Multiple sequence alignment - TraesCS4A01G327500

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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 TraesCS4A01G327500 chr4A 100.000 4885 0 0 1 4885 613815530 613820414 0.000000e+00 9022
1 TraesCS4A01G327500 chr4A 92.611 203 15 0 2660 2862 97759900 97759698 4.780000e-75 292
2 TraesCS4A01G327500 chr4A 80.714 280 52 2 130 408 599611630 599611352 2.960000e-52 217
3 TraesCS4A01G327500 chr5B 94.996 2258 58 11 406 2659 696026386 696028592 0.000000e+00 3493
4 TraesCS4A01G327500 chr5B 94.404 1108 52 8 3668 4772 696029080 696030180 0.000000e+00 1694
5 TraesCS4A01G327500 chr5B 92.157 408 13 6 1 408 696025916 696026304 4.270000e-155 558
6 TraesCS4A01G327500 chr5B 97.152 316 7 2 3334 3648 696028584 696028898 2.590000e-147 532
7 TraesCS4A01G327500 chr5B 95.763 118 4 1 4769 4885 696077619 696077736 6.450000e-44 189
8 TraesCS4A01G327500 chr1A 96.593 675 11 2 2660 3334 280584690 280585352 0.000000e+00 1109
9 TraesCS4A01G327500 chr5D 83.404 946 96 23 1526 2440 554853733 554852818 0.000000e+00 821
10 TraesCS4A01G327500 chr5D 90.576 573 42 7 848 1415 554854501 554853936 0.000000e+00 749
11 TraesCS4A01G327500 chr5D 93.930 313 17 2 3337 3648 554851465 554851154 5.720000e-129 472
12 TraesCS4A01G327500 chr5D 89.302 215 18 3 2446 2659 554851670 554851460 1.040000e-66 265
13 TraesCS4A01G327500 chr7A 94.072 388 22 1 2947 3334 17715738 17716124 5.450000e-164 588
14 TraesCS4A01G327500 chr7A 94.648 355 19 0 2980 3334 107015289 107015643 7.150000e-153 551
15 TraesCS4A01G327500 chr7A 92.019 213 16 1 2648 2859 2548846 2549058 1.030000e-76 298
16 TraesCS4A01G327500 chr2A 94.809 366 18 1 2970 3334 67672983 67672618 1.970000e-158 569
17 TraesCS4A01G327500 chr7D 93.803 355 22 0 2980 3334 9053349 9053703 7.200000e-148 534
18 TraesCS4A01G327500 chr7D 93.803 355 22 0 2980 3334 629192838 629192484 7.200000e-148 534
19 TraesCS4A01G327500 chr7D 79.643 280 56 1 130 408 81078922 81078643 2.980000e-47 200
20 TraesCS4A01G327500 chr2B 91.710 386 31 1 2949 3334 594195300 594195684 7.200000e-148 534
21 TraesCS4A01G327500 chr2B 85.223 291 38 5 2660 2949 753626053 753625767 1.330000e-75 294
22 TraesCS4A01G327500 chr2B 79.643 280 55 2 130 408 61372742 61373020 2.980000e-47 200
23 TraesCS4A01G327500 chr6A 93.521 355 23 0 2980 3334 49843313 49843667 3.350000e-146 529
24 TraesCS4A01G327500 chr6A 80.072 276 53 2 133 408 599757173 599756900 2.310000e-48 204
25 TraesCS4A01G327500 chr6A 79.577 284 49 7 130 408 64507656 64507935 1.390000e-45 195
26 TraesCS4A01G327500 chr2D 92.603 365 24 2 2972 3334 638453472 638453835 5.600000e-144 521
27 TraesCS4A01G327500 chr2D 84.545 220 32 2 190 408 122538212 122538430 2.960000e-52 217
28 TraesCS4A01G327500 chr2D 81.783 258 42 5 143 396 119823748 119823492 1.380000e-50 211
29 TraesCS4A01G327500 chr2D 100.000 85 0 0 2864 2948 524527208 524527124 1.820000e-34 158
30 TraesCS4A01G327500 chr5A 94.581 203 10 1 2660 2861 606360473 606360271 3.670000e-81 313
31 TraesCS4A01G327500 chr3B 86.207 290 36 3 2660 2948 108413668 108413382 1.320000e-80 311
32 TraesCS4A01G327500 chr3B 85.274 292 32 6 2660 2946 813919148 813918863 1.720000e-74 291
33 TraesCS4A01G327500 chr3A 93.103 203 14 0 2660 2862 726855050 726854848 1.030000e-76 298
34 TraesCS4A01G327500 chr1D 92.718 206 14 1 2658 2862 40933690 40933485 3.700000e-76 296
35 TraesCS4A01G327500 chr1D 81.139 281 50 3 130 408 24205970 24206249 6.360000e-54 222
36 TraesCS4A01G327500 chr1D 100.000 85 0 0 2864 2948 451283635 451283551 1.820000e-34 158
37 TraesCS4A01G327500 chr7B 80.000 270 51 3 130 398 741446213 741445946 3.860000e-46 196
38 TraesCS4A01G327500 chrUn 100.000 85 0 0 2864 2948 19190210 19190294 1.820000e-34 158
39 TraesCS4A01G327500 chrUn 100.000 85 0 0 2864 2948 35368552 35368636 1.820000e-34 158
40 TraesCS4A01G327500 chr3D 100.000 85 0 0 2864 2948 573041177 573041093 1.820000e-34 158


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 TraesCS4A01G327500 chr4A 613815530 613820414 4884 False 9022.00 9022 100.00000 1 4885 1 chr4A.!!$F1 4884
1 TraesCS4A01G327500 chr5B 696025916 696030180 4264 False 1569.25 3493 94.67725 1 4772 4 chr5B.!!$F2 4771
2 TraesCS4A01G327500 chr1A 280584690 280585352 662 False 1109.00 1109 96.59300 2660 3334 1 chr1A.!!$F1 674
3 TraesCS4A01G327500 chr5D 554851154 554854501 3347 True 576.75 821 89.30300 848 3648 4 chr5D.!!$R1 2800

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
297 298 0.033601 ACCACAACAGCCACCAAAGA 60.034 50.0 0.00 0.0 0.00 2.52 F
738 823 0.108615 CTGTCGACCCACCTCATCAC 60.109 60.0 14.12 0.0 0.00 3.06 F
1508 1671 0.248565 GGGACTGGTCGTTTACTCCC 59.751 60.0 0.00 0.0 34.06 4.30 F
1510 1673 0.883833 GACTGGTCGTTTACTCCCGA 59.116 55.0 0.00 0.0 0.00 5.14 F
2729 4087 0.029474 ATTAGGGGACGGGGATGGAA 60.029 55.0 0.00 0.0 0.00 3.53 F
3230 4588 0.392595 GGGGACGGGCAGAAAACTAG 60.393 60.0 0.00 0.0 0.00 2.57 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1490 1653 0.108945 CGGGAGTAAACGACCAGTCC 60.109 60.000 0.0 0.0 34.08 3.85 R
2728 4086 0.676782 CCGCGGGGATGAAAAGACTT 60.677 55.000 20.1 0.0 34.06 3.01 R
2729 4087 1.078426 CCGCGGGGATGAAAAGACT 60.078 57.895 20.1 0.0 34.06 3.24 R
3187 4545 1.747745 CCATCGGGTTTCGGGGAAC 60.748 63.158 0.0 0.0 39.77 3.62 R
3600 4958 0.616964 TCAGCAGCCTGATCTCCAGT 60.617 55.000 0.0 0.0 42.98 4.00 R
4818 6340 0.108804 TCCTCGTCCGACATTGAAGC 60.109 55.000 0.0 0.0 0.00 3.86 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
67 68 8.611654 TCATTGATATGATGAACACCATAGTG 57.388 34.615 0.00 0.00 41.62 2.74
90 91 0.523968 GCCACGTACATGCATGCTTG 60.524 55.000 26.53 26.93 0.00 4.01
91 92 1.085893 CCACGTACATGCATGCTTGA 58.914 50.000 33.07 17.61 0.00 3.02
117 118 0.828677 AAGCCACCTACATACCGACC 59.171 55.000 0.00 0.00 0.00 4.79
161 162 2.930826 ACCGACCTGTCAAAACTGAT 57.069 45.000 0.00 0.00 0.00 2.90
262 263 1.898574 CTTGACAGCAACGCCCCTT 60.899 57.895 0.00 0.00 0.00 3.95
276 277 1.415200 CCCCTTACCTCCTCTAGCAC 58.585 60.000 0.00 0.00 0.00 4.40
283 284 0.904865 CCTCCTCTAGCACCACCACA 60.905 60.000 0.00 0.00 0.00 4.17
284 285 0.976641 CTCCTCTAGCACCACCACAA 59.023 55.000 0.00 0.00 0.00 3.33
285 286 0.685097 TCCTCTAGCACCACCACAAC 59.315 55.000 0.00 0.00 0.00 3.32
286 287 0.396435 CCTCTAGCACCACCACAACA 59.604 55.000 0.00 0.00 0.00 3.33
287 288 1.609061 CCTCTAGCACCACCACAACAG 60.609 57.143 0.00 0.00 0.00 3.16
288 289 0.250295 TCTAGCACCACCACAACAGC 60.250 55.000 0.00 0.00 0.00 4.40
289 290 1.228124 TAGCACCACCACAACAGCC 60.228 57.895 0.00 0.00 0.00 4.85
290 291 1.988982 TAGCACCACCACAACAGCCA 61.989 55.000 0.00 0.00 0.00 4.75
291 292 3.119193 CACCACCACAACAGCCAC 58.881 61.111 0.00 0.00 0.00 5.01
292 293 2.123897 ACCACCACAACAGCCACC 60.124 61.111 0.00 0.00 0.00 4.61
293 294 2.123939 CCACCACAACAGCCACCA 60.124 61.111 0.00 0.00 0.00 4.17
294 295 1.756172 CCACCACAACAGCCACCAA 60.756 57.895 0.00 0.00 0.00 3.67
295 296 1.326213 CCACCACAACAGCCACCAAA 61.326 55.000 0.00 0.00 0.00 3.28
296 297 0.102844 CACCACAACAGCCACCAAAG 59.897 55.000 0.00 0.00 0.00 2.77
297 298 0.033601 ACCACAACAGCCACCAAAGA 60.034 50.000 0.00 0.00 0.00 2.52
298 299 1.110442 CCACAACAGCCACCAAAGAA 58.890 50.000 0.00 0.00 0.00 2.52
299 300 1.688197 CCACAACAGCCACCAAAGAAT 59.312 47.619 0.00 0.00 0.00 2.40
300 301 2.890311 CCACAACAGCCACCAAAGAATA 59.110 45.455 0.00 0.00 0.00 1.75
334 335 1.002250 CTTCACACCCGAGTTCGACG 61.002 60.000 2.59 0.00 43.02 5.12
381 382 0.807667 CGGATCTTCAAGGTGGCTCG 60.808 60.000 0.00 0.00 0.00 5.03
398 399 4.576993 GCCAAAGGCGAAACCATG 57.423 55.556 0.00 0.00 43.14 3.66
429 514 2.277084 CCATACCTGCCTTTCACGTAC 58.723 52.381 0.00 0.00 0.00 3.67
449 534 6.536224 ACGTACCATAAACCTTAGCACATAAC 59.464 38.462 0.00 0.00 0.00 1.89
461 546 6.016777 CCTTAGCACATAACCCATCATCTTTC 60.017 42.308 0.00 0.00 0.00 2.62
509 594 3.231818 CATCCTCTACCGGAATACCTGT 58.768 50.000 9.46 0.00 36.49 4.00
582 667 1.656652 GATGAATCAGGTCCACCACG 58.343 55.000 0.00 0.00 38.89 4.94
622 707 2.419159 CCATCCTTGCTCGAACAGATGA 60.419 50.000 15.76 3.84 34.40 2.92
661 746 3.721172 ATGGAGCCGATGACCCCCT 62.721 63.158 0.00 0.00 0.00 4.79
676 761 1.153628 CCCTTCATCACCGACGACC 60.154 63.158 0.00 0.00 0.00 4.79
711 796 6.470557 TTTGACCTAAAACTATACACACGC 57.529 37.500 0.00 0.00 0.00 5.34
713 798 3.514645 ACCTAAAACTATACACACGCGG 58.485 45.455 12.47 1.27 0.00 6.46
714 799 2.861935 CCTAAAACTATACACACGCGGG 59.138 50.000 6.92 6.92 0.00 6.13
720 805 0.468585 TATACACACGCGGGGGATCT 60.469 55.000 22.47 3.03 0.00 2.75
722 807 4.082523 CACACGCGGGGGATCTGT 62.083 66.667 15.46 0.91 0.00 3.41
738 823 0.108615 CTGTCGACCCACCTCATCAC 60.109 60.000 14.12 0.00 0.00 3.06
739 824 1.218316 GTCGACCCACCTCATCACC 59.782 63.158 3.51 0.00 0.00 4.02
774 859 4.816984 GAGGAGGGGAGCCGTCGA 62.817 72.222 0.00 0.00 39.08 4.20
777 862 2.754658 GAGGGGAGCCGTCGAAGA 60.755 66.667 0.00 0.00 0.00 2.87
819 904 2.969628 TCAAGATCGCCTCTTCCTTC 57.030 50.000 0.00 0.00 42.48 3.46
822 907 0.741915 AGATCGCCTCTTCCTTCGAC 59.258 55.000 0.00 0.00 33.59 4.20
871 956 0.461339 AGTCGAGGTTTGCACGTGTT 60.461 50.000 18.38 0.00 0.00 3.32
889 974 1.211212 GTTAACAGCCTAATCCCCGGT 59.789 52.381 0.00 0.00 0.00 5.28
971 1056 1.268899 CCCGATCGATATATACGCCCC 59.731 57.143 18.66 0.00 0.00 5.80
972 1057 2.228059 CCGATCGATATATACGCCCCT 58.772 52.381 18.66 0.00 0.00 4.79
973 1058 3.405831 CCGATCGATATATACGCCCCTA 58.594 50.000 18.66 0.00 0.00 3.53
998 1083 3.244700 CCCCTGCCAAAGAATCGATCTAT 60.245 47.826 0.00 0.00 37.42 1.98
1115 1200 2.732619 CCGAGCTACCCCTGTTCCC 61.733 68.421 0.00 0.00 0.00 3.97
1238 1323 1.895020 TTTACTGGATCCACGCGGCT 61.895 55.000 11.44 0.00 0.00 5.52
1498 1661 7.336396 AGTAAAAGTATGTATTGGGACTGGTC 58.664 38.462 0.00 0.00 0.00 4.02
1505 1668 3.579586 TGTATTGGGACTGGTCGTTTACT 59.420 43.478 0.00 0.00 0.00 2.24
1506 1669 2.825861 TTGGGACTGGTCGTTTACTC 57.174 50.000 0.00 0.00 0.00 2.59
1507 1670 0.971386 TGGGACTGGTCGTTTACTCC 59.029 55.000 0.00 0.00 0.00 3.85
1508 1671 0.248565 GGGACTGGTCGTTTACTCCC 59.751 60.000 0.00 0.00 34.06 4.30
1510 1673 0.883833 GACTGGTCGTTTACTCCCGA 59.116 55.000 0.00 0.00 0.00 5.14
1675 1856 1.760268 CTGATCGCGCTCCAGCTTTC 61.760 60.000 7.59 0.00 39.32 2.62
1794 1981 8.850156 ACATCTGGTAATTAAGAATAACCATGC 58.150 33.333 0.00 0.00 39.40 4.06
1795 1982 8.849168 CATCTGGTAATTAAGAATAACCATGCA 58.151 33.333 0.00 0.00 39.40 3.96
1870 2057 2.480419 CAGCTAGCTAAGTTGTGCGTTT 59.520 45.455 18.86 0.00 32.12 3.60
1880 2067 9.716507 AGCTAAGTTGTGCGTTTATTATATTTG 57.283 29.630 0.00 0.00 0.00 2.32
1901 2088 2.668280 GCGCGTGTTTCCTGGAGAC 61.668 63.158 8.43 10.29 0.00 3.36
2251 2465 7.573968 AAATAATAATGGAGTGGTCAAGCTC 57.426 36.000 0.00 0.00 0.00 4.09
2617 3973 0.886043 GGTTGCTCGGGGTACGTTTT 60.886 55.000 0.00 0.00 44.69 2.43
2728 4086 0.868894 TATTAGGGGACGGGGATGGA 59.131 55.000 0.00 0.00 0.00 3.41
2729 4087 0.029474 ATTAGGGGACGGGGATGGAA 60.029 55.000 0.00 0.00 0.00 3.53
3046 4404 8.383619 GCCGTTGAAATACATTCTATATAGCTG 58.616 37.037 4.75 7.57 38.92 4.24
3179 4537 8.026607 TGAATATTTTGATTTTCTCGTGGGTTC 58.973 33.333 0.00 0.00 0.00 3.62
3180 4538 4.577834 TTTTGATTTTCTCGTGGGTTCC 57.422 40.909 0.00 0.00 0.00 3.62
3181 4539 2.194201 TGATTTTCTCGTGGGTTCCC 57.806 50.000 0.12 0.12 0.00 3.97
3182 4540 1.271707 TGATTTTCTCGTGGGTTCCCC 60.272 52.381 5.34 0.00 45.71 4.81
3230 4588 0.392595 GGGGACGGGCAGAAAACTAG 60.393 60.000 0.00 0.00 0.00 2.57
3321 4679 2.510691 CGATGGGTTTCGTCCCCG 60.511 66.667 9.69 4.70 45.86 5.73
3334 4692 0.394352 GTCCCCGTTGCCATCTTGAT 60.394 55.000 0.00 0.00 0.00 2.57
3335 4693 0.394216 TCCCCGTTGCCATCTTGATG 60.394 55.000 3.77 3.77 0.00 3.07
3336 4694 0.680921 CCCCGTTGCCATCTTGATGT 60.681 55.000 9.41 0.00 0.00 3.06
3337 4695 0.452987 CCCGTTGCCATCTTGATGTG 59.547 55.000 9.41 3.16 0.00 3.21
3338 4696 1.167851 CCGTTGCCATCTTGATGTGT 58.832 50.000 9.41 0.00 0.00 3.72
3339 4697 2.355197 CCGTTGCCATCTTGATGTGTA 58.645 47.619 9.41 0.00 0.00 2.90
3340 4698 2.945008 CCGTTGCCATCTTGATGTGTAT 59.055 45.455 9.41 0.00 0.00 2.29
3341 4699 4.126437 CCGTTGCCATCTTGATGTGTATA 58.874 43.478 9.41 0.00 0.00 1.47
3342 4700 4.024893 CCGTTGCCATCTTGATGTGTATAC 60.025 45.833 9.41 0.00 0.00 1.47
3343 4701 4.024893 CGTTGCCATCTTGATGTGTATACC 60.025 45.833 9.41 0.00 0.00 2.73
3344 4702 5.126067 GTTGCCATCTTGATGTGTATACCT 58.874 41.667 9.41 0.00 0.00 3.08
3345 4703 5.372343 TGCCATCTTGATGTGTATACCTT 57.628 39.130 9.41 0.00 0.00 3.50
3371 4729 7.279615 TCAACTTCTGATTGTCAAGAACCTAA 58.720 34.615 0.00 0.00 0.00 2.69
3488 4846 2.131183 GCCATGATAGCACTTCTCGTC 58.869 52.381 0.00 0.00 0.00 4.20
3600 4958 5.820947 GTGTGTTCCTACTTTGAAAGGAGAA 59.179 40.000 18.54 10.02 42.39 2.87
3626 4984 4.387598 GAGATCAGGCTGCTGATGTATTT 58.612 43.478 10.34 0.00 43.38 1.40
3638 4996 4.213059 GCTGATGTATTTCTGCCTCTAAGC 59.787 45.833 0.00 0.00 35.30 3.09
3655 5013 1.769026 AGCGGACTAGCTCAGAATCA 58.231 50.000 0.00 0.00 45.67 2.57
3657 5015 1.407258 GCGGACTAGCTCAGAATCAGT 59.593 52.381 0.00 0.00 0.00 3.41
3658 5016 2.159170 GCGGACTAGCTCAGAATCAGTT 60.159 50.000 0.00 0.00 0.00 3.16
3660 5018 3.129462 CGGACTAGCTCAGAATCAGTTCA 59.871 47.826 0.00 0.00 36.79 3.18
3661 5019 4.202101 CGGACTAGCTCAGAATCAGTTCAT 60.202 45.833 0.00 0.00 36.79 2.57
3662 5020 5.669477 GGACTAGCTCAGAATCAGTTCATT 58.331 41.667 0.00 0.00 36.79 2.57
3665 5023 7.201866 GGACTAGCTCAGAATCAGTTCATTAGA 60.202 40.741 0.00 0.00 36.79 2.10
3666 5024 7.715657 ACTAGCTCAGAATCAGTTCATTAGAG 58.284 38.462 0.00 0.00 36.79 2.43
3690 5210 9.630098 GAGATGAAAAACAAGCAGAATCATTTA 57.370 29.630 0.00 0.00 0.00 1.40
3736 5256 7.628234 AGAGAGAAAATCAGCTCTTTATCCAA 58.372 34.615 0.00 0.00 41.33 3.53
3754 5274 4.285863 TCCAAACATCTCCCAAACTTTGT 58.714 39.130 0.88 0.00 0.00 2.83
3779 5299 6.876789 TGTCATACAAGTCGAAACACCATAAT 59.123 34.615 0.00 0.00 0.00 1.28
3830 5350 9.738832 TTTTGAATAGTTTTTAGTGCTTACCAC 57.261 29.630 0.00 0.00 45.01 4.16
3841 5361 2.289547 GTGCTTACCACAATGTCACGTT 59.710 45.455 0.00 0.00 44.06 3.99
3850 5370 5.124138 ACCACAATGTCACGTTGTAAAAAGA 59.876 36.000 15.15 0.00 37.69 2.52
3890 5410 8.784994 TGTAAGTCGAATAACAGCCAAATAAAA 58.215 29.630 0.00 0.00 0.00 1.52
3891 5411 9.615295 GTAAGTCGAATAACAGCCAAATAAAAA 57.385 29.630 0.00 0.00 0.00 1.94
3932 5452 1.969923 CATCAACCCCACCAACACAAT 59.030 47.619 0.00 0.00 0.00 2.71
3936 5456 2.433970 CAACCCCACCAACACAATTTCT 59.566 45.455 0.00 0.00 0.00 2.52
3952 5472 9.480053 ACACAATTTCTCATCCAACAAATAAAG 57.520 29.630 0.00 0.00 0.00 1.85
3993 5513 8.398665 GCTTCTCTTATGTTTAGGGTTATTGTG 58.601 37.037 0.00 0.00 0.00 3.33
4014 5534 7.214467 TGTGGTCTTTTAGAAAAATAGGCTG 57.786 36.000 0.00 0.00 0.00 4.85
4019 5539 8.023706 GGTCTTTTAGAAAAATAGGCTGTCTTG 58.976 37.037 0.00 0.00 0.00 3.02
4032 5552 3.628032 GGCTGTCTTGCCCTTTTATAGAC 59.372 47.826 0.00 0.00 46.82 2.59
4035 5555 6.113411 GCTGTCTTGCCCTTTTATAGACTAA 58.887 40.000 0.00 0.00 36.91 2.24
4036 5556 6.768381 GCTGTCTTGCCCTTTTATAGACTAAT 59.232 38.462 0.00 0.00 36.91 1.73
4091 5611 4.222366 TCATGGGCAAAATCATTGTAGCAA 59.778 37.500 0.00 0.00 0.00 3.91
4195 5717 3.902881 AATGCACACAGTTGGGAAAAA 57.097 38.095 0.00 0.00 0.00 1.94
4219 5741 6.396450 ACTAAAATCAGAAGTACCCTCGTTC 58.604 40.000 0.00 0.00 0.00 3.95
4236 5758 5.048991 CCTCGTTCCCGATAATATTTTTGGG 60.049 44.000 20.21 20.21 43.27 4.12
4243 5765 7.228590 TCCCGATAATATTTTTGGGTTCCTAG 58.771 38.462 23.46 4.37 37.88 3.02
4259 5781 7.016661 TGGGTTCCTAGCATTTTTATTTTTCCA 59.983 33.333 0.00 0.00 0.00 3.53
4373 5895 5.385509 TGAAGTGTCTCGTATGTGAATCA 57.614 39.130 0.00 0.00 0.00 2.57
4440 5962 5.947566 AGTCAGAGTCTTCTTACTAGGAACC 59.052 44.000 0.00 0.00 36.40 3.62
4442 5964 7.037442 AGTCAGAGTCTTCTTACTAGGAACCTA 60.037 40.741 0.00 0.50 36.40 3.08
4604 6126 5.086621 AGGAAAATAAGAAGTGCCCAACAT 58.913 37.500 0.00 0.00 0.00 2.71
4605 6127 5.047092 AGGAAAATAAGAAGTGCCCAACATG 60.047 40.000 0.00 0.00 0.00 3.21
4772 6294 5.995565 ATTATTTCATCCTCATGCCATGG 57.004 39.130 7.63 7.63 0.00 3.66
4773 6295 1.405872 TTTCATCCTCATGCCATGGC 58.594 50.000 30.54 30.54 42.35 4.40
4774 6296 0.554305 TTCATCCTCATGCCATGGCT 59.446 50.000 35.53 19.42 42.51 4.75
4775 6297 1.437397 TCATCCTCATGCCATGGCTA 58.563 50.000 35.53 22.71 42.51 3.93
4776 6298 1.990327 TCATCCTCATGCCATGGCTAT 59.010 47.619 35.53 23.84 42.51 2.97
4777 6299 2.026542 TCATCCTCATGCCATGGCTATC 60.027 50.000 35.53 9.29 42.51 2.08
4778 6300 1.437397 TCCTCATGCCATGGCTATCA 58.563 50.000 35.53 17.68 42.51 2.15
4779 6301 1.072806 TCCTCATGCCATGGCTATCAC 59.927 52.381 35.53 8.10 42.51 3.06
4780 6302 1.202842 CCTCATGCCATGGCTATCACA 60.203 52.381 35.53 16.49 42.51 3.58
4781 6303 2.554564 CCTCATGCCATGGCTATCACAT 60.555 50.000 35.53 18.09 42.51 3.21
4782 6304 2.488153 CTCATGCCATGGCTATCACATG 59.512 50.000 35.53 27.44 44.03 3.21
4783 6305 2.158579 TCATGCCATGGCTATCACATGT 60.159 45.455 35.53 8.94 43.15 3.21
4784 6306 1.682740 TGCCATGGCTATCACATGTG 58.317 50.000 35.53 20.18 43.15 3.21
4785 6307 1.064537 TGCCATGGCTATCACATGTGT 60.065 47.619 35.53 14.61 43.15 3.72
4786 6308 1.335810 GCCATGGCTATCACATGTGTG 59.664 52.381 29.98 16.45 43.15 3.82
4787 6309 1.335810 CCATGGCTATCACATGTGTGC 59.664 52.381 24.63 23.56 45.25 4.57
4788 6310 2.018515 CATGGCTATCACATGTGTGCA 58.981 47.619 27.78 19.54 45.25 4.57
4789 6311 1.741528 TGGCTATCACATGTGTGCAG 58.258 50.000 27.78 21.98 45.25 4.41
4790 6312 1.003464 TGGCTATCACATGTGTGCAGT 59.997 47.619 27.78 14.92 45.25 4.40
4791 6313 2.235898 TGGCTATCACATGTGTGCAGTA 59.764 45.455 27.78 17.59 45.25 2.74
4792 6314 3.118298 TGGCTATCACATGTGTGCAGTAT 60.118 43.478 27.78 17.18 45.25 2.12
4793 6315 3.879295 GGCTATCACATGTGTGCAGTATT 59.121 43.478 27.78 10.71 45.25 1.89
4794 6316 5.056480 GGCTATCACATGTGTGCAGTATTA 58.944 41.667 27.78 10.69 45.25 0.98
4795 6317 5.178252 GGCTATCACATGTGTGCAGTATTAG 59.822 44.000 27.78 17.34 45.25 1.73
4796 6318 5.333645 GCTATCACATGTGTGCAGTATTAGC 60.334 44.000 24.63 18.06 45.25 3.09
4797 6319 3.270027 TCACATGTGTGCAGTATTAGCC 58.730 45.455 24.63 0.00 45.25 3.93
4798 6320 3.009026 CACATGTGTGCAGTATTAGCCA 58.991 45.455 18.03 0.00 39.39 4.75
4799 6321 3.628942 CACATGTGTGCAGTATTAGCCAT 59.371 43.478 18.03 0.00 39.39 4.40
4800 6322 3.628942 ACATGTGTGCAGTATTAGCCATG 59.371 43.478 0.00 0.00 36.16 3.66
4801 6323 3.348647 TGTGTGCAGTATTAGCCATGT 57.651 42.857 0.00 0.00 0.00 3.21
4802 6324 3.009026 TGTGTGCAGTATTAGCCATGTG 58.991 45.455 0.00 0.00 0.00 3.21
4803 6325 3.270027 GTGTGCAGTATTAGCCATGTGA 58.730 45.455 0.00 0.00 0.00 3.58
4804 6326 3.879295 GTGTGCAGTATTAGCCATGTGAT 59.121 43.478 0.00 0.00 0.00 3.06
4805 6327 4.024556 GTGTGCAGTATTAGCCATGTGATC 60.025 45.833 0.00 0.00 0.00 2.92
4806 6328 4.129380 GTGCAGTATTAGCCATGTGATCA 58.871 43.478 0.00 0.00 0.00 2.92
4807 6329 4.212847 GTGCAGTATTAGCCATGTGATCAG 59.787 45.833 0.00 0.00 0.00 2.90
4808 6330 4.101430 TGCAGTATTAGCCATGTGATCAGA 59.899 41.667 0.00 0.00 0.00 3.27
4809 6331 5.221783 TGCAGTATTAGCCATGTGATCAGAT 60.222 40.000 0.00 0.00 0.00 2.90
4810 6332 6.014327 TGCAGTATTAGCCATGTGATCAGATA 60.014 38.462 4.82 0.00 0.00 1.98
4811 6333 7.046652 GCAGTATTAGCCATGTGATCAGATAT 58.953 38.462 4.82 0.00 0.00 1.63
4812 6334 7.224362 GCAGTATTAGCCATGTGATCAGATATC 59.776 40.741 4.82 0.00 0.00 1.63
4813 6335 8.255905 CAGTATTAGCCATGTGATCAGATATCA 58.744 37.037 4.82 0.00 0.00 2.15
4814 6336 8.819845 AGTATTAGCCATGTGATCAGATATCAA 58.180 33.333 4.82 0.00 0.00 2.57
4815 6337 9.440773 GTATTAGCCATGTGATCAGATATCAAA 57.559 33.333 4.82 0.00 0.00 2.69
4817 6339 8.557592 TTAGCCATGTGATCAGATATCAAATC 57.442 34.615 4.82 7.80 0.00 2.17
4818 6340 5.642491 AGCCATGTGATCAGATATCAAATCG 59.358 40.000 4.82 0.00 0.00 3.34
4819 6341 5.673068 GCCATGTGATCAGATATCAAATCGC 60.673 44.000 17.49 17.49 0.00 4.58
4820 6342 5.642491 CCATGTGATCAGATATCAAATCGCT 59.358 40.000 21.62 11.35 31.53 4.93
4821 6343 6.148976 CCATGTGATCAGATATCAAATCGCTT 59.851 38.462 21.62 16.31 31.53 4.68
4822 6344 6.775939 TGTGATCAGATATCAAATCGCTTC 57.224 37.500 21.62 10.59 31.53 3.86
4823 6345 6.282930 TGTGATCAGATATCAAATCGCTTCA 58.717 36.000 21.62 12.14 31.53 3.02
4824 6346 6.762661 TGTGATCAGATATCAAATCGCTTCAA 59.237 34.615 21.62 7.81 31.53 2.69
4825 6347 7.443272 TGTGATCAGATATCAAATCGCTTCAAT 59.557 33.333 21.62 0.00 31.53 2.57
4826 6348 7.745155 GTGATCAGATATCAAATCGCTTCAATG 59.255 37.037 17.23 0.42 0.00 2.82
4827 6349 7.443272 TGATCAGATATCAAATCGCTTCAATGT 59.557 33.333 5.32 0.00 0.00 2.71
4828 6350 7.182361 TCAGATATCAAATCGCTTCAATGTC 57.818 36.000 5.32 0.00 0.00 3.06
4829 6351 6.069563 CAGATATCAAATCGCTTCAATGTCG 58.930 40.000 5.32 0.00 0.00 4.35
4830 6352 3.680642 ATCAAATCGCTTCAATGTCGG 57.319 42.857 0.00 0.00 0.00 4.79
4831 6353 2.694213 TCAAATCGCTTCAATGTCGGA 58.306 42.857 0.00 0.00 0.00 4.55
4832 6354 2.415168 TCAAATCGCTTCAATGTCGGAC 59.585 45.455 0.00 0.00 0.00 4.79
4833 6355 0.999406 AATCGCTTCAATGTCGGACG 59.001 50.000 3.34 0.00 0.00 4.79
4834 6356 0.172578 ATCGCTTCAATGTCGGACGA 59.827 50.000 3.34 0.00 0.00 4.20
4835 6357 0.456142 TCGCTTCAATGTCGGACGAG 60.456 55.000 3.34 0.00 0.00 4.18
4836 6358 1.413767 CGCTTCAATGTCGGACGAGG 61.414 60.000 3.34 0.00 0.00 4.63
4837 6359 0.108804 GCTTCAATGTCGGACGAGGA 60.109 55.000 3.34 0.00 0.00 3.71
4838 6360 1.914634 CTTCAATGTCGGACGAGGAG 58.085 55.000 3.34 0.00 0.00 3.69
4839 6361 0.108804 TTCAATGTCGGACGAGGAGC 60.109 55.000 3.34 0.00 0.00 4.70
4840 6362 1.519455 CAATGTCGGACGAGGAGCC 60.519 63.158 3.34 0.00 0.00 4.70
4841 6363 2.722201 AATGTCGGACGAGGAGCCC 61.722 63.158 3.34 0.00 0.00 5.19
4844 6366 4.377760 TCGGACGAGGAGCCCCTT 62.378 66.667 0.00 0.00 44.53 3.95
4845 6367 2.441532 CGGACGAGGAGCCCCTTA 60.442 66.667 0.00 0.00 44.53 2.69
4846 6368 2.056223 CGGACGAGGAGCCCCTTAA 61.056 63.158 0.00 0.00 44.53 1.85
4847 6369 1.823976 GGACGAGGAGCCCCTTAAG 59.176 63.158 0.00 0.00 44.53 1.85
4848 6370 0.686769 GGACGAGGAGCCCCTTAAGA 60.687 60.000 3.36 0.00 44.53 2.10
4849 6371 1.192428 GACGAGGAGCCCCTTAAGAA 58.808 55.000 3.36 0.00 44.53 2.52
4850 6372 1.553704 GACGAGGAGCCCCTTAAGAAA 59.446 52.381 3.36 0.00 44.53 2.52
4851 6373 1.982958 ACGAGGAGCCCCTTAAGAAAA 59.017 47.619 3.36 0.00 44.53 2.29
4852 6374 2.374170 ACGAGGAGCCCCTTAAGAAAAA 59.626 45.455 3.36 0.00 44.53 1.94
4853 6375 3.010250 ACGAGGAGCCCCTTAAGAAAAAT 59.990 43.478 3.36 0.00 44.53 1.82
4854 6376 4.226620 ACGAGGAGCCCCTTAAGAAAAATA 59.773 41.667 3.36 0.00 44.53 1.40
4855 6377 5.104067 ACGAGGAGCCCCTTAAGAAAAATAT 60.104 40.000 3.36 0.00 44.53 1.28
4856 6378 5.239525 CGAGGAGCCCCTTAAGAAAAATATG 59.760 44.000 3.36 0.00 44.53 1.78
4857 6379 6.092346 AGGAGCCCCTTAAGAAAAATATGT 57.908 37.500 3.36 0.00 40.78 2.29
4858 6380 6.503041 AGGAGCCCCTTAAGAAAAATATGTT 58.497 36.000 3.36 0.00 40.78 2.71
4859 6381 6.607600 AGGAGCCCCTTAAGAAAAATATGTTC 59.392 38.462 3.36 0.00 40.78 3.18
4860 6382 6.379988 GGAGCCCCTTAAGAAAAATATGTTCA 59.620 38.462 3.36 0.00 0.00 3.18
4861 6383 7.093509 GGAGCCCCTTAAGAAAAATATGTTCAA 60.094 37.037 3.36 0.00 0.00 2.69
4862 6384 8.379428 AGCCCCTTAAGAAAAATATGTTCAAT 57.621 30.769 3.36 0.00 0.00 2.57
4863 6385 9.487442 AGCCCCTTAAGAAAAATATGTTCAATA 57.513 29.630 3.36 0.00 0.00 1.90
4864 6386 9.529325 GCCCCTTAAGAAAAATATGTTCAATAC 57.471 33.333 3.36 0.00 0.00 1.89
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
19 20 4.028993 ACACGTAGGACCATGGAAAATT 57.971 40.909 21.47 0.00 0.00 1.82
67 68 1.268032 GCATGCATGTACGTGGCTTAC 60.268 52.381 26.79 2.80 0.00 2.34
117 118 4.335315 TGTAAGTGGCTTCAGTTTTGACTG 59.665 41.667 0.20 0.20 35.77 3.51
128 129 2.167900 AGGTCGGTATGTAAGTGGCTTC 59.832 50.000 0.00 0.00 0.00 3.86
136 137 4.992319 CAGTTTTGACAGGTCGGTATGTAA 59.008 41.667 0.00 0.00 0.00 2.41
161 162 5.633601 CAGAGACTAGTGTTTTGTTATGCGA 59.366 40.000 0.00 0.00 0.00 5.10
262 263 0.708209 TGGTGGTGCTAGAGGAGGTA 59.292 55.000 0.00 0.00 0.00 3.08
276 277 1.326213 TTTGGTGGCTGTTGTGGTGG 61.326 55.000 0.00 0.00 0.00 4.61
283 284 4.339814 TCGTTTTATTCTTTGGTGGCTGTT 59.660 37.500 0.00 0.00 0.00 3.16
284 285 3.886505 TCGTTTTATTCTTTGGTGGCTGT 59.113 39.130 0.00 0.00 0.00 4.40
285 286 4.497473 TCGTTTTATTCTTTGGTGGCTG 57.503 40.909 0.00 0.00 0.00 4.85
286 287 4.082245 CCATCGTTTTATTCTTTGGTGGCT 60.082 41.667 0.00 0.00 0.00 4.75
287 288 4.082463 TCCATCGTTTTATTCTTTGGTGGC 60.082 41.667 0.00 0.00 0.00 5.01
288 289 5.637006 TCCATCGTTTTATTCTTTGGTGG 57.363 39.130 0.00 0.00 0.00 4.61
289 290 6.747280 GTGATCCATCGTTTTATTCTTTGGTG 59.253 38.462 0.00 0.00 0.00 4.17
290 291 6.127730 GGTGATCCATCGTTTTATTCTTTGGT 60.128 38.462 0.00 0.00 0.00 3.67
291 292 6.095440 AGGTGATCCATCGTTTTATTCTTTGG 59.905 38.462 0.00 0.00 35.89 3.28
292 293 7.088589 AGGTGATCCATCGTTTTATTCTTTG 57.911 36.000 0.00 0.00 35.89 2.77
293 294 7.393234 TGAAGGTGATCCATCGTTTTATTCTTT 59.607 33.333 0.00 0.00 34.54 2.52
294 295 6.884295 TGAAGGTGATCCATCGTTTTATTCTT 59.116 34.615 0.00 0.00 34.54 2.52
295 296 6.316390 GTGAAGGTGATCCATCGTTTTATTCT 59.684 38.462 0.00 0.00 34.54 2.40
296 297 6.093495 TGTGAAGGTGATCCATCGTTTTATTC 59.907 38.462 0.00 0.00 34.54 1.75
297 298 5.943416 TGTGAAGGTGATCCATCGTTTTATT 59.057 36.000 0.00 0.00 34.54 1.40
298 299 5.354234 GTGTGAAGGTGATCCATCGTTTTAT 59.646 40.000 0.00 0.00 34.54 1.40
299 300 4.693566 GTGTGAAGGTGATCCATCGTTTTA 59.306 41.667 0.00 0.00 34.54 1.52
300 301 3.502211 GTGTGAAGGTGATCCATCGTTTT 59.498 43.478 0.00 0.00 34.54 2.43
334 335 0.179181 CATATCAATGATGGCGCCGC 60.179 55.000 23.90 17.28 34.84 6.53
381 382 0.388520 GTCATGGTTTCGCCTTTGGC 60.389 55.000 0.00 0.00 46.75 4.52
398 399 2.427095 GGCAGGTATGGTTTCAATGGTC 59.573 50.000 0.00 0.00 0.00 4.02
429 514 5.197451 TGGGTTATGTGCTAAGGTTTATGG 58.803 41.667 0.00 0.00 0.00 2.74
461 546 1.306148 ATCAGCATCGGCAACATCTG 58.694 50.000 0.00 0.00 44.61 2.90
467 552 3.119209 TGCAAATTAATCAGCATCGGCAA 60.119 39.130 9.86 0.00 44.61 4.52
509 594 2.192187 TGGCGCACATGCAGTTTGA 61.192 52.632 10.83 0.00 42.21 2.69
565 650 0.320374 GTCGTGGTGGACCTGATTCA 59.680 55.000 0.00 0.00 36.82 2.57
582 667 2.813908 GGTGGTGATGCCGTCGTC 60.814 66.667 0.00 0.00 41.21 4.20
661 746 1.210931 GTCGGTCGTCGGTGATGAA 59.789 57.895 0.00 0.00 39.77 2.57
711 796 3.537874 GGGTCGACAGATCCCCCG 61.538 72.222 18.91 0.00 41.91 5.73
720 805 1.541310 GGTGATGAGGTGGGTCGACA 61.541 60.000 18.91 0.00 0.00 4.35
722 807 2.348104 CGGTGATGAGGTGGGTCGA 61.348 63.158 0.00 0.00 0.00 4.20
774 859 1.004918 CGTCGCCAGGGAGTTTCTT 60.005 57.895 0.00 0.00 0.00 2.52
795 880 2.829741 AAGAGGCGATCTTGATAGCC 57.170 50.000 21.70 21.70 46.80 3.93
837 922 3.058914 CCTCGACTGGTAAACAAGCAAAG 60.059 47.826 0.00 0.00 34.56 2.77
871 956 1.125633 GACCGGGGATTAGGCTGTTA 58.874 55.000 6.32 0.00 0.00 2.41
889 974 2.047655 GGCGTCGATGTGGTTGGA 60.048 61.111 6.48 0.00 0.00 3.53
971 1056 2.743183 CGATTCTTTGGCAGGGGAGTAG 60.743 54.545 0.00 0.00 0.00 2.57
972 1057 1.209504 CGATTCTTTGGCAGGGGAGTA 59.790 52.381 0.00 0.00 0.00 2.59
973 1058 0.035056 CGATTCTTTGGCAGGGGAGT 60.035 55.000 0.00 0.00 0.00 3.85
1115 1200 2.358737 AGCGCCTTGTTCCGGAAG 60.359 61.111 19.50 5.79 0.00 3.46
1490 1653 0.108945 CGGGAGTAAACGACCAGTCC 60.109 60.000 0.00 0.00 34.08 3.85
1498 1661 1.000060 TCAACCAGTCGGGAGTAAACG 60.000 52.381 0.00 0.00 41.15 3.60
1505 1668 0.178973 TGAGAGTCAACCAGTCGGGA 60.179 55.000 0.00 0.00 41.15 5.14
1506 1669 0.898320 ATGAGAGTCAACCAGTCGGG 59.102 55.000 0.00 0.00 44.81 5.14
1507 1670 1.273606 ACATGAGAGTCAACCAGTCGG 59.726 52.381 0.00 0.00 38.77 4.79
1508 1671 2.288457 ACACATGAGAGTCAACCAGTCG 60.288 50.000 0.00 0.00 0.00 4.18
1510 1673 4.955811 TTACACATGAGAGTCAACCAGT 57.044 40.909 0.00 0.00 0.00 4.00
1511 1674 7.905604 TTAATTACACATGAGAGTCAACCAG 57.094 36.000 0.00 0.00 0.00 4.00
1513 1676 9.774742 GAAATTAATTACACATGAGAGTCAACC 57.225 33.333 0.00 0.00 0.00 3.77
1542 1723 7.255486 GGACCTATCCCTGCATATGTTAAAAAC 60.255 40.741 4.29 0.00 39.39 2.43
1800 1987 1.131504 TGCGCGCGGATAAAAAGAATT 59.868 42.857 33.06 0.00 0.00 2.17
1801 1988 0.730265 TGCGCGCGGATAAAAAGAAT 59.270 45.000 33.06 0.00 0.00 2.40
1806 1993 2.137129 TAGTATGCGCGCGGATAAAA 57.863 45.000 39.19 28.23 30.50 1.52
1813 2000 3.907178 ATGAATATTAGTATGCGCGCG 57.093 42.857 28.44 28.44 0.00 6.86
1814 2001 9.358123 CTTATTTATGAATATTAGTATGCGCGC 57.642 33.333 27.26 27.26 0.00 6.86
1870 2057 6.702723 AGGAAACACGCGCTACAAATATAATA 59.297 34.615 5.73 0.00 0.00 0.98
1880 2067 1.352156 CTCCAGGAAACACGCGCTAC 61.352 60.000 5.73 0.00 0.00 3.58
1901 2088 4.279420 TGACGATCTTGTCTCCTCCATATG 59.721 45.833 0.00 0.00 39.64 1.78
2251 2465 3.121030 CGCTTCCAACTGCCGAGG 61.121 66.667 0.00 0.00 0.00 4.63
2395 2611 1.722011 ACCACGCCAAGATTTCGTAG 58.278 50.000 0.00 0.00 34.81 3.51
2396 2612 2.231964 AGTACCACGCCAAGATTTCGTA 59.768 45.455 0.00 0.00 34.81 3.43
2728 4086 0.676782 CCGCGGGGATGAAAAGACTT 60.677 55.000 20.10 0.00 34.06 3.01
2729 4087 1.078426 CCGCGGGGATGAAAAGACT 60.078 57.895 20.10 0.00 34.06 3.24
2755 4113 2.955660 CGGGTTGTATAATGTGCCCAAT 59.044 45.455 0.00 0.00 35.99 3.16
2789 4147 3.219281 ACTATTGAAACGGGTGCAAACT 58.781 40.909 0.00 0.00 0.00 2.66
2827 4185 3.157750 TGTATTTTGCCGGGTTTACCT 57.842 42.857 2.18 0.00 36.97 3.08
3074 4432 7.031372 TCAGCATCATAACTTGAGCAAATTTC 58.969 34.615 0.00 0.00 37.89 2.17
3187 4545 1.747745 CCATCGGGTTTCGGGGAAC 60.748 63.158 0.00 0.00 39.77 3.62
3188 4546 2.672295 CCATCGGGTTTCGGGGAA 59.328 61.111 0.00 0.00 39.77 3.97
3189 4547 3.404438 CCCATCGGGTTTCGGGGA 61.404 66.667 0.00 0.00 41.14 4.81
3321 4679 5.126067 AGGTATACACATCAAGATGGCAAC 58.874 41.667 14.04 0.00 42.91 4.17
3334 4692 7.936847 ACAATCAGAAGTTGAAAGGTATACACA 59.063 33.333 5.01 0.00 39.77 3.72
3335 4693 8.324163 ACAATCAGAAGTTGAAAGGTATACAC 57.676 34.615 5.01 0.00 39.77 2.90
3336 4694 8.154203 TGACAATCAGAAGTTGAAAGGTATACA 58.846 33.333 5.01 0.00 39.77 2.29
3337 4695 8.547967 TGACAATCAGAAGTTGAAAGGTATAC 57.452 34.615 0.00 0.00 39.77 1.47
3338 4696 9.219603 CTTGACAATCAGAAGTTGAAAGGTATA 57.780 33.333 0.00 0.00 39.77 1.47
3339 4697 7.939039 TCTTGACAATCAGAAGTTGAAAGGTAT 59.061 33.333 0.00 0.00 39.77 2.73
3340 4698 7.279615 TCTTGACAATCAGAAGTTGAAAGGTA 58.720 34.615 0.00 0.00 39.77 3.08
3341 4699 6.122277 TCTTGACAATCAGAAGTTGAAAGGT 58.878 36.000 0.00 0.00 39.77 3.50
3342 4700 6.624352 TCTTGACAATCAGAAGTTGAAAGG 57.376 37.500 0.00 0.00 39.77 3.11
3343 4701 6.914757 GGTTCTTGACAATCAGAAGTTGAAAG 59.085 38.462 0.00 0.00 39.77 2.62
3344 4702 6.603201 AGGTTCTTGACAATCAGAAGTTGAAA 59.397 34.615 0.00 0.00 39.77 2.69
3345 4703 6.122277 AGGTTCTTGACAATCAGAAGTTGAA 58.878 36.000 0.00 0.00 39.77 2.69
3371 4729 2.806244 CGTAGCCAAACAAGCAGTTAGT 59.194 45.455 0.00 0.00 40.26 2.24
3600 4958 0.616964 TCAGCAGCCTGATCTCCAGT 60.617 55.000 0.00 0.00 42.98 4.00
3626 4984 1.681538 CTAGTCCGCTTAGAGGCAGA 58.318 55.000 0.00 0.00 0.00 4.26
3638 4996 3.129462 TGAACTGATTCTGAGCTAGTCCG 59.871 47.826 0.00 0.00 35.69 4.79
3653 5011 8.292448 GCTTGTTTTTCATCTCTAATGAACTGA 58.708 33.333 0.13 0.00 37.71 3.41
3654 5012 8.077991 TGCTTGTTTTTCATCTCTAATGAACTG 58.922 33.333 0.13 0.00 37.71 3.16
3655 5013 8.169977 TGCTTGTTTTTCATCTCTAATGAACT 57.830 30.769 0.13 0.00 37.71 3.01
3657 5015 8.394971 TCTGCTTGTTTTTCATCTCTAATGAA 57.605 30.769 0.00 0.00 36.37 2.57
3658 5016 7.984422 TCTGCTTGTTTTTCATCTCTAATGA 57.016 32.000 0.00 0.00 0.00 2.57
3660 5018 9.017509 TGATTCTGCTTGTTTTTCATCTCTAAT 57.982 29.630 0.00 0.00 0.00 1.73
3661 5019 8.394971 TGATTCTGCTTGTTTTTCATCTCTAA 57.605 30.769 0.00 0.00 0.00 2.10
3662 5020 7.984422 TGATTCTGCTTGTTTTTCATCTCTA 57.016 32.000 0.00 0.00 0.00 2.43
3665 5023 9.985730 TTAAATGATTCTGCTTGTTTTTCATCT 57.014 25.926 0.00 0.00 0.00 2.90
3736 5256 4.277476 TGACACAAAGTTTGGGAGATGTT 58.723 39.130 24.46 0.03 37.55 2.71
3754 5274 4.061357 TGGTGTTTCGACTTGTATGACA 57.939 40.909 0.00 0.00 0.00 3.58
3820 5340 1.871039 ACGTGACATTGTGGTAAGCAC 59.129 47.619 0.00 0.00 0.00 4.40
3830 5350 6.964370 TCACTTCTTTTTACAACGTGACATTG 59.036 34.615 0.00 0.00 0.00 2.82
3891 5411 6.664816 TGATGGCTTCATCTTCCACTATTTTT 59.335 34.615 0.00 0.00 45.59 1.94
3932 5452 6.916360 AGCCTTTATTTGTTGGATGAGAAA 57.084 33.333 0.00 0.00 0.00 2.52
3936 5456 6.096705 CACCATAGCCTTTATTTGTTGGATGA 59.903 38.462 0.00 0.00 0.00 2.92
3993 5513 7.689446 AGACAGCCTATTTTTCTAAAAGACC 57.311 36.000 0.00 0.00 0.00 3.85
4011 5531 4.518249 AGTCTATAAAAGGGCAAGACAGC 58.482 43.478 0.00 0.00 39.20 4.40
4032 5552 7.938563 AAGCAAGTCTCGCTCTTAATATTAG 57.061 36.000 0.00 0.00 39.29 1.73
4035 5555 6.041069 ACCTAAGCAAGTCTCGCTCTTAATAT 59.959 38.462 0.00 0.00 39.29 1.28
4036 5556 5.360144 ACCTAAGCAAGTCTCGCTCTTAATA 59.640 40.000 0.00 0.00 39.29 0.98
4053 5573 3.429410 GCCCATGAATTGACAACCTAAGC 60.429 47.826 0.00 0.00 0.00 3.09
4176 5698 2.765699 AGTTTTTCCCAACTGTGTGCAT 59.234 40.909 0.00 0.00 35.57 3.96
4195 5717 5.997384 ACGAGGGTACTTCTGATTTTAGT 57.003 39.130 0.00 0.00 0.00 2.24
4219 5741 6.072119 GCTAGGAACCCAAAAATATTATCGGG 60.072 42.308 12.35 12.35 39.72 5.14
4348 5870 5.900339 TTCACATACGAGACACTTCAAAC 57.100 39.130 0.00 0.00 0.00 2.93
4373 5895 6.133356 CCTAGGAGAGTAAGAAGAAGGTGAT 58.867 44.000 1.05 0.00 0.00 3.06
4588 6110 5.606348 AAAAACATGTTGGGCACTTCTTA 57.394 34.783 12.82 0.00 0.00 2.10
4627 6149 9.844257 AAATCCATGGTTTTTAATGAAAGTTGA 57.156 25.926 12.58 0.00 0.00 3.18
4743 6265 8.361889 TGGCATGAGGATGAAATAATACAAATG 58.638 33.333 0.00 0.00 0.00 2.32
4777 6299 6.884435 ACATGGCTAATACTGCACACATGTG 61.884 44.000 24.25 24.25 44.00 3.21
4778 6300 3.348647 TGGCTAATACTGCACACATGT 57.651 42.857 0.00 0.00 0.00 3.21
4779 6301 3.628942 ACATGGCTAATACTGCACACATG 59.371 43.478 0.00 0.00 40.04 3.21
4780 6302 3.628942 CACATGGCTAATACTGCACACAT 59.371 43.478 0.00 0.00 0.00 3.21
4781 6303 3.009026 CACATGGCTAATACTGCACACA 58.991 45.455 0.00 0.00 0.00 3.72
4782 6304 3.270027 TCACATGGCTAATACTGCACAC 58.730 45.455 0.00 0.00 0.00 3.82
4783 6305 3.625649 TCACATGGCTAATACTGCACA 57.374 42.857 0.00 0.00 0.00 4.57
4784 6306 4.129380 TGATCACATGGCTAATACTGCAC 58.871 43.478 0.00 0.00 0.00 4.57
4785 6307 4.101430 TCTGATCACATGGCTAATACTGCA 59.899 41.667 0.00 0.00 0.00 4.41
4786 6308 4.635223 TCTGATCACATGGCTAATACTGC 58.365 43.478 0.00 0.00 0.00 4.40
4787 6309 8.255905 TGATATCTGATCACATGGCTAATACTG 58.744 37.037 3.98 0.00 0.00 2.74
4788 6310 8.371571 TGATATCTGATCACATGGCTAATACT 57.628 34.615 3.98 0.00 0.00 2.12
4789 6311 9.440773 TTTGATATCTGATCACATGGCTAATAC 57.559 33.333 3.98 0.00 0.00 1.89
4791 6313 9.175312 GATTTGATATCTGATCACATGGCTAAT 57.825 33.333 3.98 0.00 0.00 1.73
4792 6314 7.332678 CGATTTGATATCTGATCACATGGCTAA 59.667 37.037 3.98 0.00 0.00 3.09
4793 6315 6.815142 CGATTTGATATCTGATCACATGGCTA 59.185 38.462 3.98 0.00 0.00 3.93
4794 6316 5.642491 CGATTTGATATCTGATCACATGGCT 59.358 40.000 3.98 0.00 0.00 4.75
4795 6317 5.673068 GCGATTTGATATCTGATCACATGGC 60.673 44.000 3.98 5.36 34.56 4.40
4796 6318 5.642491 AGCGATTTGATATCTGATCACATGG 59.358 40.000 3.98 0.00 0.00 3.66
4797 6319 6.723131 AGCGATTTGATATCTGATCACATG 57.277 37.500 3.98 0.00 0.00 3.21
4798 6320 6.932960 TGAAGCGATTTGATATCTGATCACAT 59.067 34.615 3.98 0.00 0.00 3.21
4799 6321 6.282930 TGAAGCGATTTGATATCTGATCACA 58.717 36.000 3.98 0.00 0.00 3.58
4800 6322 6.775939 TGAAGCGATTTGATATCTGATCAC 57.224 37.500 3.98 2.24 0.00 3.06
4801 6323 7.443272 ACATTGAAGCGATTTGATATCTGATCA 59.557 33.333 3.98 0.00 0.00 2.92
4802 6324 7.804712 ACATTGAAGCGATTTGATATCTGATC 58.195 34.615 3.98 6.56 0.00 2.92
4803 6325 7.359849 CGACATTGAAGCGATTTGATATCTGAT 60.360 37.037 3.98 0.00 0.00 2.90
4804 6326 6.074142 CGACATTGAAGCGATTTGATATCTGA 60.074 38.462 3.98 0.00 0.00 3.27
4805 6327 6.069563 CGACATTGAAGCGATTTGATATCTG 58.930 40.000 3.98 0.00 0.00 2.90
4806 6328 5.178252 CCGACATTGAAGCGATTTGATATCT 59.822 40.000 3.98 0.00 0.00 1.98
4807 6329 5.177511 TCCGACATTGAAGCGATTTGATATC 59.822 40.000 0.00 0.00 0.00 1.63
4808 6330 5.050091 GTCCGACATTGAAGCGATTTGATAT 60.050 40.000 0.00 0.00 0.00 1.63
4809 6331 4.270084 GTCCGACATTGAAGCGATTTGATA 59.730 41.667 0.00 0.00 0.00 2.15
4810 6332 3.063997 GTCCGACATTGAAGCGATTTGAT 59.936 43.478 0.00 0.00 0.00 2.57
4811 6333 2.415168 GTCCGACATTGAAGCGATTTGA 59.585 45.455 0.00 0.00 0.00 2.69
4812 6334 2.774007 GTCCGACATTGAAGCGATTTG 58.226 47.619 0.00 0.00 0.00 2.32
4813 6335 1.393539 CGTCCGACATTGAAGCGATTT 59.606 47.619 0.00 0.00 0.00 2.17
4814 6336 0.999406 CGTCCGACATTGAAGCGATT 59.001 50.000 0.00 0.00 0.00 3.34
4815 6337 0.172578 TCGTCCGACATTGAAGCGAT 59.827 50.000 0.00 0.00 0.00 4.58
4816 6338 0.456142 CTCGTCCGACATTGAAGCGA 60.456 55.000 0.00 0.00 0.00 4.93
4817 6339 1.413767 CCTCGTCCGACATTGAAGCG 61.414 60.000 0.00 0.00 0.00 4.68
4818 6340 0.108804 TCCTCGTCCGACATTGAAGC 60.109 55.000 0.00 0.00 0.00 3.86
4819 6341 1.914634 CTCCTCGTCCGACATTGAAG 58.085 55.000 0.00 0.00 0.00 3.02
4820 6342 0.108804 GCTCCTCGTCCGACATTGAA 60.109 55.000 0.00 0.00 0.00 2.69
4821 6343 1.511305 GCTCCTCGTCCGACATTGA 59.489 57.895 0.00 0.00 0.00 2.57
4822 6344 1.519455 GGCTCCTCGTCCGACATTG 60.519 63.158 0.00 0.00 0.00 2.82
4823 6345 2.722201 GGGCTCCTCGTCCGACATT 61.722 63.158 0.00 0.00 0.00 2.71
4824 6346 3.148279 GGGCTCCTCGTCCGACAT 61.148 66.667 0.00 0.00 0.00 3.06
4827 6349 2.503846 TTAAGGGGCTCCTCGTCCGA 62.504 60.000 5.00 0.00 44.07 4.55
4828 6350 2.017559 CTTAAGGGGCTCCTCGTCCG 62.018 65.000 5.00 0.00 44.07 4.79
4829 6351 0.686769 TCTTAAGGGGCTCCTCGTCC 60.687 60.000 5.00 0.00 44.07 4.79
4830 6352 1.192428 TTCTTAAGGGGCTCCTCGTC 58.808 55.000 5.00 0.00 44.07 4.20
4831 6353 1.652947 TTTCTTAAGGGGCTCCTCGT 58.347 50.000 5.00 0.00 44.07 4.18
4832 6354 2.781681 TTTTCTTAAGGGGCTCCTCG 57.218 50.000 5.00 0.00 44.07 4.63
4833 6355 6.129874 ACATATTTTTCTTAAGGGGCTCCTC 58.870 40.000 5.00 0.00 44.07 3.71
4835 6357 6.379988 TGAACATATTTTTCTTAAGGGGCTCC 59.620 38.462 0.00 0.00 0.00 4.70
4836 6358 7.404671 TGAACATATTTTTCTTAAGGGGCTC 57.595 36.000 1.85 0.00 0.00 4.70
4837 6359 7.790782 TTGAACATATTTTTCTTAAGGGGCT 57.209 32.000 1.85 0.00 0.00 5.19
4838 6360 9.529325 GTATTGAACATATTTTTCTTAAGGGGC 57.471 33.333 1.85 0.00 0.00 5.80


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

AutoCloner maintained by Alex Coulton.