Multiple sequence alignment - TraesCS4B01G047300

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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 TraesCS4B01G047300 chr4B 100.000 8543 0 0 1 8543 34714153 34722695 0.000000e+00 15777.0
1 TraesCS4B01G047300 chr4B 85.887 1403 107 32 1 1338 34707407 34708783 0.000000e+00 1410.0
2 TraesCS4B01G047300 chr4B 100.000 28 0 0 102 129 622773642 622773669 1.500000e-02 52.8
3 TraesCS4B01G047300 chr4D 96.167 3261 95 14 2214 5456 22940231 22943479 0.000000e+00 5302.0
4 TraesCS4B01G047300 chr4D 93.493 2428 69 15 5519 7868 22943478 22945894 0.000000e+00 3526.0
5 TraesCS4B01G047300 chr4D 87.435 573 24 30 706 1260 22938535 22939077 4.380000e-172 616.0
6 TraesCS4B01G047300 chr4D 90.074 403 16 13 8124 8511 22946640 22947033 1.280000e-137 501.0
7 TraesCS4B01G047300 chr4D 87.470 415 29 8 1523 1936 22939463 22939855 2.810000e-124 457.0
8 TraesCS4B01G047300 chr4D 87.879 297 20 8 1941 2223 22939911 22940205 1.370000e-87 335.0
9 TraesCS4B01G047300 chr4D 81.994 361 23 19 706 1063 22934821 22935142 1.410000e-67 268.0
10 TraesCS4B01G047300 chr4A 92.711 3608 188 35 2214 5768 579437312 579433727 0.000000e+00 5136.0
11 TraesCS4B01G047300 chr4A 88.699 2929 158 65 5769 8543 579433643 579430734 0.000000e+00 3415.0
12 TraesCS4B01G047300 chr4A 85.942 1252 81 41 328 1527 579439449 579438241 0.000000e+00 1249.0
13 TraesCS4B01G047300 chr4A 92.464 345 24 2 1529 1872 579438196 579437853 7.710000e-135 492.0
14 TraesCS4B01G047300 chr4A 90.698 344 17 7 1873 2216 579437673 579437345 2.190000e-120 444.0
15 TraesCS4B01G047300 chr4A 86.997 323 37 4 2 323 579474122 579473804 8.150000e-95 359.0
16 TraesCS4B01G047300 chr2D 79.899 592 70 18 148 692 82094410 82093821 1.040000e-103 388.0
17 TraesCS4B01G047300 chr2D 86.973 261 34 0 432 692 112538521 112538781 2.330000e-75 294.0
18 TraesCS4B01G047300 chr2D 76.599 594 87 16 147 690 639674889 639675480 6.530000e-71 279.0
19 TraesCS4B01G047300 chr7D 79.518 581 78 20 145 690 590860238 590859664 8.100000e-100 375.0
20 TraesCS4B01G047300 chr7D 78.082 584 79 21 155 690 632121428 632120846 2.970000e-84 324.0
21 TraesCS4B01G047300 chr7D 89.266 177 15 4 149 323 595869699 595869525 1.440000e-52 219.0
22 TraesCS4B01G047300 chr6D 82.687 387 42 13 328 692 409782008 409781625 3.850000e-83 320.0
23 TraesCS4B01G047300 chr6D 82.308 390 40 14 328 692 304688938 304688553 2.320000e-80 311.0
24 TraesCS4B01G047300 chr3D 78.237 556 82 19 169 692 610077108 610076560 3.850000e-83 320.0
25 TraesCS4B01G047300 chr3D 87.283 173 21 1 2949 3121 335667484 335667313 6.770000e-46 196.0
26 TraesCS4B01G047300 chr3D 82.297 209 29 6 328 531 575672235 575672440 3.170000e-39 174.0
27 TraesCS4B01G047300 chr3A 78.041 592 71 26 154 692 681556543 681555958 1.380000e-82 318.0
28 TraesCS4B01G047300 chr3A 84.689 209 24 6 328 531 711134431 711134636 1.450000e-47 202.0
29 TraesCS4B01G047300 chr3A 86.705 173 22 1 2949 3121 453656385 453656214 3.150000e-44 191.0
30 TraesCS4B01G047300 chr3A 83.908 174 27 1 2950 3123 582348868 582348696 1.910000e-36 165.0
31 TraesCS4B01G047300 chr5D 88.538 253 29 0 440 692 536239808 536239556 3.000000e-79 307.0
32 TraesCS4B01G047300 chr5D 89.143 175 18 1 2949 3123 315935985 315936158 5.190000e-52 217.0
33 TraesCS4B01G047300 chr5D 88.439 173 20 0 155 327 539235087 539234915 8.690000e-50 209.0
34 TraesCS4B01G047300 chr5D 86.932 176 21 2 2948 3123 287807014 287806841 6.770000e-46 196.0
35 TraesCS4B01G047300 chr5D 86.705 173 22 1 2949 3121 395733850 395733679 3.150000e-44 191.0
36 TraesCS4B01G047300 chr5A 87.692 260 32 0 433 692 687161680 687161421 3.870000e-78 303.0
37 TraesCS4B01G047300 chr5A 74.850 334 61 19 339 666 569680285 569679969 6.960000e-26 130.0
38 TraesCS4B01G047300 chr5A 84.906 106 13 3 330 434 210840648 210840545 4.220000e-18 104.0
39 TraesCS4B01G047300 chr7B 77.753 454 49 23 155 558 108270101 108270552 1.850000e-56 231.0
40 TraesCS4B01G047300 chr7B 86.111 180 25 0 148 327 666419022 666418843 2.430000e-45 195.0
41 TraesCS4B01G047300 chr5B 87.500 176 20 2 2948 3123 326916393 326916220 1.450000e-47 202.0
42 TraesCS4B01G047300 chr5B 87.429 175 21 1 2949 3123 364139543 364139716 5.230000e-47 200.0
43 TraesCS4B01G047300 chr5B 74.346 573 96 21 169 692 455813056 455812486 6.770000e-46 196.0
44 TraesCS4B01G047300 chr2B 84.127 189 28 2 148 334 640770408 640770220 1.890000e-41 182.0
45 TraesCS4B01G047300 chr6A 75.321 312 48 13 148 434 36992758 36993065 1.160000e-23 122.0
46 TraesCS4B01G047300 chr1A 74.267 307 54 17 148 431 223452047 223452351 1.170000e-18 106.0


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS4B01G047300 chr4B 34714153 34722695 8542 False 15777.000000 15777 100.0000 1 8543 1 chr4B.!!$F2 8542
1 TraesCS4B01G047300 chr4B 34707407 34708783 1376 False 1410.000000 1410 85.8870 1 1338 1 chr4B.!!$F1 1337
2 TraesCS4B01G047300 chr4D 22934821 22947033 12212 False 1572.142857 5302 89.2160 706 8511 7 chr4D.!!$F1 7805
3 TraesCS4B01G047300 chr4A 579430734 579439449 8715 True 2147.200000 5136 90.1028 328 8543 5 chr4A.!!$R2 8215
4 TraesCS4B01G047300 chr2D 82093821 82094410 589 True 388.000000 388 79.8990 148 692 1 chr2D.!!$R1 544
5 TraesCS4B01G047300 chr2D 639674889 639675480 591 False 279.000000 279 76.5990 147 690 1 chr2D.!!$F2 543
6 TraesCS4B01G047300 chr7D 590859664 590860238 574 True 375.000000 375 79.5180 145 690 1 chr7D.!!$R1 545
7 TraesCS4B01G047300 chr7D 632120846 632121428 582 True 324.000000 324 78.0820 155 690 1 chr7D.!!$R3 535
8 TraesCS4B01G047300 chr3D 610076560 610077108 548 True 320.000000 320 78.2370 169 692 1 chr3D.!!$R2 523
9 TraesCS4B01G047300 chr3A 681555958 681556543 585 True 318.000000 318 78.0410 154 692 1 chr3A.!!$R3 538

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
119 120 0.179156 CGGCATGGTGAGCAATGTTC 60.179 55.000 0.00 0.0 0.00 3.18 F
1602 4794 0.616111 AGGAGGGCGAGTGTGATTCT 60.616 55.000 0.00 0.0 0.00 2.40 F
2032 5467 1.240256 GTCTCTGGTGACTGACGACT 58.760 55.000 0.00 0.0 35.57 4.18 F
2925 6398 0.316204 ATGCTGTTCAGGTGCTTTGC 59.684 50.000 1.97 0.0 0.00 3.68 F
3202 6689 0.168128 ATGCTTCGCGTACCTTTTGC 59.832 50.000 5.77 0.0 0.00 3.68 F
3999 7491 2.094545 GGCTACTGGTGCCTTCATTTTG 60.095 50.000 6.03 0.0 46.38 2.44 F
5557 9057 0.038744 ACAATGGGCAAGTCTGGAGG 59.961 55.000 0.00 0.0 0.00 4.30 F
7093 10737 1.000163 CCCGACTGGTATGGAATCTCG 60.000 57.143 0.00 0.0 0.00 4.04 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1635 4828 0.302890 CGAAACTGATGATCTGCGCC 59.697 55.000 4.18 0.0 0.00 6.53 R
2925 6398 0.464452 AAGGAGAGGGCGGTTTATCG 59.536 55.000 0.00 0.0 0.00 2.92 R
3187 6674 1.799994 GGTTAGCAAAAGGTACGCGAA 59.200 47.619 15.93 0.0 0.00 4.70 R
4784 8280 0.249868 CTCCAGCAACACCGTGAAGA 60.250 55.000 5.28 0.0 0.00 2.87 R
4990 8488 2.574322 CGATCAACCAGTTCTTTTGCG 58.426 47.619 0.00 0.0 0.00 4.85 R
5565 9065 0.034337 AAGCCTGGCAAAACAGCATG 59.966 50.000 22.65 0.0 46.00 4.06 R
7382 11090 0.541863 AGTTGGATCTTACCAGCGGG 59.458 55.000 0.00 0.0 44.01 6.13 R
8148 12434 0.034896 TTCCTCGTCCTGAACTTGCC 59.965 55.000 0.00 0.0 0.00 4.52 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
30 31 2.223688 TGTGAAGCCCAAATGAAACACG 60.224 45.455 0.00 0.00 0.00 4.49
32 33 0.318614 AAGCCCAAATGAAACACGCG 60.319 50.000 3.53 3.53 0.00 6.01
60 61 8.008279 GTCAAAGTTAAAACCGACAAGATACTC 58.992 37.037 0.00 0.00 0.00 2.59
87 88 6.538742 GCTAACATATTAAAGAGCCACTCACA 59.461 38.462 0.00 0.00 32.06 3.58
88 89 6.992063 AACATATTAAAGAGCCACTCACAG 57.008 37.500 0.00 0.00 32.06 3.66
91 92 0.670546 TAAAGAGCCACTCACAGCGC 60.671 55.000 0.00 0.00 32.06 5.92
96 97 4.374702 CCACTCACAGCGCGCAAC 62.375 66.667 35.10 3.43 0.00 4.17
97 98 3.639008 CACTCACAGCGCGCAACA 61.639 61.111 35.10 12.93 0.00 3.33
98 99 2.894879 ACTCACAGCGCGCAACAA 60.895 55.556 35.10 14.86 0.00 2.83
116 117 1.940883 AAGCGGCATGGTGAGCAATG 61.941 55.000 1.45 0.00 0.00 2.82
118 119 1.885157 CGGCATGGTGAGCAATGTT 59.115 52.632 0.00 0.00 0.00 2.71
119 120 0.179156 CGGCATGGTGAGCAATGTTC 60.179 55.000 0.00 0.00 0.00 3.18
127 128 5.471556 TGGTGAGCAATGTTCAAATCATT 57.528 34.783 0.33 0.00 36.16 2.57
129 130 4.560035 GGTGAGCAATGTTCAAATCATTCG 59.440 41.667 0.33 0.00 33.92 3.34
134 135 5.808540 AGCAATGTTCAAATCATTCGAATGG 59.191 36.000 32.03 19.00 37.03 3.16
139 140 7.622893 TGTTCAAATCATTCGAATGGTATGA 57.377 32.000 32.03 27.40 37.03 2.15
274 275 2.443958 AGGGCTCCCTTTTTAGATGC 57.556 50.000 0.54 0.00 45.70 3.91
346 371 2.042843 CTCCCCGTCTAGCCCTGT 60.043 66.667 0.00 0.00 0.00 4.00
377 402 2.947852 GCATCTAGCATCGTCGGTTAT 58.052 47.619 0.00 0.00 44.79 1.89
407 432 1.906824 GTGTCTCCGGTGGACCTGA 60.907 63.158 20.99 6.39 33.22 3.86
437 486 3.937706 AGATTTGCTCGGATCTTGTCTTG 59.062 43.478 0.00 0.00 28.42 3.02
626 676 4.663389 GCTTCAGTGTTTGTAATCGTCGTC 60.663 45.833 0.00 0.00 0.00 4.20
648 698 8.380867 TCGTCAGGTGGTCTATAAATCTAGATA 58.619 37.037 5.46 0.00 30.75 1.98
697 747 4.893524 TCGTACTACCATGATTGACCTCAT 59.106 41.667 0.00 0.00 36.29 2.90
700 750 7.232737 TCGTACTACCATGATTGACCTCATATT 59.767 37.037 0.00 0.00 34.11 1.28
791 3819 1.411246 ACTACCGCTGACAGTTTCACA 59.589 47.619 3.99 0.00 0.00 3.58
909 3951 2.768834 GACTAGAAAAGGCGCCCAG 58.231 57.895 26.15 13.15 0.00 4.45
994 4036 2.821810 GAGAAGCCAAGCCGAGCC 60.822 66.667 0.00 0.00 0.00 4.70
1035 4077 3.396822 ATCCTCCTCCCCCTCCACG 62.397 68.421 0.00 0.00 0.00 4.94
1122 4164 3.917760 CGATCTCCCCACCGCCTC 61.918 72.222 0.00 0.00 0.00 4.70
1123 4165 3.551407 GATCTCCCCACCGCCTCC 61.551 72.222 0.00 0.00 0.00 4.30
1124 4166 4.414956 ATCTCCCCACCGCCTCCA 62.415 66.667 0.00 0.00 0.00 3.86
1349 4412 2.916702 TCCGGATGGATCTCATTGTG 57.083 50.000 0.00 0.00 40.17 3.33
1350 4413 1.202687 TCCGGATGGATCTCATTGTGC 60.203 52.381 0.00 0.00 40.17 4.57
1351 4414 1.233019 CGGATGGATCTCATTGTGCC 58.767 55.000 0.00 0.00 35.97 5.01
1353 4416 1.475751 GGATGGATCTCATTGTGCCGT 60.476 52.381 0.00 0.00 35.97 5.68
1354 4417 1.600957 GATGGATCTCATTGTGCCGTG 59.399 52.381 0.00 0.00 35.97 4.94
1355 4418 1.026182 TGGATCTCATTGTGCCGTGC 61.026 55.000 0.00 0.00 0.00 5.34
1356 4419 1.718757 GGATCTCATTGTGCCGTGCC 61.719 60.000 0.00 0.00 0.00 5.01
1357 4420 2.040213 GATCTCATTGTGCCGTGCCG 62.040 60.000 0.00 0.00 0.00 5.69
1359 4422 3.313007 CTCATTGTGCCGTGCCGTG 62.313 63.158 0.00 0.00 0.00 4.94
1375 4438 4.323477 TGCCAGCGCCGTTAGGTT 62.323 61.111 2.29 0.00 40.50 3.50
1376 4439 3.497031 GCCAGCGCCGTTAGGTTC 61.497 66.667 2.29 0.00 40.50 3.62
1377 4440 3.186047 CCAGCGCCGTTAGGTTCG 61.186 66.667 2.29 0.00 40.50 3.95
1378 4441 2.431942 CAGCGCCGTTAGGTTCGT 60.432 61.111 2.29 0.00 40.50 3.85
1379 4442 2.126189 AGCGCCGTTAGGTTCGTC 60.126 61.111 2.29 0.00 40.50 4.20
1380 4443 3.539107 GCGCCGTTAGGTTCGTCG 61.539 66.667 0.00 0.00 40.50 5.12
1381 4444 2.877582 CGCCGTTAGGTTCGTCGG 60.878 66.667 0.00 0.00 44.86 4.79
1385 4448 1.286880 CGTTAGGTTCGTCGGGTGT 59.713 57.895 0.00 0.00 0.00 4.16
1489 4627 3.480133 CGGGAGGGATTTCGGCCT 61.480 66.667 0.00 0.00 0.00 5.19
1490 4628 2.511403 GGGAGGGATTTCGGCCTC 59.489 66.667 0.00 0.00 0.00 4.70
1527 4675 1.685148 GGGCTGATCTCCAATGGTTC 58.315 55.000 0.00 0.00 0.00 3.62
1602 4794 0.616111 AGGAGGGCGAGTGTGATTCT 60.616 55.000 0.00 0.00 0.00 2.40
1610 4802 3.684788 GGCGAGTGTGATTCTAATTGTGT 59.315 43.478 0.00 0.00 0.00 3.72
1611 4803 4.201724 GGCGAGTGTGATTCTAATTGTGTC 60.202 45.833 0.00 0.00 0.00 3.67
1659 4852 4.780324 GCGCAGATCATCAGTTTCGTTAAG 60.780 45.833 0.30 0.00 0.00 1.85
1773 4966 2.945668 GCCATACTGGAATGTCCTGTTC 59.054 50.000 11.46 0.00 44.87 3.18
1928 5300 2.376808 ACAGGACGAAGCAGAAGATG 57.623 50.000 0.00 0.00 0.00 2.90
2032 5467 1.240256 GTCTCTGGTGACTGACGACT 58.760 55.000 0.00 0.00 35.57 4.18
2033 5468 2.224450 TGTCTCTGGTGACTGACGACTA 60.224 50.000 0.00 0.00 37.36 2.59
2041 5476 3.119101 GGTGACTGACGACTATCCATGTT 60.119 47.826 0.00 0.00 0.00 2.71
2054 5489 7.002250 ACTATCCATGTTAGATGTGATCCAG 57.998 40.000 6.87 0.00 0.00 3.86
2080 5515 5.238868 TCATGTTTGGGTGCAATTTTGATTG 59.761 36.000 0.00 0.00 34.79 2.67
2091 5527 4.168760 CAATTTTGATTGCGGGAGAGTTC 58.831 43.478 0.00 0.00 0.00 3.01
2109 5545 7.222805 GGAGAGTTCTTTTTCATTGTTTTCACC 59.777 37.037 0.00 0.00 0.00 4.02
2123 5559 9.927668 CATTGTTTTCACCCTTCATAAATAAGT 57.072 29.630 0.00 0.00 0.00 2.24
2216 5652 6.175471 CAGCCAAATCTATGCCATCTGTATA 58.825 40.000 0.00 0.00 0.00 1.47
2218 5654 7.012138 CAGCCAAATCTATGCCATCTGTATATC 59.988 40.741 0.00 0.00 0.00 1.63
2260 5731 3.942130 AACATTTTGTTCCTAGCCAGC 57.058 42.857 0.00 0.00 35.27 4.85
2265 5736 3.780804 TTTGTTCCTAGCCAGCTAACA 57.219 42.857 0.34 1.84 0.00 2.41
2300 5772 9.907229 AAGGAAGATAAAAGGGTGATAGTTTAG 57.093 33.333 0.00 0.00 0.00 1.85
2349 5821 9.529325 AATGATTGAATGTTCATGAATGATGAC 57.471 29.630 12.12 0.00 41.02 3.06
2351 5823 7.340999 TGATTGAATGTTCATGAATGATGACCT 59.659 33.333 12.12 0.00 41.02 3.85
2405 5877 8.958119 TGTTAGTTCTGTTATTTCTCTGTTGT 57.042 30.769 0.00 0.00 0.00 3.32
2422 5894 6.884187 TCTGTTGTACTACTTTCGATTTTGC 58.116 36.000 8.88 0.00 0.00 3.68
2605 6077 6.855836 TGCTGCTTGTTAGAAAATAATCCTG 58.144 36.000 0.00 0.00 0.00 3.86
2607 6079 7.609918 TGCTGCTTGTTAGAAAATAATCCTGTA 59.390 33.333 0.00 0.00 0.00 2.74
2608 6080 7.910683 GCTGCTTGTTAGAAAATAATCCTGTAC 59.089 37.037 0.00 0.00 0.00 2.90
2622 6094 1.469940 CCTGTACTGCTAGGCACGAAG 60.470 57.143 0.00 0.00 33.79 3.79
2678 6150 8.607713 TCCATTTCCTGGTATCAACTTTAACTA 58.392 33.333 0.00 0.00 46.08 2.24
2820 6293 4.272018 CCAGTGTTTCTTGTCTTGTCTCTG 59.728 45.833 0.00 0.00 0.00 3.35
2839 6312 2.237143 CTGCAGTCCTTCCTCATAACCA 59.763 50.000 5.25 0.00 0.00 3.67
2925 6398 0.316204 ATGCTGTTCAGGTGCTTTGC 59.684 50.000 1.97 0.00 0.00 3.68
2934 6407 0.802494 AGGTGCTTTGCGATAAACCG 59.198 50.000 0.00 0.00 32.83 4.44
2945 6418 1.538419 CGATAAACCGCCCTCTCCTTC 60.538 57.143 0.00 0.00 0.00 3.46
2954 6427 2.373224 GCCCTCTCCTTCCTCAAAATG 58.627 52.381 0.00 0.00 0.00 2.32
2956 6429 3.615155 CCCTCTCCTTCCTCAAAATGAC 58.385 50.000 0.00 0.00 0.00 3.06
3191 6678 1.206523 GAGTAACCCGTATGCTTCGC 58.793 55.000 0.00 0.00 0.00 4.70
3202 6689 0.168128 ATGCTTCGCGTACCTTTTGC 59.832 50.000 5.77 0.00 0.00 3.68
3375 6862 8.662781 TGTTCTATGCAACTCCTTTATATGTC 57.337 34.615 0.00 0.00 0.00 3.06
3586 7073 6.348050 GCAGATGTAAGTCTTGTTTCTTCCAG 60.348 42.308 0.00 0.00 0.00 3.86
3715 7207 7.676947 ACATATAGTAGTTTGGTTGTGACACT 58.323 34.615 7.20 0.00 0.00 3.55
3733 7225 2.430694 CACTATACAGTGCCTACCAGCA 59.569 50.000 0.00 0.00 45.44 4.41
3787 7279 6.321717 CCGCACATTGTATTAAACTGTTCAT 58.678 36.000 0.00 0.00 0.00 2.57
3999 7491 2.094545 GGCTACTGGTGCCTTCATTTTG 60.095 50.000 6.03 0.00 46.38 2.44
4089 7581 2.376109 CATCTCTGGCAAATCAAGGCT 58.624 47.619 0.00 0.00 0.00 4.58
4298 7790 7.712797 TGTATTTTTGTTCTCTTTCTGTTCCC 58.287 34.615 0.00 0.00 0.00 3.97
4573 8068 5.812286 GGGGAAACACTAGAACCTCATAAA 58.188 41.667 0.00 0.00 0.00 1.40
4576 8071 6.713450 GGGAAACACTAGAACCTCATAAAACA 59.287 38.462 0.00 0.00 0.00 2.83
4784 8280 6.018343 CGGTTTGCAATTTTAGTTTTGATGGT 60.018 34.615 0.00 0.00 0.00 3.55
4990 8488 2.108970 CCAGACCCTAACCTCACCTAC 58.891 57.143 0.00 0.00 0.00 3.18
5095 8593 1.238439 CTGACCGCAACATGGTTCTT 58.762 50.000 0.00 0.00 40.63 2.52
5343 8841 8.561738 TTTTCTTTCTGATTAATACTTCCGCT 57.438 30.769 0.00 0.00 0.00 5.52
5365 8864 5.220491 GCTAGTCGAATCAAGGCTTTAAGTG 60.220 44.000 0.00 0.00 0.00 3.16
5401 8900 1.798223 GTCTGCAGTAAACACGCATGA 59.202 47.619 14.67 0.00 34.63 3.07
5412 8911 5.403897 AAACACGCATGATTTCCTATACG 57.596 39.130 0.00 0.00 0.00 3.06
5455 8954 1.133136 TCAGGGACTAGGCAGGATACC 60.133 57.143 0.00 0.00 36.02 2.73
5457 8956 1.666580 GGACTAGGCAGGATACCGC 59.333 63.158 0.00 0.00 37.17 5.68
5462 8961 0.467844 TAGGCAGGATACCGCGGTAA 60.468 55.000 39.14 23.61 33.99 2.85
5472 8971 1.477553 ACCGCGGTAACTCTCCATTA 58.522 50.000 33.34 0.00 0.00 1.90
5473 8972 1.826720 ACCGCGGTAACTCTCCATTAA 59.173 47.619 33.34 0.00 0.00 1.40
5474 8973 2.199236 CCGCGGTAACTCTCCATTAAC 58.801 52.381 19.50 0.00 0.00 2.01
5490 8989 2.945447 TAACGATGGTAACTGGTCGG 57.055 50.000 0.00 0.00 39.67 4.79
5491 8990 0.971386 AACGATGGTAACTGGTCGGT 59.029 50.000 0.00 0.00 39.67 4.69
5509 9008 5.375417 TCGGTTACGATCAGTTAACAGAA 57.625 39.130 8.61 0.00 45.59 3.02
5512 9011 6.309494 TCGGTTACGATCAGTTAACAGAAATG 59.691 38.462 8.61 2.61 45.59 2.32
5513 9012 6.248631 GGTTACGATCAGTTAACAGAAATGC 58.751 40.000 8.61 0.00 0.00 3.56
5557 9057 0.038744 ACAATGGGCAAGTCTGGAGG 59.961 55.000 0.00 0.00 0.00 4.30
5558 9058 1.000396 AATGGGCAAGTCTGGAGGC 60.000 57.895 0.00 0.00 0.00 4.70
5559 9059 1.504275 AATGGGCAAGTCTGGAGGCT 61.504 55.000 0.00 0.00 0.00 4.58
5560 9060 2.045536 GGGCAAGTCTGGAGGCTG 60.046 66.667 0.00 0.00 0.00 4.85
5561 9061 2.045536 GGCAAGTCTGGAGGCTGG 60.046 66.667 0.00 0.00 0.00 4.85
5562 9062 2.596851 GGCAAGTCTGGAGGCTGGA 61.597 63.158 0.00 0.00 0.00 3.86
5563 9063 1.078567 GCAAGTCTGGAGGCTGGAG 60.079 63.158 0.00 0.00 0.00 3.86
5564 9064 1.078567 CAAGTCTGGAGGCTGGAGC 60.079 63.158 0.00 0.00 41.14 4.70
5595 9115 1.005332 TGCCAGGCTTGCTACCATTTA 59.995 47.619 14.15 0.00 0.00 1.40
5704 9237 3.064134 GCTGGCTTACTAGCTTAAACTGC 59.936 47.826 0.00 0.00 46.90 4.40
5799 9415 8.361889 CCATCTTATGATTTGCATCCATGTTTA 58.638 33.333 0.00 0.00 38.44 2.01
5808 9424 9.531942 GATTTGCATCCATGTTTATGTTGAATA 57.468 29.630 0.00 0.00 32.21 1.75
6066 9682 1.201429 AGGTGCCTACTGGGTGGAAG 61.201 60.000 0.00 0.00 37.43 3.46
6218 9834 4.029520 TGCCTTATGGTAAAATGCCATGT 58.970 39.130 9.83 0.00 45.47 3.21
6250 9866 5.871396 TGTAACACCTCTCTTGGGATATC 57.129 43.478 0.00 0.00 0.00 1.63
6366 9984 2.328473 TCGACATGAAGCTGAAAGACG 58.672 47.619 0.00 0.00 34.07 4.18
6428 10046 2.303311 GGGGTTGCTGATATCCTCTACC 59.697 54.545 12.94 12.94 0.00 3.18
6549 10167 4.567159 GGAGATAAGCTTGTTACGGTTGAG 59.433 45.833 9.86 0.00 0.00 3.02
6630 10248 7.551585 ACTATGAGGTACTTCATTCAACTGAG 58.448 38.462 23.67 15.53 41.55 3.35
6631 10249 5.152623 TGAGGTACTTCATTCAACTGAGG 57.847 43.478 3.11 0.00 41.55 3.86
6632 10250 4.593206 TGAGGTACTTCATTCAACTGAGGT 59.407 41.667 3.11 0.00 41.55 3.85
6826 10470 6.604795 ACTTCATGCACATATTTAAGCCTCTT 59.395 34.615 0.00 0.00 0.00 2.85
6842 10486 3.814945 CCTCTTCGATTTGCTGTGAAAC 58.185 45.455 0.00 0.00 37.35 2.78
6845 10489 5.179368 CCTCTTCGATTTGCTGTGAAACTAA 59.821 40.000 0.00 0.00 38.04 2.24
6987 10631 2.350522 CCTACTGTTGCAGATGTGGTC 58.649 52.381 2.91 0.00 35.18 4.02
7084 10728 2.040178 GAGATGGTTCCCGACTGGTAT 58.960 52.381 0.00 0.00 34.77 2.73
7093 10737 1.000163 CCCGACTGGTATGGAATCTCG 60.000 57.143 0.00 0.00 0.00 4.04
7121 10813 7.358023 GCTGTTATTTATTGGTGAACACGTTTG 60.358 37.037 0.00 0.00 0.00 2.93
7224 10932 2.041620 CAGAGTTGATCCTTTTGGGGGA 59.958 50.000 0.00 0.00 40.87 4.81
7382 11090 1.272781 CGTCGAGTGATGCTCTTTCC 58.727 55.000 0.00 0.00 41.98 3.13
7385 11093 0.807667 CGAGTGATGCTCTTTCCCCG 60.808 60.000 0.00 0.00 41.98 5.73
7425 11150 6.480763 TCCTCATGCTTCTAACAAATAACCA 58.519 36.000 0.00 0.00 0.00 3.67
7584 11310 0.178068 AGGCCGCGTATGAAGTTCAT 59.822 50.000 21.57 21.57 40.72 2.57
7612 11338 3.002759 GCCTCATGTTCGATAGCCTTTTC 59.997 47.826 0.00 0.00 0.00 2.29
7626 11354 4.849518 AGCCTTTTCTTACATCTCCCTTC 58.150 43.478 0.00 0.00 0.00 3.46
7673 11401 1.860078 GTCTCCGTTTCGTTGCCTG 59.140 57.895 0.00 0.00 0.00 4.85
7771 11512 6.909895 GTGCAATGCAATATATTGACGTGTTA 59.090 34.615 26.22 11.44 41.47 2.41
7854 11604 6.038714 AGGAATTTCTGAAGGATATTGTTCGC 59.961 38.462 0.00 0.00 0.00 4.70
7886 11636 3.967332 TCCTTTGGTACCGTTAGGAAG 57.033 47.619 20.99 11.74 41.02 3.46
7939 12175 3.886938 TCCCTATGGAATGGGCTATTCT 58.113 45.455 20.87 7.00 44.87 2.40
7947 12183 5.935945 TGGAATGGGCTATTCTATCGAAAA 58.064 37.500 20.87 0.00 43.81 2.29
7950 12186 7.505585 TGGAATGGGCTATTCTATCGAAAATTT 59.494 33.333 20.87 0.00 43.81 1.82
7975 12211 2.242882 AAGCCAAATGAGCCCTTGAT 57.757 45.000 0.00 0.00 0.00 2.57
7976 12212 1.481871 AGCCAAATGAGCCCTTGATG 58.518 50.000 0.00 0.00 0.00 3.07
7982 12218 4.020839 CCAAATGAGCCCTTGATGTTTTCT 60.021 41.667 0.00 0.00 0.00 2.52
7996 12232 7.715265 TGATGTTTTCTTCTCTGTCTACAAC 57.285 36.000 0.00 0.00 0.00 3.32
8001 12237 9.010029 TGTTTTCTTCTCTGTCTACAACTTTTT 57.990 29.630 0.00 0.00 0.00 1.94
8015 12251 8.836413 TCTACAACTTTTTCTTACCAATGTGAG 58.164 33.333 0.00 0.00 0.00 3.51
8063 12318 5.637006 TGTTGTTGTTGATTACCCTATGC 57.363 39.130 0.00 0.00 0.00 3.14
8064 12319 5.073428 TGTTGTTGTTGATTACCCTATGCA 58.927 37.500 0.00 0.00 0.00 3.96
8065 12320 5.714333 TGTTGTTGTTGATTACCCTATGCAT 59.286 36.000 3.79 3.79 0.00 3.96
8066 12321 6.210385 TGTTGTTGTTGATTACCCTATGCATT 59.790 34.615 3.54 0.00 0.00 3.56
8085 12340 3.611433 GCAACGATTGATGCAGACC 57.389 52.632 10.18 0.00 42.88 3.85
8091 12346 3.084039 ACGATTGATGCAGACCACAAAT 58.916 40.909 0.00 0.00 0.00 2.32
8105 12391 4.151883 ACCACAAATAAGTGCCATGAACT 58.848 39.130 0.00 0.00 38.18 3.01
8107 12393 4.925054 CCACAAATAAGTGCCATGAACTTG 59.075 41.667 18.64 9.10 38.32 3.16
8111 12397 1.331214 AAGTGCCATGAACTTGGGTG 58.669 50.000 11.58 0.00 36.52 4.61
8117 12403 1.548081 CATGAACTTGGGTGCCATGA 58.452 50.000 0.00 0.00 38.46 3.07
8148 12434 0.524862 GAGATGTTTGCAGGCCACAG 59.475 55.000 5.01 0.00 0.00 3.66
8149 12435 0.896940 AGATGTTTGCAGGCCACAGG 60.897 55.000 5.01 0.00 0.00 4.00
8180 12466 1.139058 ACGAGGAACATACATCCAGCC 59.861 52.381 0.00 0.00 39.55 4.85
8198 12485 2.892852 AGCCACACAAGCACATTACATT 59.107 40.909 0.00 0.00 0.00 2.71
8199 12486 4.078537 AGCCACACAAGCACATTACATTA 58.921 39.130 0.00 0.00 0.00 1.90
8202 12489 5.622007 GCCACACAAGCACATTACATTACAT 60.622 40.000 0.00 0.00 0.00 2.29
8256 12561 1.797046 CAGTCTCATCACTGCACACAC 59.203 52.381 0.00 0.00 37.58 3.82
8376 12695 2.021068 ATGGTGGTCTCGGCGATCAG 62.021 60.000 11.27 0.00 32.22 2.90
8502 12821 4.277593 CGCCACGCCCTGCAAAAA 62.278 61.111 0.00 0.00 0.00 1.94
8532 12851 1.589716 AATGCAGCCGGAAAGCAGTC 61.590 55.000 18.44 0.00 42.14 3.51
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
30 31 3.031126 GTCGGTTTTAACTTTGACACGC 58.969 45.455 0.00 0.00 0.00 5.34
32 33 5.871539 TCTTGTCGGTTTTAACTTTGACAC 58.128 37.500 12.12 0.00 36.26 3.67
60 61 6.763135 TGAGTGGCTCTTTAATATGTTAGCTG 59.237 38.462 0.00 0.00 0.00 4.24
93 94 1.210931 CTCACCATGCCGCTTGTTG 59.789 57.895 5.61 1.87 0.00 3.33
96 97 1.940883 ATTGCTCACCATGCCGCTTG 61.941 55.000 0.00 0.00 0.00 4.01
97 98 1.679977 ATTGCTCACCATGCCGCTT 60.680 52.632 0.00 0.00 0.00 4.68
98 99 2.044650 ATTGCTCACCATGCCGCT 60.045 55.556 0.00 0.00 0.00 5.52
101 102 0.889994 TGAACATTGCTCACCATGCC 59.110 50.000 0.00 0.00 0.00 4.40
104 105 5.670792 ATGATTTGAACATTGCTCACCAT 57.329 34.783 0.00 0.00 0.00 3.55
220 221 4.315941 GGATCCATCGCGTCCCCC 62.316 72.222 6.95 0.00 0.00 5.40
263 264 6.969669 AAACTCGAAAACGCATCTAAAAAG 57.030 33.333 0.00 0.00 0.00 2.27
274 275 6.744082 ACAAACCTTAAGAAAACTCGAAAACG 59.256 34.615 3.36 0.00 0.00 3.60
336 361 1.550130 CCACCGGAAACAGGGCTAGA 61.550 60.000 9.46 0.00 0.00 2.43
346 371 0.392461 GCTAGATGCACCACCGGAAA 60.392 55.000 9.46 0.00 42.31 3.13
377 402 2.746697 GAGACACACCTCCACAGGA 58.253 57.895 0.00 0.00 43.65 3.86
407 432 5.440610 AGATCCGAGCAAATCTACCAAAAT 58.559 37.500 0.00 0.00 30.50 1.82
437 486 4.320348 CGTAGATCGGAAGGATACAACCTC 60.320 50.000 0.00 0.00 36.15 3.85
675 725 4.649088 TGAGGTCAATCATGGTAGTACG 57.351 45.455 0.00 0.00 0.00 3.67
753 3778 5.297527 CGGTAGTTTTGTAGGAGTGGTTTTT 59.702 40.000 0.00 0.00 0.00 1.94
811 3839 1.899437 ATAGCATATCCGTGGGGGCG 61.899 60.000 0.00 0.00 34.94 6.13
910 3952 3.847602 CTCGCTCCTGCTCTGGGG 61.848 72.222 0.00 0.00 36.97 4.96
911 3953 4.527583 GCTCGCTCCTGCTCTGGG 62.528 72.222 0.00 0.00 36.97 4.45
918 3960 4.903355 CTCGCTCGCTCGCTCCTG 62.903 72.222 0.00 0.00 0.00 3.86
962 4004 4.292306 TGGCTTCTCCCTTTTTCTCCTTAT 59.708 41.667 0.00 0.00 0.00 1.73
965 4007 2.065799 TGGCTTCTCCCTTTTTCTCCT 58.934 47.619 0.00 0.00 0.00 3.69
967 4009 2.230025 GCTTGGCTTCTCCCTTTTTCTC 59.770 50.000 0.00 0.00 0.00 2.87
968 4010 2.242926 GCTTGGCTTCTCCCTTTTTCT 58.757 47.619 0.00 0.00 0.00 2.52
969 4011 1.273606 GGCTTGGCTTCTCCCTTTTTC 59.726 52.381 0.00 0.00 0.00 2.29
975 4017 2.124942 CTCGGCTTGGCTTCTCCC 60.125 66.667 0.00 0.00 0.00 4.30
1122 4164 3.151022 GAGGAGGCGAGGAGGTGG 61.151 72.222 0.00 0.00 0.00 4.61
1123 4165 3.151022 GGAGGAGGCGAGGAGGTG 61.151 72.222 0.00 0.00 0.00 4.00
1124 4166 3.351885 AGGAGGAGGCGAGGAGGT 61.352 66.667 0.00 0.00 0.00 3.85
1191 4248 2.434884 AACACCATCTCCGCTGCG 60.435 61.111 16.34 16.34 0.00 5.18
1338 4401 1.723870 GGCACGGCACAATGAGATC 59.276 57.895 0.00 0.00 0.00 2.75
1339 4402 3.909662 GGCACGGCACAATGAGAT 58.090 55.556 0.00 0.00 0.00 2.75
1359 4422 3.497031 GAACCTAACGGCGCTGGC 61.497 66.667 22.44 0.00 38.90 4.85
1360 4423 3.186047 CGAACCTAACGGCGCTGG 61.186 66.667 22.44 9.50 0.00 4.85
1361 4424 2.431942 ACGAACCTAACGGCGCTG 60.432 61.111 16.39 16.39 34.93 5.18
1362 4425 2.126189 GACGAACCTAACGGCGCT 60.126 61.111 6.90 0.00 34.93 5.92
1365 4428 2.507769 CCCGACGAACCTAACGGC 60.508 66.667 0.00 0.00 43.37 5.68
1366 4429 1.444895 CACCCGACGAACCTAACGG 60.445 63.158 0.00 0.00 44.16 4.44
1367 4430 0.730494 GACACCCGACGAACCTAACG 60.730 60.000 0.00 0.00 0.00 3.18
1368 4431 0.389037 GGACACCCGACGAACCTAAC 60.389 60.000 0.00 0.00 0.00 2.34
1369 4432 1.535204 GGGACACCCGACGAACCTAA 61.535 60.000 0.00 0.00 32.13 2.69
1370 4433 1.978617 GGGACACCCGACGAACCTA 60.979 63.158 0.00 0.00 32.13 3.08
1371 4434 3.308705 GGGACACCCGACGAACCT 61.309 66.667 0.00 0.00 32.13 3.50
1527 4675 4.424430 CCGAAACGCGCTGAACCG 62.424 66.667 5.73 1.12 39.11 4.44
1596 4788 6.042777 GGATCAGACGACACAATTAGAATCA 58.957 40.000 0.00 0.00 0.00 2.57
1602 4794 2.159156 CCCGGATCAGACGACACAATTA 60.159 50.000 0.73 0.00 0.00 1.40
1610 4802 1.000019 AACCTCCCGGATCAGACGA 60.000 57.895 0.73 0.00 0.00 4.20
1611 4803 1.437986 GAACCTCCCGGATCAGACG 59.562 63.158 0.73 0.00 32.67 4.18
1632 4825 1.094073 AACTGATGATCTGCGCCAGC 61.094 55.000 4.18 0.00 45.41 4.85
1635 4828 0.302890 CGAAACTGATGATCTGCGCC 59.697 55.000 4.18 0.00 0.00 6.53
1773 4966 0.680921 ACATGCCAGATCCCAAACGG 60.681 55.000 0.00 0.00 0.00 4.44
1846 5039 2.046217 GGGTCCCCGCAGAAGAAC 60.046 66.667 0.00 0.00 0.00 3.01
1881 5253 1.732259 CCACGTGAATGCACTCCTTAC 59.268 52.381 19.30 0.00 42.93 2.34
1974 5398 2.708216 TTTGAGCAACAGGTCAGTGA 57.292 45.000 0.00 0.00 40.47 3.41
2032 5467 7.071071 TGAACTGGATCACATCTAACATGGATA 59.929 37.037 0.00 0.00 0.00 2.59
2033 5468 5.901413 ACTGGATCACATCTAACATGGAT 57.099 39.130 0.00 0.00 0.00 3.41
2041 5476 5.882000 CCAAACATGAACTGGATCACATCTA 59.118 40.000 0.00 0.00 31.38 1.98
2054 5489 4.574013 TCAAAATTGCACCCAAACATGAAC 59.426 37.500 0.00 0.00 34.05 3.18
2080 5515 3.253432 ACAATGAAAAAGAACTCTCCCGC 59.747 43.478 0.00 0.00 0.00 6.13
2091 5527 7.790823 ATGAAGGGTGAAAACAATGAAAAAG 57.209 32.000 0.00 0.00 0.00 2.27
2188 5624 0.740737 GGCATAGATTTGGCTGCGTT 59.259 50.000 0.00 0.00 39.00 4.84
2190 5626 0.956633 ATGGCATAGATTTGGCTGCG 59.043 50.000 0.00 0.00 42.34 5.18
2246 5717 4.009675 CAATGTTAGCTGGCTAGGAACAA 58.990 43.478 11.68 0.00 0.00 2.83
2265 5736 6.959954 ACCCTTTTATCTTCCTTTAAGGCAAT 59.040 34.615 6.05 2.38 34.61 3.56
2369 5841 2.737252 CAGAACTAACAAGAGAACGGCC 59.263 50.000 0.00 0.00 0.00 6.13
2405 5877 4.693566 CCACTGGCAAAATCGAAAGTAGTA 59.306 41.667 0.00 0.00 0.00 1.82
2407 5879 4.083581 CCACTGGCAAAATCGAAAGTAG 57.916 45.455 0.00 0.00 0.00 2.57
2422 5894 1.271871 TGAATTGTACTGGGCCACTGG 60.272 52.381 0.00 0.00 0.00 4.00
2605 6077 2.094649 ACTTCTTCGTGCCTAGCAGTAC 60.095 50.000 0.00 0.00 40.08 2.73
2607 6079 0.969894 ACTTCTTCGTGCCTAGCAGT 59.030 50.000 0.00 0.00 40.08 4.40
2608 6080 2.531206 GTACTTCTTCGTGCCTAGCAG 58.469 52.381 0.00 0.00 40.08 4.24
2678 6150 9.838339 AGATCTGGTTATTTTTCGTTATCTGAT 57.162 29.630 0.00 0.00 0.00 2.90
2820 6293 2.237392 AGTGGTTATGAGGAAGGACTGC 59.763 50.000 0.00 0.00 0.00 4.40
2839 6312 6.599638 GCACCTACAAGGAAAGAAATGATAGT 59.400 38.462 0.00 0.00 37.67 2.12
2925 6398 0.464452 AAGGAGAGGGCGGTTTATCG 59.536 55.000 0.00 0.00 0.00 2.92
2934 6407 2.025887 TCATTTTGAGGAAGGAGAGGGC 60.026 50.000 0.00 0.00 0.00 5.19
2945 6418 6.467677 TCCTAGAACTTCAGTCATTTTGAGG 58.532 40.000 0.00 0.00 0.00 3.86
3187 6674 1.799994 GGTTAGCAAAAGGTACGCGAA 59.200 47.619 15.93 0.00 0.00 4.70
3191 6678 2.188062 TGGGGTTAGCAAAAGGTACG 57.812 50.000 0.00 0.00 0.00 3.67
3715 7207 3.118408 CCTTTGCTGGTAGGCACTGTATA 60.118 47.826 0.00 0.00 42.27 1.47
3726 7218 2.906389 ACTCAGACATCCTTTGCTGGTA 59.094 45.455 0.00 0.00 33.18 3.25
3733 7225 5.053978 AGGTTTGAACTCAGACATCCTTT 57.946 39.130 3.15 0.00 33.14 3.11
3787 7279 8.429641 GGATCAATAGGATTAGTTGGTAACTCA 58.570 37.037 0.00 0.00 38.49 3.41
3964 7456 1.971167 TAGCCTTTGCGCCCTGTTG 60.971 57.895 4.18 0.00 44.33 3.33
3999 7491 2.985847 GGGTTGTGGCTGGCTGTC 60.986 66.667 2.00 0.00 0.00 3.51
4089 7581 5.416013 TGTTGATTTACACAGAACACCAACA 59.584 36.000 0.00 0.00 38.95 3.33
4218 7710 4.439057 TCCGCAATGAGGTATTCAGTAAC 58.561 43.478 2.35 0.00 39.68 2.50
4298 7790 4.301072 TTCCACTACCTTGGGATCAAAG 57.699 45.455 0.00 0.00 37.24 2.77
4601 8097 7.640616 TTGAATGCACACTGTTAATGAAATG 57.359 32.000 0.00 0.00 0.00 2.32
4719 8215 7.095017 GCTATTTGCTGTTAATAGGAGGATGAC 60.095 40.741 1.09 0.00 36.52 3.06
4784 8280 0.249868 CTCCAGCAACACCGTGAAGA 60.250 55.000 5.28 0.00 0.00 2.87
4883 8379 7.335171 TCCATGTTCAACTTGTGATGATAGAAG 59.665 37.037 2.95 0.00 35.70 2.85
4885 8381 6.710278 TCCATGTTCAACTTGTGATGATAGA 58.290 36.000 2.95 0.00 35.70 1.98
4886 8382 6.596888 ACTCCATGTTCAACTTGTGATGATAG 59.403 38.462 2.95 0.00 35.70 2.08
4990 8488 2.574322 CGATCAACCAGTTCTTTTGCG 58.426 47.619 0.00 0.00 0.00 4.85
5095 8593 8.749026 TGTAGTCAAAACATTACCTTTTACCA 57.251 30.769 0.00 0.00 0.00 3.25
5124 8622 6.145535 CCTCAAGTGCTTTTGTAGATTTGAC 58.854 40.000 1.64 0.00 0.00 3.18
5343 8841 5.175859 CCACTTAAAGCCTTGATTCGACTA 58.824 41.667 0.00 0.00 0.00 2.59
5365 8864 1.131883 CAGACAGCAGTGCTATTTGCC 59.868 52.381 19.26 0.00 41.17 4.52
5401 8900 4.134563 GGATGCACAACCGTATAGGAAAT 58.865 43.478 0.00 0.00 45.00 2.17
5412 8911 3.591196 TGCTTATTTGGATGCACAACC 57.409 42.857 0.00 0.00 0.00 3.77
5455 8954 1.850441 CGTTAATGGAGAGTTACCGCG 59.150 52.381 0.00 0.00 0.00 6.46
5472 8971 0.971386 ACCGACCAGTTACCATCGTT 59.029 50.000 0.00 0.00 32.70 3.85
5473 8972 0.971386 AACCGACCAGTTACCATCGT 59.029 50.000 0.00 0.00 32.70 3.73
5474 8973 2.533266 GTAACCGACCAGTTACCATCG 58.467 52.381 3.70 0.00 44.11 3.84
5490 8989 7.061752 AGCATTTCTGTTAACTGATCGTAAC 57.938 36.000 14.99 6.76 0.00 2.50
5491 8990 7.667043 AAGCATTTCTGTTAACTGATCGTAA 57.333 32.000 14.99 7.68 0.00 3.18
5495 8994 5.574443 GGCAAAGCATTTCTGTTAACTGATC 59.426 40.000 14.99 6.33 35.03 2.92
5509 9008 2.961062 GAGTATCCATGGGCAAAGCATT 59.039 45.455 13.02 0.00 0.00 3.56
5557 9057 0.389426 CAAAACAGCATGGCTCCAGC 60.389 55.000 0.00 0.00 43.62 4.85
5558 9058 0.389426 GCAAAACAGCATGGCTCCAG 60.389 55.000 0.00 0.00 43.62 3.86
5559 9059 1.667151 GCAAAACAGCATGGCTCCA 59.333 52.632 0.00 0.00 43.62 3.86
5560 9060 1.079612 GGCAAAACAGCATGGCTCC 60.080 57.895 0.00 0.00 43.62 4.70
5561 9061 0.389426 CTGGCAAAACAGCATGGCTC 60.389 55.000 0.00 0.00 43.62 4.70
5562 9062 1.669440 CTGGCAAAACAGCATGGCT 59.331 52.632 0.00 0.00 43.62 4.75
5563 9063 1.375013 CCTGGCAAAACAGCATGGC 60.375 57.895 0.00 0.00 43.62 4.40
5564 9064 1.375013 GCCTGGCAAAACAGCATGG 60.375 57.895 15.17 0.00 43.62 3.66
5565 9065 0.034337 AAGCCTGGCAAAACAGCATG 59.966 50.000 22.65 0.00 46.00 4.06
5704 9237 5.078411 ACCAGTCAGACAAACATAGCTAG 57.922 43.478 2.66 0.00 0.00 3.42
5799 9415 5.125417 GGGCACACAGTACATTATTCAACAT 59.875 40.000 0.00 0.00 0.00 2.71
5808 9424 2.949177 TCTTGGGCACACAGTACATT 57.051 45.000 0.00 0.00 0.00 2.71
5818 9434 1.065551 GGCGATTGTAATCTTGGGCAC 59.934 52.381 3.40 0.00 33.24 5.01
6218 9834 4.716784 AGAGAGGTGTTACATGCCAGAATA 59.283 41.667 0.00 0.00 0.00 1.75
6232 9848 3.312890 CTGGATATCCCAAGAGAGGTGT 58.687 50.000 19.34 0.00 46.07 4.16
6250 9866 5.181056 ACAAAAGGAAAAACAAGTTTGCTGG 59.819 36.000 0.00 0.00 38.92 4.85
6287 9903 4.356405 TCAGAACATCATGTCACCTGTT 57.644 40.909 12.01 0.00 34.68 3.16
6366 9984 6.346919 CCAGTTAGCGCTATGAATATCAACAC 60.347 42.308 19.60 8.62 0.00 3.32
6428 10046 5.523916 CGGATGTGGTCAGAACCTAAAATAG 59.476 44.000 0.00 0.00 46.60 1.73
6549 10167 2.227388 CCAGTGCTGAAGAACAATGTCC 59.773 50.000 0.02 0.00 30.23 4.02
6630 10248 6.315144 TCAAATGTGCAGTATATACACACACC 59.685 38.462 29.24 12.70 46.23 4.16
6631 10249 7.302350 TCAAATGTGCAGTATATACACACAC 57.698 36.000 29.24 23.98 46.23 3.82
6632 10250 9.606631 TTATCAAATGTGCAGTATATACACACA 57.393 29.630 28.99 28.99 46.23 3.72
6826 10470 4.610456 CGCTTTAGTTTCACAGCAAATCGA 60.610 41.667 0.00 0.00 32.17 3.59
6842 10486 7.139392 TCAGTGCTTATGATAGTACGCTTTAG 58.861 38.462 0.00 0.00 36.10 1.85
6845 10489 5.515797 TCAGTGCTTATGATAGTACGCTT 57.484 39.130 0.00 0.00 36.10 4.68
6987 10631 2.376808 ACTCAAACTCATCAGCCGAG 57.623 50.000 0.00 0.00 36.53 4.63
7084 10728 6.038161 CCAATAAATAACAGCACGAGATTCCA 59.962 38.462 0.00 0.00 0.00 3.53
7093 10737 5.567534 CGTGTTCACCAATAAATAACAGCAC 59.432 40.000 0.00 0.00 31.19 4.40
7121 10813 5.517411 GCTACTTGTGTTGGTTTGGTTAAAC 59.483 40.000 0.00 0.00 44.27 2.01
7224 10932 3.030291 TCACCTTCACCAGCATTTGTTT 58.970 40.909 0.00 0.00 0.00 2.83
7370 11078 1.078214 CAGCGGGGAAAGAGCATCA 60.078 57.895 0.00 0.00 37.82 3.07
7382 11090 0.541863 AGTTGGATCTTACCAGCGGG 59.458 55.000 0.00 0.00 44.01 6.13
7385 11093 2.501723 TGAGGAGTTGGATCTTACCAGC 59.498 50.000 0.00 0.00 41.19 4.85
7425 11150 2.036992 TGCATCCTCGCCAAAATGTTTT 59.963 40.909 0.00 0.00 0.00 2.43
7530 11256 8.196802 TCTAGGTCAAAATTTATGTGATCACG 57.803 34.615 20.54 3.50 0.00 4.35
7584 11310 2.787473 ATCGAACATGAGGCCAGAAA 57.213 45.000 5.01 0.00 0.00 2.52
7612 11338 3.515502 TCAGGTGTGAAGGGAGATGTAAG 59.484 47.826 0.00 0.00 0.00 2.34
7626 11354 5.125257 TGGCACATACATTTATTCAGGTGTG 59.875 40.000 0.00 0.00 38.86 3.82
7673 11401 0.531200 ACCGGCAGCAGAGTAAGTAC 59.469 55.000 0.00 0.00 0.00 2.73
7786 11527 7.634671 TCAAGATAAGATTGGTACACGAGTA 57.365 36.000 0.00 0.00 39.29 2.59
7792 11533 7.629157 TGGATGTTCAAGATAAGATTGGTACA 58.371 34.615 0.00 0.00 31.79 2.90
7899 12126 8.678199 CATAGGGAATTCAAAGGAAAGTAAGAC 58.322 37.037 7.93 0.00 36.43 3.01
7936 12172 6.882140 TGGCTTACTCCAAATTTTCGATAGAA 59.118 34.615 0.00 0.00 43.00 2.10
7950 12186 1.340991 GGGCTCATTTGGCTTACTCCA 60.341 52.381 0.00 0.00 0.00 3.86
7958 12194 1.188863 ACATCAAGGGCTCATTTGGC 58.811 50.000 0.00 0.00 0.00 4.52
7967 12203 3.823304 ACAGAGAAGAAAACATCAAGGGC 59.177 43.478 0.00 0.00 0.00 5.19
7975 12211 8.561738 AAAAGTTGTAGACAGAGAAGAAAACA 57.438 30.769 0.00 0.00 0.00 2.83
7976 12212 9.491934 GAAAAAGTTGTAGACAGAGAAGAAAAC 57.508 33.333 0.00 0.00 0.00 2.43
7982 12218 8.262227 TGGTAAGAAAAAGTTGTAGACAGAGAA 58.738 33.333 0.00 0.00 0.00 2.87
7996 12232 9.748708 TTTCAATCTCACATTGGTAAGAAAAAG 57.251 29.630 0.00 0.00 0.00 2.27
8001 12237 6.227522 TCGTTTCAATCTCACATTGGTAAGA 58.772 36.000 0.00 0.00 0.00 2.10
8005 12241 5.964958 AATCGTTTCAATCTCACATTGGT 57.035 34.783 0.00 0.00 0.00 3.67
8039 12293 5.861787 GCATAGGGTAATCAACAACAACAAC 59.138 40.000 0.00 0.00 0.00 3.32
8041 12295 5.073428 TGCATAGGGTAATCAACAACAACA 58.927 37.500 0.00 0.00 0.00 3.33
8042 12296 5.637006 TGCATAGGGTAATCAACAACAAC 57.363 39.130 0.00 0.00 0.00 3.32
8063 12318 2.850060 GTCTGCATCAATCGTTGCAATG 59.150 45.455 12.66 12.66 44.95 2.82
8064 12319 2.159338 GGTCTGCATCAATCGTTGCAAT 60.159 45.455 0.59 0.00 44.95 3.56
8065 12320 1.199789 GGTCTGCATCAATCGTTGCAA 59.800 47.619 0.00 0.00 44.95 4.08
8066 12321 0.804364 GGTCTGCATCAATCGTTGCA 59.196 50.000 0.00 0.00 43.80 4.08
8085 12340 4.925054 CCAAGTTCATGGCACTTATTTGTG 59.075 41.667 9.96 0.00 40.62 3.33
8091 12346 2.513753 CACCCAAGTTCATGGCACTTA 58.486 47.619 9.96 0.00 39.26 2.24
8105 12391 0.250945 TAAGCGTTCATGGCACCCAA 60.251 50.000 0.00 0.00 36.95 4.12
8107 12393 0.170339 GTTAAGCGTTCATGGCACCC 59.830 55.000 0.00 0.00 0.00 4.61
8111 12397 0.793861 TCGTGTTAAGCGTTCATGGC 59.206 50.000 0.00 0.00 0.00 4.40
8148 12434 0.034896 TTCCTCGTCCTGAACTTGCC 59.965 55.000 0.00 0.00 0.00 4.52
8149 12435 1.149148 GTTCCTCGTCCTGAACTTGC 58.851 55.000 0.00 0.00 38.24 4.01
8180 12466 6.858104 CATGTAATGTAATGTGCTTGTGTG 57.142 37.500 0.00 0.00 40.20 3.82
8256 12561 0.871057 TGTGTGTGTGTGTGTGTGTG 59.129 50.000 0.00 0.00 0.00 3.82
8376 12695 2.413142 CCCTACGTCGTCACCTCCC 61.413 68.421 0.00 0.00 0.00 4.30
8502 12821 1.932511 CGGCTGCATTGTTTGTTTGTT 59.067 42.857 0.50 0.00 0.00 2.83


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

AutoCloner maintained by Alex Coulton.