Multiple sequence alignment - TraesCS4D01G288400

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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 TraesCS4D01G288400 chr4D 100.000 5159 0 0 1 5159 459432084 459426926 0.000000e+00 9527.0
1 TraesCS4D01G288400 chr4D 80.442 317 32 11 382 695 459432472 459432761 1.130000e-51 215.0
2 TraesCS4D01G288400 chr4B 92.680 3839 158 38 797 4570 574227092 574223312 0.000000e+00 5419.0
3 TraesCS4D01G288400 chr4B 84.653 606 75 12 4565 5159 574223147 574222549 5.750000e-164 588.0
4 TraesCS4D01G288400 chr4A 89.771 2923 208 46 717 3578 9377786 9380678 0.000000e+00 3657.0
5 TraesCS4D01G288400 chr4A 91.125 1600 116 18 3573 5159 9380756 9382342 0.000000e+00 2145.0
6 TraesCS4D01G288400 chr7A 96.396 333 12 0 1 333 622381519 622381851 2.720000e-152 549.0
7 TraesCS4D01G288400 chr7A 80.398 352 39 10 348 695 194801041 194801366 1.860000e-59 241.0
8 TraesCS4D01G288400 chr3B 92.188 192 13 2 143 333 673835796 673835986 2.370000e-68 270.0
9 TraesCS4D01G288400 chr3B 89.189 185 18 2 512 696 419574694 419574512 4.020000e-56 230.0
10 TraesCS4D01G288400 chr3B 79.612 103 18 3 4895 4995 265841302 265841403 2.580000e-08 71.3
11 TraesCS4D01G288400 chr1D 80.992 363 37 7 348 705 271296127 271295792 5.120000e-65 259.0
12 TraesCS4D01G288400 chr1D 91.429 175 15 0 522 696 15874728 15874902 1.860000e-59 241.0
13 TraesCS4D01G288400 chr1D 88.660 194 21 1 141 333 271296303 271296110 8.640000e-58 235.0
14 TraesCS4D01G288400 chr3D 89.637 193 20 0 141 333 54966505 54966313 3.990000e-61 246.0
15 TraesCS4D01G288400 chr3D 83.929 112 16 2 4982 5092 584217183 584217293 7.060000e-19 106.0
16 TraesCS4D01G288400 chr7D 89.119 193 21 0 141 333 155832675 155832483 1.860000e-59 241.0
17 TraesCS4D01G288400 chr7D 90.449 178 15 1 522 699 77511821 77511646 3.110000e-57 233.0
18 TraesCS4D01G288400 chr7D 90.449 178 15 1 522 699 77512392 77512217 3.110000e-57 233.0
19 TraesCS4D01G288400 chr7D 95.775 142 6 0 1 142 178014362 178014503 4.020000e-56 230.0
20 TraesCS4D01G288400 chr7D 83.209 268 20 6 424 691 178013977 178013735 6.720000e-54 222.0
21 TraesCS4D01G288400 chr7D 94.366 142 8 0 1 142 77512906 77513047 8.700000e-53 219.0
22 TraesCS4D01G288400 chr7D 79.155 355 44 11 351 702 305129787 305130114 8.700000e-53 219.0
23 TraesCS4D01G288400 chr7D 94.366 142 6 1 1 142 305129422 305129283 3.130000e-52 217.0
24 TraesCS4D01G288400 chr7D 93.662 142 9 0 1 142 95843852 95843993 4.050000e-51 213.0
25 TraesCS4D01G288400 chr7D 81.481 162 23 6 351 507 77512541 77512382 5.420000e-25 126.0
26 TraesCS4D01G288400 chr5D 90.270 185 17 1 522 705 513395555 513395739 1.860000e-59 241.0
27 TraesCS4D01G288400 chr5D 95.683 139 6 0 4 142 243098098 243097960 1.870000e-54 224.0
28 TraesCS4D01G288400 chr5D 94.964 139 7 0 4 142 434388726 434388588 8.700000e-53 219.0
29 TraesCS4D01G288400 chr5D 81.034 174 24 7 351 518 513395406 513395576 4.190000e-26 130.0
30 TraesCS4D01G288400 chr1A 91.329 173 15 0 522 694 2689398 2689570 2.400000e-58 237.0
31 TraesCS4D01G288400 chr6D 88.265 196 23 0 138 333 454793828 454794023 8.640000e-58 235.0
32 TraesCS4D01G288400 chr6A 88.601 193 22 0 141 333 182594311 182594119 8.640000e-58 235.0
33 TraesCS4D01G288400 chr6A 88.083 193 23 0 141 333 208012535 208012343 4.020000e-56 230.0
34 TraesCS4D01G288400 chr6A 94.245 139 8 0 4 142 208016126 208015988 4.050000e-51 213.0
35 TraesCS4D01G288400 chr2A 90.341 176 17 0 522 697 104678581 104678406 1.120000e-56 231.0
36 TraesCS4D01G288400 chr2A 79.603 353 41 11 348 696 243178815 243179140 1.870000e-54 224.0
37 TraesCS4D01G288400 chr2A 94.366 142 8 0 1 142 699616768 699616909 8.700000e-53 219.0
38 TraesCS4D01G288400 chr2D 89.888 178 18 0 522 699 79043975 79044152 4.020000e-56 230.0
39 TraesCS4D01G288400 chr7B 87.629 194 23 1 141 333 713628658 713628465 1.870000e-54 224.0
40 TraesCS4D01G288400 chr7B 81.022 274 25 8 423 696 559345121 559345367 5.270000e-45 193.0


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 TraesCS4D01G288400 chr4D 459426926 459432084 5158 True 9527.0 9527 100.0000 1 5159 1 chr4D.!!$R1 5158
1 TraesCS4D01G288400 chr4B 574222549 574227092 4543 True 3003.5 5419 88.6665 797 5159 2 chr4B.!!$R1 4362
2 TraesCS4D01G288400 chr4A 9377786 9382342 4556 False 2901.0 3657 90.4480 717 5159 2 chr4A.!!$F1 4442
3 TraesCS4D01G288400 chr1D 271295792 271296303 511 True 247.0 259 84.8260 141 705 2 chr1D.!!$R1 564
4 TraesCS4D01G288400 chr6A 208012343 208016126 3783 True 221.5 230 91.1640 4 333 2 chr6A.!!$R2 329

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
169 3624 0.169009 GCGGTCTGCCTCATTTGTTC 59.831 55.000 0.00 0.00 37.76 3.18 F
1218 4704 0.184692 TGGTTCCTGTGGATTGCACA 59.815 50.000 10.73 10.73 0.00 4.57 F
2666 6178 1.001641 ATGCAAGTCCACTCTGGGC 60.002 57.895 0.00 0.00 44.07 5.36 F
3809 7430 1.255882 GTGTGCATTCATCCCACCAA 58.744 50.000 0.00 0.00 0.00 3.67 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1229 4715 0.321830 TAAACTGGGTAAGGTGCCGC 60.322 55.000 0.0 0.0 0.0 6.53 R
3001 6518 0.028902 GAACAAACACCAGCGTCCAC 59.971 55.000 0.0 0.0 0.0 4.02 R
3956 7577 1.022903 ATCCAACTCCTCCCTCTCCT 58.977 55.000 0.0 0.0 0.0 3.69 R
5098 8931 1.272490 CGTTGTGACCAGCCTAAGAGA 59.728 52.381 0.0 0.0 0.0 3.10 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
28 29 1.077501 CAGGACGCCCCAACATGAT 60.078 57.895 0.00 0.00 37.41 2.45
32 33 2.303022 AGGACGCCCCAACATGATATAG 59.697 50.000 0.00 0.00 37.41 1.31
69 70 7.928167 TCCTGCATTGTGAGTATACTAATTCTG 59.072 37.037 5.09 2.97 0.00 3.02
87 88 1.087202 TGAGTGTGCGTGTGTGGTTC 61.087 55.000 0.00 0.00 0.00 3.62
94 95 3.682377 TGTGCGTGTGTGGTTCAATATAG 59.318 43.478 0.00 0.00 0.00 1.31
118 119 5.444218 GCTTGTAGAGGTCGAAATTTGTACG 60.444 44.000 0.00 0.00 0.00 3.67
139 3594 8.464404 TGTACGTAGAATTTGTAGTAGCTGAAT 58.536 33.333 0.00 0.00 0.00 2.57
169 3624 0.169009 GCGGTCTGCCTCATTTGTTC 59.831 55.000 0.00 0.00 37.76 3.18
179 3634 4.937620 TGCCTCATTTGTTCATGTCTACTC 59.062 41.667 0.00 0.00 0.00 2.59
180 3635 4.937620 GCCTCATTTGTTCATGTCTACTCA 59.062 41.667 0.00 0.00 0.00 3.41
205 3660 2.035632 AGACAGATTCTTCTAGCCGGG 58.964 52.381 2.18 0.00 0.00 5.73
211 3666 3.785859 CTTCTAGCCGGGCAGCCA 61.786 66.667 23.09 2.01 0.00 4.75
233 3688 3.572682 ACTCGTGTAGATCTGTTGTCCAA 59.427 43.478 5.18 0.00 0.00 3.53
253 3708 4.808895 CCAAACTAACTTTCAAACCCAAGC 59.191 41.667 0.00 0.00 0.00 4.01
277 3732 6.545504 TCAACTAGCTAGCAACAAGAAAAG 57.454 37.500 20.91 2.49 0.00 2.27
287 3742 5.297547 AGCAACAAGAAAAGATACGAGACA 58.702 37.500 0.00 0.00 0.00 3.41
290 3745 7.602644 AGCAACAAGAAAAGATACGAGACATTA 59.397 33.333 0.00 0.00 0.00 1.90
301 3756 4.537135 ACGAGACATTACTGTGTTGGAT 57.463 40.909 3.13 0.00 34.95 3.41
392 3848 9.109393 TCCTTATAAACAACATGTCATTAGCTC 57.891 33.333 0.00 0.00 0.00 4.09
408 3864 0.670546 GCTCAGTTGGTTAGCTCGCA 60.671 55.000 0.00 0.00 33.40 5.10
410 3866 0.320421 TCAGTTGGTTAGCTCGCACC 60.320 55.000 0.00 0.00 0.00 5.01
411 3867 0.602638 CAGTTGGTTAGCTCGCACCA 60.603 55.000 8.02 8.02 41.55 4.17
413 3869 0.727398 GTTGGTTAGCTCGCACCATC 59.273 55.000 12.01 8.50 42.81 3.51
414 3870 0.392461 TTGGTTAGCTCGCACCATCC 60.392 55.000 12.01 0.00 42.81 3.51
417 3873 0.811616 GTTAGCTCGCACCATCCTGG 60.812 60.000 0.00 0.00 45.02 4.45
419 3875 1.395045 TAGCTCGCACCATCCTGGAG 61.395 60.000 1.52 0.00 40.96 3.86
420 3876 2.503061 CTCGCACCATCCTGGAGG 59.497 66.667 1.52 0.91 40.96 4.30
440 3896 0.531311 ACGTGGTCTTGGGTTCGAAC 60.531 55.000 20.14 20.14 0.00 3.95
455 3911 1.767692 GAACCCCTGCTCTCCCAAA 59.232 57.895 0.00 0.00 0.00 3.28
460 3916 2.381961 ACCCCTGCTCTCCCAAATTTTA 59.618 45.455 0.00 0.00 0.00 1.52
466 3922 5.220931 CCTGCTCTCCCAAATTTTATTCTCG 60.221 44.000 0.00 0.00 0.00 4.04
467 3923 4.096382 TGCTCTCCCAAATTTTATTCTCGC 59.904 41.667 0.00 0.00 0.00 5.03
507 3963 7.147266 CCTTACAAATGGGATAGGGGTAGTTTA 60.147 40.741 0.00 0.00 0.00 2.01
508 3964 6.262056 ACAAATGGGATAGGGGTAGTTTAG 57.738 41.667 0.00 0.00 0.00 1.85
509 3965 5.734634 ACAAATGGGATAGGGGTAGTTTAGT 59.265 40.000 0.00 0.00 0.00 2.24
510 3966 6.126565 ACAAATGGGATAGGGGTAGTTTAGTC 60.127 42.308 0.00 0.00 0.00 2.59
511 3967 4.630382 TGGGATAGGGGTAGTTTAGTCA 57.370 45.455 0.00 0.00 0.00 3.41
512 3968 5.166013 TGGGATAGGGGTAGTTTAGTCAT 57.834 43.478 0.00 0.00 0.00 3.06
513 3969 5.152934 TGGGATAGGGGTAGTTTAGTCATC 58.847 45.833 0.00 0.00 0.00 2.92
514 3970 5.102783 TGGGATAGGGGTAGTTTAGTCATCT 60.103 44.000 0.00 0.00 0.00 2.90
515 3971 6.105139 TGGGATAGGGGTAGTTTAGTCATCTA 59.895 42.308 0.00 0.00 0.00 1.98
516 3972 7.015064 GGGATAGGGGTAGTTTAGTCATCTAA 58.985 42.308 0.00 0.00 34.76 2.10
517 3973 7.039152 GGGATAGGGGTAGTTTAGTCATCTAAC 60.039 44.444 0.00 0.00 36.09 2.34
518 3974 7.508296 GGATAGGGGTAGTTTAGTCATCTAACA 59.492 40.741 0.00 0.00 36.09 2.41
519 3975 9.091220 GATAGGGGTAGTTTAGTCATCTAACAT 57.909 37.037 0.00 0.00 36.09 2.71
520 3976 7.362802 AGGGGTAGTTTAGTCATCTAACATC 57.637 40.000 0.00 0.00 36.09 3.06
521 3977 6.901300 AGGGGTAGTTTAGTCATCTAACATCA 59.099 38.462 0.00 0.00 36.09 3.07
522 3978 7.070074 AGGGGTAGTTTAGTCATCTAACATCAG 59.930 40.741 0.00 0.00 36.09 2.90
523 3979 7.210873 GGGTAGTTTAGTCATCTAACATCAGG 58.789 42.308 0.00 0.00 36.09 3.86
524 3980 7.210873 GGTAGTTTAGTCATCTAACATCAGGG 58.789 42.308 0.00 0.00 36.09 4.45
525 3981 6.240549 AGTTTAGTCATCTAACATCAGGGG 57.759 41.667 0.00 0.00 36.09 4.79
526 3982 5.726793 AGTTTAGTCATCTAACATCAGGGGT 59.273 40.000 0.00 0.00 36.09 4.95
527 3983 6.901300 AGTTTAGTCATCTAACATCAGGGGTA 59.099 38.462 0.00 0.00 36.09 3.69
528 3984 6.978674 TTAGTCATCTAACATCAGGGGTAG 57.021 41.667 0.00 0.00 32.03 3.18
529 3985 4.884961 AGTCATCTAACATCAGGGGTAGT 58.115 43.478 0.00 0.00 0.00 2.73
530 3986 5.281314 AGTCATCTAACATCAGGGGTAGTT 58.719 41.667 0.00 0.00 0.00 2.24
531 3987 5.726793 AGTCATCTAACATCAGGGGTAGTTT 59.273 40.000 0.00 0.00 0.00 2.66
532 3988 6.049790 GTCATCTAACATCAGGGGTAGTTTC 58.950 44.000 0.00 0.00 0.00 2.78
533 3989 4.730949 TCTAACATCAGGGGTAGTTTCG 57.269 45.455 0.00 0.00 0.00 3.46
543 3999 4.081862 CAGGGGTAGTTTCGTCATCTAACA 60.082 45.833 0.00 0.00 0.00 2.41
552 4008 7.099764 AGTTTCGTCATCTAACATCAGTCAAT 58.900 34.615 0.00 0.00 0.00 2.57
573 4029 8.780846 TCAATGTGTATTGACTAAACGGTAAT 57.219 30.769 0.00 0.00 45.77 1.89
574 4030 8.875803 TCAATGTGTATTGACTAAACGGTAATC 58.124 33.333 0.00 0.00 45.77 1.75
575 4031 8.661257 CAATGTGTATTGACTAAACGGTAATCA 58.339 33.333 0.00 0.00 45.21 2.57
583 4039 9.840427 ATTGACTAAACGGTAATCATGAAAAAG 57.160 29.630 0.00 0.00 0.00 2.27
590 4046 5.414765 ACGGTAATCATGAAAAAGGGTCTTC 59.585 40.000 0.00 0.00 0.00 2.87
608 4064 5.934625 GGTCTTCTTGAGCTTGATCTAACAA 59.065 40.000 0.00 0.00 39.86 2.83
611 4067 8.014517 GTCTTCTTGAGCTTGATCTAACAAAAG 58.985 37.037 0.00 0.00 0.00 2.27
612 4068 6.808008 TCTTGAGCTTGATCTAACAAAAGG 57.192 37.500 0.00 0.00 0.00 3.11
667 4124 4.259690 GGCAAAACTGAGTAGCGTTATACG 60.260 45.833 0.00 0.00 45.88 3.06
696 4153 6.732896 TGGCAAAACTGATAAAAACCCTAA 57.267 33.333 0.00 0.00 0.00 2.69
699 4156 7.713073 TGGCAAAACTGATAAAAACCCTAAAAG 59.287 33.333 0.00 0.00 0.00 2.27
701 4158 9.320352 GCAAAACTGATAAAAACCCTAAAAGAA 57.680 29.630 0.00 0.00 0.00 2.52
727 4184 5.854010 TCTTCCTAAAGTAGATCACGCAT 57.146 39.130 0.00 0.00 33.95 4.73
730 4187 5.707242 TCCTAAAGTAGATCACGCATAGG 57.293 43.478 0.00 1.71 35.03 2.57
756 4213 7.255486 GGAGTACCTATTTTGTGCTTTTGACTT 60.255 37.037 0.00 0.00 0.00 3.01
771 4228 6.863645 GCTTTTGACTTTGTTATTCCCTCTTC 59.136 38.462 0.00 0.00 0.00 2.87
780 4237 6.575162 TGTTATTCCCTCTTCTTTTCAAGC 57.425 37.500 0.00 0.00 0.00 4.01
784 4241 3.660865 TCCCTCTTCTTTTCAAGCGTAC 58.339 45.455 0.00 0.00 0.00 3.67
884 4346 0.676736 GCCCTCACCTTCTCTATCGG 59.323 60.000 0.00 0.00 0.00 4.18
971 4433 3.181407 TGCATCCCACTCCTATCTATCCA 60.181 47.826 0.00 0.00 0.00 3.41
1023 4485 2.844146 CGCGTGTTGTCTCGTTCC 59.156 61.111 0.00 0.00 33.82 3.62
1029 4491 4.367023 TTGTCTCGTTCCCCGCCG 62.367 66.667 0.00 0.00 36.19 6.46
1184 4654 1.761667 CCTCTCTGCTCCCCTCCTG 60.762 68.421 0.00 0.00 0.00 3.86
1186 4656 0.260230 CTCTCTGCTCCCCTCCTGTA 59.740 60.000 0.00 0.00 0.00 2.74
1195 4665 3.682999 GCTCCCCTCCTGTAGTGAAATTC 60.683 52.174 0.00 0.00 0.00 2.17
1203 4673 5.127491 TCCTGTAGTGAAATTCGTTTGGTT 58.873 37.500 0.00 0.00 0.00 3.67
1207 4677 4.568152 AGTGAAATTCGTTTGGTTCCTG 57.432 40.909 0.00 0.00 0.00 3.86
1208 4678 3.951680 AGTGAAATTCGTTTGGTTCCTGT 59.048 39.130 0.00 0.00 0.00 4.00
1209 4679 4.041723 GTGAAATTCGTTTGGTTCCTGTG 58.958 43.478 0.00 0.00 0.00 3.66
1216 4702 1.686052 GTTTGGTTCCTGTGGATTGCA 59.314 47.619 0.00 0.00 0.00 4.08
1218 4704 0.184692 TGGTTCCTGTGGATTGCACA 59.815 50.000 10.73 10.73 0.00 4.57
1222 4708 1.896220 TCCTGTGGATTGCACAACTC 58.104 50.000 12.27 0.00 31.61 3.01
1245 4731 3.246112 TGCGGCACCTTACCCAGT 61.246 61.111 0.00 0.00 0.00 4.00
1255 4741 1.003928 CCTTACCCAGTTTAGCCCGTT 59.996 52.381 0.00 0.00 0.00 4.44
1260 4746 1.814394 CCCAGTTTAGCCCGTTTTACC 59.186 52.381 0.00 0.00 0.00 2.85
1436 4935 1.275010 TCCGCTACTGTCTGCATTCAA 59.725 47.619 0.00 0.00 0.00 2.69
1488 4987 6.521427 GCCTACAAGATTGATGAGATATGGGT 60.521 42.308 0.00 0.00 0.00 4.51
1493 4992 8.443176 ACAAGATTGATGAGATATGGGTATTGT 58.557 33.333 0.00 0.00 0.00 2.71
1529 5028 2.437281 TGTTGTGAATGGGGCAAACAAT 59.563 40.909 0.00 0.00 33.67 2.71
1537 5036 6.092533 GTGAATGGGGCAAACAATTTAATCAG 59.907 38.462 0.00 0.00 0.00 2.90
1644 5143 5.625568 TGTCATCTCAGATGTTCATGGAT 57.374 39.130 14.56 0.00 0.00 3.41
1679 5178 7.893236 CGCTGCTACGTGATATTATTAAACATC 59.107 37.037 0.00 0.00 0.00 3.06
1689 5188 9.066892 TGATATTATTAAACATCAGGAAGGTGC 57.933 33.333 1.81 0.00 0.00 5.01
1821 5320 7.690256 ACACAGAATATTAGAAGTGGACCTTT 58.310 34.615 11.38 0.00 32.03 3.11
1822 5321 8.164070 ACACAGAATATTAGAAGTGGACCTTTT 58.836 33.333 11.38 0.00 32.03 2.27
1823 5322 9.014297 CACAGAATATTAGAAGTGGACCTTTTT 57.986 33.333 0.00 0.00 32.03 1.94
1879 5378 3.267597 ATTTGTTGCCGCGCCTGTC 62.268 57.895 0.00 0.00 0.00 3.51
1933 5432 9.932699 GTACAAGTATATCTCGTATGCGATAAT 57.067 33.333 6.30 6.42 46.80 1.28
2003 5510 4.565652 GGACTTGTGTCAGTCATGGGTAAT 60.566 45.833 3.39 0.00 44.53 1.89
2151 5660 2.959030 TGACCTACAGGCTACAGCTATG 59.041 50.000 0.54 3.63 41.70 2.23
2321 5833 3.243267 GGAGACATAGAAGACGGAGAAGC 60.243 52.174 0.00 0.00 0.00 3.86
2548 6060 2.565210 TGACAGTTTGCTTGTGCTTG 57.435 45.000 0.00 0.00 40.48 4.01
2608 6120 6.094325 TGTTTGTACTTCTGTAGTTGGTTTGG 59.906 38.462 0.00 0.00 38.33 3.28
2611 6123 6.416415 TGTACTTCTGTAGTTGGTTTGGAAA 58.584 36.000 0.00 0.00 38.33 3.13
2666 6178 1.001641 ATGCAAGTCCACTCTGGGC 60.002 57.895 0.00 0.00 44.07 5.36
2692 6204 9.409312 CTGTTGTGAACATATCAATAAAAAGCA 57.591 29.630 0.00 0.00 41.26 3.91
2861 6375 5.010933 TCTACCAAAAACCACAACTGTTCA 58.989 37.500 0.00 0.00 0.00 3.18
2944 6461 2.034687 CCTGCAGGTGTTCCCAGG 59.965 66.667 25.53 0.00 37.02 4.45
2967 6484 3.074412 ACAACAAAGCTGAGGGATAACG 58.926 45.455 0.00 0.00 0.00 3.18
3083 6604 5.365025 ACTCTATCTCATTACCTGTGTGCAT 59.635 40.000 0.00 0.00 0.00 3.96
3107 6628 4.570369 GCCACAATTACAAGTTGCACTTTT 59.430 37.500 1.81 0.00 36.03 2.27
3189 6726 9.190858 GCATATGTGTTTTGAACTTTTGTATGA 57.809 29.630 4.29 0.00 0.00 2.15
3199 6736 9.515020 TTTGAACTTTTGTATGATCACTTGTTC 57.485 29.630 0.00 7.01 0.00 3.18
3251 6788 6.643770 TGTTAAATCGACTCCTTCACTTGTAC 59.356 38.462 0.00 0.00 0.00 2.90
3252 6789 5.470047 AAATCGACTCCTTCACTTGTACT 57.530 39.130 0.00 0.00 0.00 2.73
3253 6790 6.585695 AAATCGACTCCTTCACTTGTACTA 57.414 37.500 0.00 0.00 0.00 1.82
3263 6800 7.997482 TCCTTCACTTGTACTAGTAGCATAAG 58.003 38.462 9.68 8.37 0.00 1.73
3809 7430 1.255882 GTGTGCATTCATCCCACCAA 58.744 50.000 0.00 0.00 0.00 3.67
3824 7445 4.042311 TCCCACCAAAACTGATAAGTAGCA 59.958 41.667 0.00 0.00 0.00 3.49
3875 7496 7.867403 GTCAATGAAACCAAACAGATACACAAT 59.133 33.333 0.00 0.00 0.00 2.71
3908 7529 8.962884 ATTTGCTTGTTTTCATAGAACCTTTT 57.037 26.923 0.00 0.00 0.00 2.27
3912 7533 6.983890 GCTTGTTTTCATAGAACCTTTTCCAA 59.016 34.615 0.00 0.00 31.28 3.53
4204 7825 3.120130 CGTGTTGGTGTTGTAGTGTGTTT 60.120 43.478 0.00 0.00 0.00 2.83
4208 7829 2.421775 TGGTGTTGTAGTGTGTTTGCTG 59.578 45.455 0.00 0.00 0.00 4.41
4210 7831 3.623960 GGTGTTGTAGTGTGTTTGCTGTA 59.376 43.478 0.00 0.00 0.00 2.74
4228 7849 5.163530 TGCTGTATTACAAATGGGAGCATTG 60.164 40.000 0.00 0.00 0.00 2.82
4276 7898 1.202867 TGCCTGGTTGCACTGATAACA 60.203 47.619 0.00 0.00 36.04 2.41
4314 7936 5.869888 CGCACAATATTATTAGAGGGGAGAC 59.130 44.000 0.00 0.00 0.00 3.36
4413 8035 6.942532 TGAGCACTTAAACTTCTGTGAAAT 57.057 33.333 0.00 0.00 32.72 2.17
4417 8039 5.790495 GCACTTAAACTTCTGTGAAATAGCG 59.210 40.000 0.00 0.00 32.72 4.26
4422 8044 2.028112 ACTTCTGTGAAATAGCGGCAGA 60.028 45.455 1.45 0.00 34.80 4.26
4478 8100 3.484953 ACACCATGGACTAGGGTTCTA 57.515 47.619 21.47 0.00 41.62 2.10
4587 8379 6.587608 CCTCTAAATCCATTTTCTGCAACAAC 59.412 38.462 0.00 0.00 0.00 3.32
4675 8468 8.830201 TTCCATATGAAAGTTGAAACAAATGG 57.170 30.769 3.65 0.00 33.10 3.16
4688 8481 0.963962 CAAATGGAGTTGCAGTGCCT 59.036 50.000 13.72 2.62 0.00 4.75
4704 8497 3.635836 AGTGCCTACTATTACCTCCGTTC 59.364 47.826 0.00 0.00 34.74 3.95
4715 8508 3.740631 ACCTCCGTTCGAACTAAAACT 57.259 42.857 24.80 1.51 0.00 2.66
4716 8509 3.387397 ACCTCCGTTCGAACTAAAACTG 58.613 45.455 24.80 8.26 0.00 3.16
4718 8511 2.798283 CTCCGTTCGAACTAAAACTGCA 59.202 45.455 24.80 0.00 0.00 4.41
4744 8538 6.472887 CAGTTATTCCAAACAGAGGGAGTAA 58.527 40.000 0.00 0.00 34.27 2.24
4767 8561 6.884280 AAACCAGTTTCCTCACTTTCATAG 57.116 37.500 0.00 0.00 0.00 2.23
4768 8562 5.825593 ACCAGTTTCCTCACTTTCATAGA 57.174 39.130 0.00 0.00 0.00 1.98
4769 8563 5.799213 ACCAGTTTCCTCACTTTCATAGAG 58.201 41.667 0.00 0.00 0.00 2.43
4813 8611 9.897744 TGATTTCTAAGCTTTATTTGAACTGTG 57.102 29.630 3.20 0.00 0.00 3.66
4817 8615 9.515020 TTCTAAGCTTTATTTGAACTGTGTTTG 57.485 29.630 3.20 0.00 0.00 2.93
4870 8703 7.552687 TCCAGTTGTTCAAAGTGGTATATGATC 59.447 37.037 10.85 0.00 40.70 2.92
4871 8704 7.554118 CCAGTTGTTCAAAGTGGTATATGATCT 59.446 37.037 4.13 0.00 36.29 2.75
4872 8705 8.393366 CAGTTGTTCAAAGTGGTATATGATCTG 58.607 37.037 0.00 0.00 0.00 2.90
4873 8706 8.321353 AGTTGTTCAAAGTGGTATATGATCTGA 58.679 33.333 0.00 0.00 0.00 3.27
4874 8707 9.113838 GTTGTTCAAAGTGGTATATGATCTGAT 57.886 33.333 0.00 0.00 0.00 2.90
4875 8708 8.667076 TGTTCAAAGTGGTATATGATCTGATG 57.333 34.615 0.00 0.00 0.00 3.07
4876 8709 8.267183 TGTTCAAAGTGGTATATGATCTGATGT 58.733 33.333 0.00 0.00 0.00 3.06
4877 8710 9.113838 GTTCAAAGTGGTATATGATCTGATGTT 57.886 33.333 0.00 0.00 0.00 2.71
4878 8711 8.893219 TCAAAGTGGTATATGATCTGATGTTC 57.107 34.615 0.00 0.00 0.00 3.18
4879 8712 8.485392 TCAAAGTGGTATATGATCTGATGTTCA 58.515 33.333 0.00 0.00 0.00 3.18
4880 8713 9.112725 CAAAGTGGTATATGATCTGATGTTCAA 57.887 33.333 0.00 0.00 0.00 2.69
4881 8714 9.685276 AAAGTGGTATATGATCTGATGTTCAAA 57.315 29.630 0.00 0.00 0.00 2.69
4882 8715 9.685276 AAGTGGTATATGATCTGATGTTCAAAA 57.315 29.630 0.00 0.00 0.00 2.44
4883 8716 9.685276 AGTGGTATATGATCTGATGTTCAAAAA 57.315 29.630 0.00 0.00 0.00 1.94
4954 8787 6.590677 TGTATTATAGTGTTTGCGCAAGTACA 59.409 34.615 28.68 25.24 41.68 2.90
4965 8798 7.535940 TGTTTGCGCAAGTACATAAAGAAATAC 59.464 33.333 23.68 12.65 41.68 1.89
4970 8803 7.399523 CGCAAGTACATAAAGAAATACAGGAC 58.600 38.462 0.00 0.00 0.00 3.85
4990 8823 4.390264 GACAAACCAGATATAGGGGAAGC 58.610 47.826 0.00 0.00 0.00 3.86
5005 8838 2.526432 GGAAGCTGTATCGGGGATCTA 58.474 52.381 0.00 0.00 0.00 1.98
5011 8844 4.707448 AGCTGTATCGGGGATCTATTACAG 59.293 45.833 12.97 12.97 37.37 2.74
5022 8855 6.239600 GGGGATCTATTACAGCAACACATCTA 60.240 42.308 0.00 0.00 0.00 1.98
5092 8925 4.550422 AGAAGATTTTTGAAAAGCCGCTC 58.450 39.130 0.00 0.00 35.01 5.03
5093 8926 4.037923 AGAAGATTTTTGAAAAGCCGCTCA 59.962 37.500 0.00 0.00 35.01 4.26
5095 8928 4.692228 AGATTTTTGAAAAGCCGCTCAAA 58.308 34.783 0.00 0.00 39.24 2.69
5098 8931 3.518634 TTTGAAAAGCCGCTCAAAGTT 57.481 38.095 0.00 0.00 36.79 2.66
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
28 29 5.573380 ATGCAGGAATTTCAGAGCCTATA 57.427 39.130 0.00 0.00 0.00 1.31
32 33 2.494870 ACAATGCAGGAATTTCAGAGCC 59.505 45.455 0.00 0.00 0.00 4.70
69 70 1.087202 TGAACCACACACGCACACTC 61.087 55.000 0.00 0.00 0.00 3.51
87 88 8.594881 AATTTCGACCTCTACAAGCTATATTG 57.405 34.615 0.00 0.00 36.22 1.90
94 95 5.444218 CGTACAAATTTCGACCTCTACAAGC 60.444 44.000 0.00 0.00 0.00 4.01
118 119 9.774742 CCAAAATTCAGCTACTACAAATTCTAC 57.225 33.333 0.00 0.00 0.00 2.59
139 3594 4.572571 AGACCGCCACGCCCAAAA 62.573 61.111 0.00 0.00 0.00 2.44
169 3624 6.647334 ATCTGTCTGGTATGAGTAGACATG 57.353 41.667 6.75 0.00 46.71 3.21
179 3634 5.537188 GGCTAGAAGAATCTGTCTGGTATG 58.463 45.833 0.00 0.00 36.40 2.39
180 3635 4.279671 CGGCTAGAAGAATCTGTCTGGTAT 59.720 45.833 0.00 0.00 36.40 2.73
205 3660 0.457851 AGATCTACACGAGTGGCTGC 59.542 55.000 8.19 0.00 34.19 5.25
211 3666 3.154710 TGGACAACAGATCTACACGAGT 58.845 45.455 0.00 0.00 0.00 4.18
218 3673 8.208224 TGAAAGTTAGTTTGGACAACAGATCTA 58.792 33.333 0.00 0.00 0.00 1.98
233 3688 4.953579 TGAGCTTGGGTTTGAAAGTTAGTT 59.046 37.500 0.00 0.00 0.00 2.24
253 3708 6.425114 TCTTTTCTTGTTGCTAGCTAGTTGAG 59.575 38.462 21.62 12.41 0.00 3.02
277 3732 5.647589 TCCAACACAGTAATGTCTCGTATC 58.352 41.667 0.00 0.00 30.55 2.24
364 3820 9.109393 GCTAATGACATGTTGTTTATAAGGAGA 57.891 33.333 0.00 0.00 0.00 3.71
365 3821 9.113838 AGCTAATGACATGTTGTTTATAAGGAG 57.886 33.333 0.00 0.00 0.00 3.69
366 3822 9.109393 GAGCTAATGACATGTTGTTTATAAGGA 57.891 33.333 0.00 0.00 0.00 3.36
367 3823 8.892723 TGAGCTAATGACATGTTGTTTATAAGG 58.107 33.333 0.00 0.00 0.00 2.69
368 3824 9.926751 CTGAGCTAATGACATGTTGTTTATAAG 57.073 33.333 0.00 0.00 0.00 1.73
369 3825 9.448438 ACTGAGCTAATGACATGTTGTTTATAA 57.552 29.630 0.00 0.00 0.00 0.98
370 3826 9.448438 AACTGAGCTAATGACATGTTGTTTATA 57.552 29.630 0.00 0.00 0.00 0.98
371 3827 7.928307 ACTGAGCTAATGACATGTTGTTTAT 57.072 32.000 0.00 0.00 0.00 1.40
372 3828 7.308529 CCAACTGAGCTAATGACATGTTGTTTA 60.309 37.037 0.00 0.00 33.81 2.01
373 3829 6.441274 CAACTGAGCTAATGACATGTTGTTT 58.559 36.000 0.00 0.00 31.85 2.83
374 3830 5.048504 CCAACTGAGCTAATGACATGTTGTT 60.049 40.000 0.00 0.60 33.81 2.83
375 3831 4.456911 CCAACTGAGCTAATGACATGTTGT 59.543 41.667 0.00 0.00 33.81 3.32
376 3832 4.456911 ACCAACTGAGCTAATGACATGTTG 59.543 41.667 0.00 5.86 34.96 3.33
382 3838 4.508662 AGCTAACCAACTGAGCTAATGAC 58.491 43.478 0.00 0.00 44.65 3.06
385 3841 3.786635 CGAGCTAACCAACTGAGCTAAT 58.213 45.455 0.00 0.00 46.42 1.73
392 3848 0.602638 TGGTGCGAGCTAACCAACTG 60.603 55.000 11.90 0.00 43.46 3.16
413 3869 1.293498 CAAGACCACGTCCTCCAGG 59.707 63.158 0.00 0.00 32.18 4.45
414 3870 1.293498 CCAAGACCACGTCCTCCAG 59.707 63.158 0.00 0.00 32.18 3.86
417 3873 0.320508 GAACCCAAGACCACGTCCTC 60.321 60.000 0.00 0.00 32.18 3.71
419 3875 1.666872 CGAACCCAAGACCACGTCC 60.667 63.158 0.00 0.00 32.18 4.79
420 3876 0.249573 TTCGAACCCAAGACCACGTC 60.250 55.000 0.00 0.00 0.00 4.34
421 3877 0.531311 GTTCGAACCCAAGACCACGT 60.531 55.000 17.68 0.00 0.00 4.49
422 3878 1.226030 GGTTCGAACCCAAGACCACG 61.226 60.000 33.02 0.00 43.43 4.94
440 3896 1.942776 AAAATTTGGGAGAGCAGGGG 58.057 50.000 0.00 0.00 0.00 4.79
444 3900 4.096382 GCGAGAATAAAATTTGGGAGAGCA 59.904 41.667 0.00 0.00 0.00 4.26
445 3901 4.336713 AGCGAGAATAAAATTTGGGAGAGC 59.663 41.667 0.00 0.00 0.00 4.09
446 3902 6.442513 AAGCGAGAATAAAATTTGGGAGAG 57.557 37.500 0.00 0.00 0.00 3.20
447 3903 6.659242 AGAAAGCGAGAATAAAATTTGGGAGA 59.341 34.615 0.00 0.00 0.00 3.71
466 3922 0.748005 TAAGGGGCGCATGAGAAAGC 60.748 55.000 10.83 0.00 0.00 3.51
467 3923 1.017387 GTAAGGGGCGCATGAGAAAG 58.983 55.000 10.83 0.00 0.00 2.62
507 3963 4.884961 ACTACCCCTGATGTTAGATGACT 58.115 43.478 0.00 0.00 0.00 3.41
508 3964 5.615925 AACTACCCCTGATGTTAGATGAC 57.384 43.478 0.00 0.00 0.00 3.06
509 3965 5.163447 CGAAACTACCCCTGATGTTAGATGA 60.163 44.000 0.00 0.00 0.00 2.92
510 3966 5.050490 CGAAACTACCCCTGATGTTAGATG 58.950 45.833 0.00 0.00 0.00 2.90
511 3967 4.715297 ACGAAACTACCCCTGATGTTAGAT 59.285 41.667 0.00 0.00 0.00 1.98
512 3968 4.091549 ACGAAACTACCCCTGATGTTAGA 58.908 43.478 0.00 0.00 0.00 2.10
513 3969 4.081862 TGACGAAACTACCCCTGATGTTAG 60.082 45.833 0.00 0.00 0.00 2.34
514 3970 3.833650 TGACGAAACTACCCCTGATGTTA 59.166 43.478 0.00 0.00 0.00 2.41
515 3971 2.635915 TGACGAAACTACCCCTGATGTT 59.364 45.455 0.00 0.00 0.00 2.71
516 3972 2.253610 TGACGAAACTACCCCTGATGT 58.746 47.619 0.00 0.00 0.00 3.06
517 3973 3.133003 AGATGACGAAACTACCCCTGATG 59.867 47.826 0.00 0.00 0.00 3.07
518 3974 3.375699 AGATGACGAAACTACCCCTGAT 58.624 45.455 0.00 0.00 0.00 2.90
519 3975 2.816411 AGATGACGAAACTACCCCTGA 58.184 47.619 0.00 0.00 0.00 3.86
520 3976 4.081862 TGTTAGATGACGAAACTACCCCTG 60.082 45.833 0.00 0.00 0.00 4.45
521 3977 4.091549 TGTTAGATGACGAAACTACCCCT 58.908 43.478 0.00 0.00 0.00 4.79
522 3978 4.460948 TGTTAGATGACGAAACTACCCC 57.539 45.455 0.00 0.00 0.00 4.95
523 3979 5.657474 TGATGTTAGATGACGAAACTACCC 58.343 41.667 0.00 0.00 0.00 3.69
524 3980 6.331061 ACTGATGTTAGATGACGAAACTACC 58.669 40.000 0.00 0.00 0.00 3.18
525 3981 7.027760 TGACTGATGTTAGATGACGAAACTAC 58.972 38.462 0.00 0.00 0.00 2.73
526 3982 7.153217 TGACTGATGTTAGATGACGAAACTA 57.847 36.000 0.00 0.00 0.00 2.24
527 3983 6.025749 TGACTGATGTTAGATGACGAAACT 57.974 37.500 0.00 0.00 0.00 2.66
528 3984 6.706055 TTGACTGATGTTAGATGACGAAAC 57.294 37.500 0.00 0.00 0.00 2.78
529 3985 6.873605 ACATTGACTGATGTTAGATGACGAAA 59.126 34.615 0.00 0.00 36.92 3.46
530 3986 6.311200 CACATTGACTGATGTTAGATGACGAA 59.689 38.462 0.00 0.00 38.15 3.85
531 3987 5.807011 CACATTGACTGATGTTAGATGACGA 59.193 40.000 0.00 0.00 38.15 4.20
532 3988 5.578336 ACACATTGACTGATGTTAGATGACG 59.422 40.000 0.00 0.00 38.15 4.35
533 3989 6.974932 ACACATTGACTGATGTTAGATGAC 57.025 37.500 0.00 0.00 38.15 3.06
552 4008 8.035984 TCATGATTACCGTTTAGTCAATACACA 58.964 33.333 0.00 0.00 0.00 3.72
563 4019 6.943718 AGACCCTTTTTCATGATTACCGTTTA 59.056 34.615 0.00 0.00 0.00 2.01
573 4029 4.520492 GCTCAAGAAGACCCTTTTTCATGA 59.480 41.667 0.00 0.00 32.24 3.07
574 4030 4.522022 AGCTCAAGAAGACCCTTTTTCATG 59.478 41.667 0.00 0.00 0.00 3.07
575 4031 4.734266 AGCTCAAGAAGACCCTTTTTCAT 58.266 39.130 0.00 0.00 0.00 2.57
583 4039 3.625649 AGATCAAGCTCAAGAAGACCC 57.374 47.619 0.00 0.00 0.00 4.46
590 4046 5.474876 ACCCTTTTGTTAGATCAAGCTCAAG 59.525 40.000 0.00 0.00 0.00 3.02
608 4064 4.039124 CACTACTCAAAAATGCCACCCTTT 59.961 41.667 0.00 0.00 0.00 3.11
611 4067 3.153919 TCACTACTCAAAAATGCCACCC 58.846 45.455 0.00 0.00 0.00 4.61
612 4068 4.846779 TTCACTACTCAAAAATGCCACC 57.153 40.909 0.00 0.00 0.00 4.61
699 4156 8.917655 GCGTGATCTACTTTAGGAAGATTATTC 58.082 37.037 0.00 0.00 36.69 1.75
701 4158 7.952671 TGCGTGATCTACTTTAGGAAGATTAT 58.047 34.615 0.00 0.00 36.69 1.28
702 4159 7.342769 TGCGTGATCTACTTTAGGAAGATTA 57.657 36.000 0.00 0.00 36.69 1.75
704 4161 5.854010 TGCGTGATCTACTTTAGGAAGAT 57.146 39.130 0.00 0.00 36.69 2.40
705 4162 5.854010 ATGCGTGATCTACTTTAGGAAGA 57.146 39.130 0.00 0.00 36.69 2.87
706 4163 6.153067 CCTATGCGTGATCTACTTTAGGAAG 58.847 44.000 0.00 0.00 38.87 3.46
707 4164 5.010719 CCCTATGCGTGATCTACTTTAGGAA 59.989 44.000 11.04 0.00 30.48 3.36
708 4165 4.523173 CCCTATGCGTGATCTACTTTAGGA 59.477 45.833 11.04 0.00 30.48 2.94
709 4166 4.523173 TCCCTATGCGTGATCTACTTTAGG 59.477 45.833 0.00 0.00 0.00 2.69
710 4167 5.241949 ACTCCCTATGCGTGATCTACTTTAG 59.758 44.000 0.00 0.00 0.00 1.85
711 4168 5.138276 ACTCCCTATGCGTGATCTACTTTA 58.862 41.667 0.00 0.00 0.00 1.85
712 4169 3.961408 ACTCCCTATGCGTGATCTACTTT 59.039 43.478 0.00 0.00 0.00 2.66
713 4170 3.567397 ACTCCCTATGCGTGATCTACTT 58.433 45.455 0.00 0.00 0.00 2.24
714 4171 3.231207 ACTCCCTATGCGTGATCTACT 57.769 47.619 0.00 0.00 0.00 2.57
715 4172 3.190953 GGTACTCCCTATGCGTGATCTAC 59.809 52.174 0.00 0.00 0.00 2.59
730 4187 6.206829 AGTCAAAAGCACAAAATAGGTACTCC 59.793 38.462 0.00 0.00 41.75 3.85
771 4228 6.257423 TGCATCAATATGTACGCTTGAAAAG 58.743 36.000 8.16 4.43 40.27 2.27
884 4346 1.776034 GCCGATGCGAGGGATTGTTC 61.776 60.000 0.00 0.00 0.00 3.18
956 4418 3.027412 CGGGGATGGATAGATAGGAGTG 58.973 54.545 0.00 0.00 0.00 3.51
957 4419 2.624557 GCGGGGATGGATAGATAGGAGT 60.625 54.545 0.00 0.00 0.00 3.85
1159 4621 3.086600 GAGCAGAGAGGGGGTGGG 61.087 72.222 0.00 0.00 0.00 4.61
1162 4624 4.423209 GGGGAGCAGAGAGGGGGT 62.423 72.222 0.00 0.00 0.00 4.95
1166 4628 1.761667 CAGGAGGGGAGCAGAGAGG 60.762 68.421 0.00 0.00 0.00 3.69
1184 4654 5.008316 ACAGGAACCAAACGAATTTCACTAC 59.992 40.000 0.00 0.00 0.00 2.73
1186 4656 3.951680 ACAGGAACCAAACGAATTTCACT 59.048 39.130 0.00 0.00 0.00 3.41
1195 4665 1.335872 GCAATCCACAGGAACCAAACG 60.336 52.381 0.00 0.00 34.34 3.60
1207 4677 2.693797 CACTGAGTTGTGCAATCCAC 57.306 50.000 0.00 0.00 44.90 4.02
1216 4702 2.974698 GCCGCAGCACTGAGTTGT 60.975 61.111 0.81 0.00 39.53 3.32
1229 4715 0.321830 TAAACTGGGTAAGGTGCCGC 60.322 55.000 0.00 0.00 0.00 6.53
1240 4726 1.814394 GGTAAAACGGGCTAAACTGGG 59.186 52.381 0.00 0.00 0.00 4.45
1245 4731 4.622260 AGTACTGGTAAAACGGGCTAAA 57.378 40.909 0.00 0.00 0.00 1.85
1342 4834 5.356882 TTGAAAATCTTGAAGCGGTGTAG 57.643 39.130 0.00 0.00 0.00 2.74
1347 4839 5.865552 ACATGATTTGAAAATCTTGAAGCGG 59.134 36.000 26.09 9.29 45.79 5.52
1391 4883 3.441496 AGACAACACCAAAACATGCAG 57.559 42.857 0.00 0.00 0.00 4.41
1395 4887 4.583073 GGACCTAAGACAACACCAAAACAT 59.417 41.667 0.00 0.00 0.00 2.71
1436 4935 4.164988 AGCCAATCTGTAACCTGAGCTAAT 59.835 41.667 0.00 0.00 0.00 1.73
1529 5028 8.539544 TCACACTATGTCCATTCTCTGATTAAA 58.460 33.333 0.00 0.00 0.00 1.52
1537 5036 6.208988 TGTAGTCACACTATGTCCATTCTC 57.791 41.667 0.00 0.00 32.65 2.87
1569 5068 7.098477 TGAAATGCATCTTTTATTTCAGGTGG 58.902 34.615 0.00 0.00 42.57 4.61
1644 5143 1.153647 CGTAGCAGCGTCCAATCCA 60.154 57.895 0.00 0.00 0.00 3.41
1689 5188 5.080969 AGATTGTGAAATGGGCATTCTTG 57.919 39.130 0.00 0.00 0.00 3.02
1821 5320 6.597280 AGTGCAGCCAAACAAGAAAATAAAAA 59.403 30.769 0.00 0.00 0.00 1.94
1822 5321 6.112058 AGTGCAGCCAAACAAGAAAATAAAA 58.888 32.000 0.00 0.00 0.00 1.52
1823 5322 5.669477 AGTGCAGCCAAACAAGAAAATAAA 58.331 33.333 0.00 0.00 0.00 1.40
1833 5332 2.930950 ACTAAGAAGTGCAGCCAAACA 58.069 42.857 0.00 0.00 33.57 2.83
1879 5378 7.744087 TCGTCCCATCAAATTCCATTATAAG 57.256 36.000 0.00 0.00 0.00 1.73
2321 5833 0.739112 GAGAACTTGAGCTGCTCCGG 60.739 60.000 25.61 19.36 0.00 5.14
2569 6081 7.439655 AGAAGTACAAACAAGACACAGAAGATC 59.560 37.037 0.00 0.00 0.00 2.75
2577 6089 7.399523 CAACTACAGAAGTACAAACAAGACAC 58.600 38.462 0.00 0.00 37.50 3.67
2608 6120 4.692228 TGGCTGTTTGAACAAATCCTTTC 58.308 39.130 3.34 0.00 38.66 2.62
2611 6123 4.751767 TTTGGCTGTTTGAACAAATCCT 57.248 36.364 3.34 0.00 38.66 3.24
2666 6178 9.409312 TGCTTTTTATTGATATGTTCACAACAG 57.591 29.630 0.00 0.00 45.95 3.16
2731 6245 3.129287 CCGTTCCTTTTCCTTGATGGATG 59.871 47.826 0.00 0.00 45.68 3.51
2747 6261 2.052782 AATGGCATAAGGTCCGTTCC 57.947 50.000 0.00 0.00 0.00 3.62
2841 6355 3.306433 GGTGAACAGTTGTGGTTTTTGGT 60.306 43.478 0.00 0.00 0.00 3.67
2861 6375 7.974501 CGTATACACAGAAGTAAGAGATTTGGT 59.025 37.037 3.32 0.00 0.00 3.67
2944 6461 4.378459 CGTTATCCCTCAGCTTTGTTGTTC 60.378 45.833 0.00 0.00 0.00 3.18
3001 6518 0.028902 GAACAAACACCAGCGTCCAC 59.971 55.000 0.00 0.00 0.00 4.02
3044 6565 6.653740 TGAGATAGAGTTAGTTCGTGAGACAA 59.346 38.462 0.00 0.00 41.84 3.18
3045 6566 6.171213 TGAGATAGAGTTAGTTCGTGAGACA 58.829 40.000 0.00 0.00 41.84 3.41
3083 6604 3.090952 GTGCAACTTGTAATTGTGGCA 57.909 42.857 0.00 0.00 40.40 4.92
3189 6726 2.844348 ACCCCTAATCGGAACAAGTGAT 59.156 45.455 0.00 0.00 33.16 3.06
3199 6736 0.463833 GCAACAGGACCCCTAATCGG 60.464 60.000 0.00 0.00 29.64 4.18
3251 6788 7.229306 TGGCCATCAAAATTCTTATGCTACTAG 59.771 37.037 0.00 0.00 0.00 2.57
3252 6789 7.059788 TGGCCATCAAAATTCTTATGCTACTA 58.940 34.615 0.00 0.00 0.00 1.82
3253 6790 5.893255 TGGCCATCAAAATTCTTATGCTACT 59.107 36.000 0.00 0.00 0.00 2.57
3302 6840 3.115554 GCGTCTGCAGTGAAAAATGTTT 58.884 40.909 14.67 0.00 42.15 2.83
3315 6853 1.795170 GCTTCCTTTTGGCGTCTGCA 61.795 55.000 0.00 0.00 45.35 4.41
3557 7095 4.842380 ACTAGTACTAACAAGGGAGGCAAA 59.158 41.667 3.76 0.00 0.00 3.68
3558 7096 4.422984 ACTAGTACTAACAAGGGAGGCAA 58.577 43.478 3.76 0.00 0.00 4.52
3700 7321 8.345565 AGCTAAATCAGTCAAAACTTAAGTGTG 58.654 33.333 9.34 10.73 31.71 3.82
3824 7445 6.369065 CGGTCAAAAGCAGTTTAGAGAATAGT 59.631 38.462 0.00 0.00 0.00 2.12
3908 7529 7.857734 TTGTAGATGCGAAATTAGATTTGGA 57.142 32.000 0.00 0.00 31.47 3.53
3956 7577 1.022903 ATCCAACTCCTCCCTCTCCT 58.977 55.000 0.00 0.00 0.00 3.69
4204 7825 3.961849 TGCTCCCATTTGTAATACAGCA 58.038 40.909 0.00 0.00 0.00 4.41
4208 7829 7.100458 AGTTCAATGCTCCCATTTGTAATAC 57.900 36.000 0.00 0.00 39.60 1.89
4210 7831 6.610075 AAGTTCAATGCTCCCATTTGTAAT 57.390 33.333 0.00 0.00 39.60 1.89
4228 7849 1.740664 GAGGCGTCCCCGAAAGTTC 60.741 63.158 0.00 0.00 39.21 3.01
4314 7936 4.511454 TCAGAAAAAGGAGACGTCAACATG 59.489 41.667 19.50 3.98 0.00 3.21
4413 8035 3.062466 AGCTGTCGTCTGCCGCTA 61.062 61.111 7.82 0.00 38.92 4.26
4417 8039 2.125753 CTCCAGCTGTCGTCTGCC 60.126 66.667 13.81 0.00 38.92 4.85
4422 8044 3.753434 CCGCTCTCCAGCTGTCGT 61.753 66.667 13.81 0.00 44.40 4.34
4425 8047 1.381056 ATCTCCGCTCTCCAGCTGT 60.381 57.895 13.81 0.00 44.40 4.40
4478 8100 4.513442 TCAAGACACAGCAACTACAAAGT 58.487 39.130 0.00 0.00 37.65 2.66
4675 8468 4.120589 GGTAATAGTAGGCACTGCAACTC 58.879 47.826 10.62 0.00 45.83 3.01
4688 8481 7.624360 TTTAGTTCGAACGGAGGTAATAGTA 57.376 36.000 21.87 2.29 0.00 1.82
4715 8508 3.820467 CTCTGTTTGGAATAACTGGTGCA 59.180 43.478 0.00 0.00 0.00 4.57
4716 8509 3.191371 CCTCTGTTTGGAATAACTGGTGC 59.809 47.826 0.00 0.00 0.00 5.01
4718 8511 3.655777 TCCCTCTGTTTGGAATAACTGGT 59.344 43.478 0.00 0.00 0.00 4.00
4730 8524 4.790718 ACTGGTTTTACTCCCTCTGTTT 57.209 40.909 0.00 0.00 0.00 2.83
4744 8538 6.601332 TCTATGAAAGTGAGGAAACTGGTTT 58.399 36.000 0.00 0.00 44.43 3.27
4767 8561 6.690194 ATCAAACATAAAGCATCACTCCTC 57.310 37.500 0.00 0.00 0.00 3.71
4768 8562 7.395489 AGAAATCAAACATAAAGCATCACTCCT 59.605 33.333 0.00 0.00 0.00 3.69
4769 8563 7.542025 AGAAATCAAACATAAAGCATCACTCC 58.458 34.615 0.00 0.00 0.00 3.85
4810 8608 5.042463 TCCATACTTCCAAGACAAACACA 57.958 39.130 0.00 0.00 0.00 3.72
4813 8611 7.214467 TCAAATCCATACTTCCAAGACAAAC 57.786 36.000 0.00 0.00 0.00 2.93
4815 8613 7.669304 TCAATCAAATCCATACTTCCAAGACAA 59.331 33.333 0.00 0.00 0.00 3.18
4816 8614 7.174413 TCAATCAAATCCATACTTCCAAGACA 58.826 34.615 0.00 0.00 0.00 3.41
4817 8615 7.630242 TCAATCAAATCCATACTTCCAAGAC 57.370 36.000 0.00 0.00 0.00 3.01
4946 8779 8.263940 TGTCCTGTATTTCTTTATGTACTTGC 57.736 34.615 0.00 0.00 0.00 4.01
4965 8798 3.973973 TCCCCTATATCTGGTTTGTCCTG 59.026 47.826 0.00 0.00 37.07 3.86
4970 8803 4.141390 ACAGCTTCCCCTATATCTGGTTTG 60.141 45.833 0.00 0.00 0.00 2.93
4990 8823 4.462834 TGCTGTAATAGATCCCCGATACAG 59.537 45.833 13.30 13.30 37.37 2.74
5005 8838 7.557358 TGGATTTCATAGATGTGTTGCTGTAAT 59.443 33.333 0.00 0.00 0.00 1.89
5011 8844 9.754382 ATTTATTGGATTTCATAGATGTGTTGC 57.246 29.630 0.00 0.00 0.00 4.17
5092 8925 3.748568 GTGACCAGCCTAAGAGAACTTTG 59.251 47.826 0.00 0.00 37.53 2.77
5093 8926 3.391296 TGTGACCAGCCTAAGAGAACTTT 59.609 43.478 0.00 0.00 37.53 2.66
5095 8928 2.609747 TGTGACCAGCCTAAGAGAACT 58.390 47.619 0.00 0.00 0.00 3.01
5098 8931 1.272490 CGTTGTGACCAGCCTAAGAGA 59.728 52.381 0.00 0.00 0.00 3.10


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

AutoCloner maintained by Alex Coulton.