39.130 4.18 0.00 0.00 3.18
2981 8850 6.846325 AAAGAAGTTATGCGCCTATAGTTC 57.154 37.500 4.18 9.12 0.00 3.01
2983 8852 9.587772 CATATAAAGAAGTTATGCGCCTATAGT 57.412 33.333 4.18 0.00 34.18 2.12
3531 9440 2.943033 GTGTATGTCATGTTGTAGGGGC 59.057 50.000 0.00 0.00 0.00 5.80
3548 9457 2.969821 ATGAGGCTTGTTTGGGTGTA 57.030 45.000 0.00 0.00 0.00 2.90
3606 9515 7.499232 CAGAAATATTTTGGGTACTCTAGGGTG 59.501 40.741 5.20 0.00 0.00 4.61
3643 9552 1.758862 AGGCCTTAAATGCAATCAGCC 59.241 47.619 0.00 7.53 44.83 4.85
3647 9556 5.067674 TGTGTATGAGGCCTTAAATGCAATC 59.932 40.000 6.77 1.74 0.00 2.67
3805 9715 5.344743 TTTGATGGTTCTCGAGCTAATCT 57.655 39.130 7.81 0.00 0.00 2.40
3867 9778 5.994416 ATAACCCCCTCAAGTGATATGTT 57.006 39.130 0.00 0.00 0.00 2.71
3869 9780 4.520492 GCAATAACCCCCTCAAGTGATATG 59.480 45.833 0.00 0.00 0.00 1.78
3912 9823 8.649841 TCATAAGAAAACGTATACTTTTCACCG 58.350 33.333 25.52 17.29 39.24 4.94
3948 9859 7.867305 TTGTAATGTTTGTCTCACTTGGTTA 57.133 32.000 0.00 0.00 0.00 2.85
4028 9947 4.201950 CCACCTAGTACTGCATTGATTTGC 60.202 45.833 5.39 0.00 43.07 3.68
4046 9965 1.000896 CTTTCATTCGGCCCCACCT 60.001 57.895 0.00 0.00 35.61 4.00
4066 9986 9.747293 GTTACTATGTTTCCTTGATAGTAGACC 57.253 37.037 0.00 0.00 36.81 3.85
4067 9987 9.448294 CGTTACTATGTTTCCTTGATAGTAGAC 57.552 37.037 0.00 0.00 36.81 2.59
4129 10050 7.224297 ACTTCAGTGGTATGTGTACTTCAAAT 58.776 34.615 0.00 0.00 0.00 2.32
4212 10133 2.427506 AGCGTGCTTCCCTCTAAAAAG 58.572 47.619 0.00 0.00 0.00 2.27
4213 10134 2.561478 AGCGTGCTTCCCTCTAAAAA 57.439 45.000 0.00 0.00 0.00 1.94
4276 10215 2.869101 TGATTTGTGATCCGTTCCCA 57.131 45.000 0.00 0.00 0.00 4.37
4377 11426 6.122964 TCTCAGTATGCTCTTAGCTTGAGTA 58.877 40.000 14.99 12.09 42.97 2.59
4385 11434 7.083858 GCTAGTGATTCTCAGTATGCTCTTAG 58.916 42.308 0.00 0.00 32.38 2.18
4399 11448 6.709846 GCTTCCATCTTAATGCTAGTGATTCT 59.290 38.462 0.00 0.00 0.00 2.40
4468 11517 1.790818 GGGGTAATCCTCCTCTTCGT 58.209 55.000 0.00 0.00 35.33 3.85
4684 11741 1.001974 CTGCTACACAGGTTGGTGCTA 59.998 52.381 0.00 0.00 43.19 3.49
4695 11761 1.613925 GTGGTGAGACTCTGCTACACA 59.386 52.381 3.68 0.00 33.82 3.72
4706 11772 1.237285 GCATGGGTGTGTGGTGAGAC 61.237 60.000 0.00 0.00 0.00 3.36
4707 11773 1.073025 GCATGGGTGTGTGGTGAGA 59.927 57.895 0.00 0.00 0.00 3.27
4712 11778 3.740397 CTGCGCATGGGTGTGTGG 61.740 66.667 12.24 0.00 38.13 4.17
4729 11797 3.132289 TGGAGGTGTCGGATAATTCAGTC 59.868 47.826 0.00 0.00 0.00 3.51
4736 11804 2.698797 GGAAGATGGAGGTGTCGGATAA 59.301 50.000 0.00 0.00 0.00 1.75
4737 11805 2.317040 GGAAGATGGAGGTGTCGGATA 58.683 52.381 0.00 0.00 0.00 2.59
4748 11816 1.061905 ATGGGATGGCGGAAGATGGA 61.062 55.000 0.00 0.00 0.00 3.41
4853 11922 1.202065 GGTCGCGTGTTGATAGACGTA 60.202 52.381 5.77 0.00 42.49 3.57
4935 12006 1.186200 CTACAGTAGTGGAGCAGCCA 58.814 55.000 0.00 0.00 46.96 4.75
4956 12027 2.072487 GCTAGAGGGGCCATGGACA 61.072 63.158 22.13 0.00 0.00 4.02
4985 12059 4.524328 CCATTAGGGGCATTATTCTTGGAC 59.476 45.833 0.00 0.00 0.00 4.02
5010 12085 3.335534 GCGTTCACGTGCCGTTCT 61.336 61.111 22.42 0.00 38.32 3.01
5041 12142 4.593956 GGAGAAAACCCTTGATCAGTCAT 58.406 43.478 0.00 0.00 33.56 3.06
5061 12162 1.618888 CCTCCTTCCACTACCTTCGGA 60.619 57.143 0.00 0.00 0.00 4.55
5093 12197 2.533266 TCCTAAAGGCATCATCGAGC 57.467 50.000 0.00 0.00 34.44 5.03
5232 12337 1.687368 GCCAGAGATGGGGCTTTGAAT 60.687 52.381 0.00 0.00 46.74 2.57
5395 13804 2.183046 GACGAGCAGGAGCAGGAC 59.817 66.667 0.00 0.00 45.49 3.85
5435 13844 1.488705 ATCTGGTGGTTTGGCTCCGA 61.489 55.000 0.00 0.00 0.00 4.55
5550 13961 2.355986 CGTCTGACCCGGATCCCAA 61.356 63.158 0.73 0.00 0.00 4.12
5636 14047 3.002583 TCCCTGTGGCGATGCTCA 61.003 61.111 0.00 0.00 0.00 4.26
5666 14077 2.710902 CGTCTGCCTCGGTCCATGA 61.711 63.158 0.00 0.00 0.00 3.07
5748 14159 0.388778 CGTGCATTTGATGGCAGCAA 60.389 50.000 15.11 15.11 41.35 3.91
5776 14187 0.668535 CAGTCATGGGATAGCGACGA 59.331 55.000 0.00 0.00 33.56 4.20
5789 14200 2.446848 CCCCCTCCATCGCAGTCAT 61.447 63.158 0.00 0.00 0.00 3.06
5820 14231 1.866015 TAGCTGCCAGCCTCTCTTTA 58.134 50.000 14.25 0.00 43.77 1.85
5823 14234 1.336632 CCTTAGCTGCCAGCCTCTCT 61.337 60.000 14.25 0.00 43.77 3.10
5827 14238 0.543749 CTAACCTTAGCTGCCAGCCT 59.456 55.000 14.25 3.40 43.77 4.58
5877 14288 0.037160 GTTTTAACCCTCCTCCCGCA 59.963 55.000 0.00 0.00 0.00 5.69
5888 14299 5.203060 TGGCTACAACCATTGTTTTAACC 57.797 39.130 0.00 0.00 42.22 2.85
5961 14372 5.957796 GCGACTAGTAATGCATGTTTTGTAC 59.042 40.000 0.00 0.00 0.00 2.90
6144 14557 8.309163 TGCAAATGATCTGAAATTTTGGTAAC 57.691 30.769 0.00 0.00 0.00 2.50
6277 14690 6.475504 ACACCTGAAGAACACATTGATGATA 58.524 36.000 0.00 0.00 0.00 2.15
6652 15065 0.846693 GCTCACCACCATTCCCCTAT 59.153 55.000 0.00 0.00 0.00 2.57
6849 15262 0.830648 TCCATCTTGCCCTCTAACCG 59.169 55.000 0.00 0.00 0.00 4.44
6850 15263 1.559682 TGTCCATCTTGCCCTCTAACC 59.440 52.381 0.00 0.00 0.00 2.85
6914 15327 0.179936 GCCTCATCTCTCCACCTTGG 59.820 60.000 0.00 0.00 39.43 3.61
6915 15328 0.179089 CGCCTCATCTCTCCACCTTG 60.179 60.000 0.00 0.00 0.00 3.61
7088 15501 8.097662 TCCAACATATATGCGGTCATACATTTA 58.902 33.333 12.79 0.00 37.94 1.40
7090 15503 6.472016 TCCAACATATATGCGGTCATACATT 58.528 36.000 12.79 0.00 37.94 2.71
7091 15504 6.048732 TCCAACATATATGCGGTCATACAT 57.951 37.500 12.79 0.00 37.94 2.29
7092 15505 5.476091 TCCAACATATATGCGGTCATACA 57.524 39.130 12.79 0.00 37.94 2.29
7093 15506 4.330074 GCTCCAACATATATGCGGTCATAC 59.670 45.833 12.79 1.16 37.94 2.39
7094 15507 4.222810 AGCTCCAACATATATGCGGTCATA 59.777 41.667 12.79 0.00 39.31 2.15
7095 15508 3.008375 AGCTCCAACATATATGCGGTCAT 59.992 43.478 12.79 2.17 36.73 3.06
7096 15509 2.368548 AGCTCCAACATATATGCGGTCA 59.631 45.455 12.79 0.00 0.00 4.02
7097 15510 2.738846 CAGCTCCAACATATATGCGGTC 59.261 50.000 12.79 9.64 0.00 4.79
7098 15511 2.368548 TCAGCTCCAACATATATGCGGT 59.631 45.455 12.79 0.00 0.00 5.68
7099 15512 3.044235 TCAGCTCCAACATATATGCGG 57.956 47.619 12.79 13.12 0.00 5.69
7100 15513 4.273235 TGTTTCAGCTCCAACATATATGCG 59.727 41.667 12.79 4.33 0.00 4.73
7101 15514 5.756195 TGTTTCAGCTCCAACATATATGC 57.244 39.130 12.79 0.00 0.00 3.14
7102 15515 7.537715 TGTTTGTTTCAGCTCCAACATATATG 58.462 34.615 11.29 11.29 32.96 1.78
7103 15516 7.701539 TGTTTGTTTCAGCTCCAACATATAT 57.298 32.000 7.85 0.00 32.96 0.86
7104 15517 7.701539 ATGTTTGTTTCAGCTCCAACATATA 57.298 32.000 7.85 3.38 32.96 0.86
7106 15519 6.403866 AATGTTTGTTTCAGCTCCAACATA 57.596 33.333 7.85 1.80 32.96 2.29
7218 15642 6.892658 TCCCATCCCAATTATAAAACATCG 57.107 37.500 0.00 0.00 0.00 3.84
7314 15854 7.996098 TTTTACTTTCATAAAGGCAGTAGCT 57.004 32.000 4.56 0.00 42.82 3.32
7315 15855 8.512138 TCTTTTTACTTTCATAAAGGCAGTAGC 58.488 33.333 4.56 0.00 42.82 3.58
7340 15880 9.668497 AAATTACTAGGGTTGTAGTGAGATTTC 57.332 33.333 0.00 0.00 34.91 2.17
7418 15963 2.752354 CCGACAGATTGTTATTTGGGCA 59.248 45.455 0.00 0.00 0.00 5.36
7435 15980 2.527100 GCATCACACAGTAGTACCGAC 58.473 52.381 0.00 0.00 0.00 4.79
7504 16215 1.766143 GCGTGGATCAGAACATCGGC 61.766 60.000 0.00 0.00 0.00 5.54
7552 16264 5.587844 GCAAGCTCTAGATTTTCTCATTCCA 59.412 40.000 0.00 0.00 0.00 3.53
7576 16289 4.445452 TTTAGTACTAGTGTTGCCTCGG 57.555 45.455 5.39 0.00 0.00 4.63
7595 16308 5.980715 CGCAGTTACTTTGTAATGGGTTTTT 59.019 36.000 0.00 0.00 0.00 1.94
7629 16342 1.745087 CTATCACCGCATTGCAAAGGT 59.255 47.619 15.95 15.95 37.49 3.50
7692 16406 3.235200 ACTCTTAGCCTGTGACTTCAGT 58.765 45.455 0.00 0.00 34.02 3.41
7713 16427 1.302366 TCTCCTCGACGCGCTAAATA 58.698 50.000 5.73 0.00 0.00 1.40
7726 16728 2.545946 GTGTTCTGTTGTGCTTCTCCTC 59.454 50.000 0.00 0.00 0.00 3.71
7729 16731 1.333258 GCGTGTTCTGTTGTGCTTCTC 60.333 52.381 0.00 0.00 0.00 2.87
7800 16802 2.172505 TGGTGATTCATCCGCCAGTATT 59.827 45.455 0.00 0.00 0.00 1.89
7803 16805 0.327924 TTGGTGATTCATCCGCCAGT 59.672 50.000 0.00 0.00 34.14 4.00
7805 16807 0.394216 CCTTGGTGATTCATCCGCCA 60.394 55.000 0.00 0.00 0.00 5.69
7808 16810 1.668419 GACCCTTGGTGATTCATCCG 58.332 55.000 0.00 0.00 35.25 4.18
7888 16890 1.302192 GTTCGCACAAGGGCCTACA 60.302 57.895 6.41 0.00 0.00 2.74
7921 16923 6.443792 TCTTTGCGAATCTTATAGCGTATGA 58.556 36.000 0.00 0.00 0.00 2.15
7927 16929 7.530861 CGGTAAATTCTTTGCGAATCTTATAGC 59.469 37.037 0.00 0.00 41.42 2.97
7936 16938 6.073167 TGTCATTACGGTAAATTCTTTGCGAA 60.073 34.615 4.47 0.00 35.78 4.70
7939 16941 7.540745 ACAATGTCATTACGGTAAATTCTTTGC 59.459 33.333 4.47 0.00 0.00 3.68
7943 16945 9.405587 CAAAACAATGTCATTACGGTAAATTCT 57.594 29.630 4.47 0.00 0.00 2.40
7950 16952 5.508200 ACACAAAACAATGTCATTACGGT 57.492 34.783 0.00 0.00 0.00 4.83
7953 16955 9.607285 CCTAGTTACACAAAACAATGTCATTAC 57.393 33.333 0.00 0.00 0.00 1.89
7964 16966 8.617809 TCTGATGAAAACCTAGTTACACAAAAC 58.382 33.333 0.00 0.00 0.00 2.43
7971 16973 6.757478 GGCTAGTCTGATGAAAACCTAGTTAC 59.243 42.308 0.00 0.00 0.00 2.50
7978 16980 3.674997 TGTGGCTAGTCTGATGAAAACC 58.325 45.455 0.00 0.00 0.00 3.27
7989 16991 0.905337 ACTCCCCACTGTGGCTAGTC 60.905 60.000 21.47 0.00 35.79 2.59
7990 16992 0.412244 TACTCCCCACTGTGGCTAGT 59.588 55.000 25.71 25.71 35.79 2.57
7991 16993 1.115467 CTACTCCCCACTGTGGCTAG 58.885 60.000 21.47 20.18 35.79 3.42
7999 17001 2.043252 ACTACTGAAGCTACTCCCCACT 59.957 50.000 0.00 0.00 0.00 4.00
8010 17012 3.055385 TGGACCCATGTTACTACTGAAGC 60.055 47.826 0.00 0.00 0.00 3.86


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

AutoCloner maintained by Alex Coulton.