Multiple sequence alignment - TraesCS7D01G322600

Loading Multiple Alignment...

Download Multiple Sequence Alignment: (Fasta) (Clustal)


BLAST Results


Shown here are the results of a BLAST search against the genome using the input sequence. The pipeline uses this to extract flanking regions for cloning. If the result of the multiple sequence alignment is not as expected, these results could be used for further investigation.

qseqid sseqid percentage.identical alignment.length no.mismatch no.gap.openings qstart qend sstart send evalue bitscore
0 TraesCS7D01G322600 chr7D 100.000 3779 0 0 1 3779 412756201 412759979 0.000000e+00 6979
1 TraesCS7D01G322600 chr7D 88.889 126 14 0 3380 3505 178613842 178613967 5.050000e-34 156
2 TraesCS7D01G322600 chr7D 98.333 60 1 0 3612 3671 22510814 22510873 5.160000e-19 106
3 TraesCS7D01G322600 chr7B 93.521 2562 95 36 841 3367 426968654 426971179 0.000000e+00 3746
4 TraesCS7D01G322600 chr7B 93.182 132 8 1 3485 3615 46022953 46022822 3.850000e-45 193
5 TraesCS7D01G322600 chr7A 91.964 2327 131 23 777 3056 473916890 473919207 0.000000e+00 3210
6 TraesCS7D01G322600 chr7A 88.618 123 13 1 3383 3505 126943231 126943110 8.460000e-32 148
7 TraesCS7D01G322600 chr7A 86.667 135 12 6 3080 3211 473919268 473919399 1.090000e-30 145
8 TraesCS7D01G322600 chr7A 87.603 121 11 3 3663 3779 473919456 473919576 1.830000e-28 137
9 TraesCS7D01G322600 chr5B 91.496 682 45 6 77 751 487232357 487233032 0.000000e+00 926
10 TraesCS7D01G322600 chr5B 93.233 133 8 1 3482 3613 31288062 31287930 1.070000e-45 195
11 TraesCS7D01G322600 chr5B 76.325 283 45 12 3383 3664 50231208 50231469 8.520000e-27 132
12 TraesCS7D01G322600 chr5B 93.671 79 5 0 1 79 487225595 487225673 6.630000e-23 119
13 TraesCS7D01G322600 chr1B 85.566 769 88 11 1 751 517098103 517097340 0.000000e+00 784
14 TraesCS7D01G322600 chr1B 76.842 285 50 12 3383 3665 117290244 117290514 3.040000e-31 147
15 TraesCS7D01G322600 chr1B 91.781 73 5 1 3612 3683 668939123 668939195 2.400000e-17 100
16 TraesCS7D01G322600 chr4D 90.437 481 35 6 1017 1490 434801513 434801989 1.150000e-174 623
17 TraesCS7D01G322600 chr4D 91.981 212 17 0 1 212 37942429 37942218 7.940000e-77 298
18 TraesCS7D01G322600 chr4D 90.580 138 11 2 3480 3615 289728431 289728294 8.340000e-42 182
19 TraesCS7D01G322600 chr4D 91.818 110 9 0 3383 3492 21101576 21101467 1.820000e-33 154
20 TraesCS7D01G322600 chr4D 91.818 110 9 0 3383 3492 97930622 97930513 1.820000e-33 154
21 TraesCS7D01G322600 chr4A 88.819 474 42 6 1017 1483 193109510 193109041 4.230000e-159 571
22 TraesCS7D01G322600 chr4A 88.608 474 43 6 1017 1483 585784034 585784503 1.970000e-157 566
23 TraesCS7D01G322600 chr4A 98.333 60 1 0 3611 3670 357678659 357678600 5.160000e-19 106
24 TraesCS7D01G322600 chr2B 90.640 203 18 1 279 481 542687437 542687638 6.220000e-68 268
25 TraesCS7D01G322600 chr2B 90.909 198 18 0 1 198 542687243 542687440 2.240000e-67 267
26 TraesCS7D01G322600 chr6D 93.750 128 7 1 3488 3614 193682455 193682582 1.390000e-44 191
27 TraesCS7D01G322600 chr3D 93.130 131 7 2 3482 3610 536894827 536894957 1.390000e-44 191
28 TraesCS7D01G322600 chr3D 90.580 138 11 2 3480 3615 140384944 140384807 8.340000e-42 182
29 TraesCS7D01G322600 chr3D 89.116 147 12 4 3472 3615 396084451 396084596 3.000000e-41 180
30 TraesCS7D01G322600 chr3D 91.818 110 9 0 3383 3492 4171274 4171165 1.820000e-33 154
31 TraesCS7D01G322600 chr2D 90.411 146 9 4 3481 3622 27264974 27265118 1.790000e-43 187
32 TraesCS7D01G322600 chr2D 98.361 61 0 1 3609 3668 89693660 89693600 5.160000e-19 106
33 TraesCS7D01G322600 chr5D 91.241 137 11 1 3479 3614 10355890 10356026 6.450000e-43 185
34 TraesCS7D01G322600 chr5D 92.523 107 8 0 3383 3489 69953553 69953659 1.820000e-33 154
35 TraesCS7D01G322600 chr5D 94.286 70 3 1 3594 3662 510094680 510094611 5.160000e-19 106
36 TraesCS7D01G322600 chr6B 78.873 284 40 10 3383 3665 204938662 204938398 1.400000e-39 174
37 TraesCS7D01G322600 chr6A 92.523 107 8 0 3383 3489 222571251 222571357 1.820000e-33 154
38 TraesCS7D01G322600 chr6A 91.549 71 6 0 3594 3664 45671697 45671627 8.640000e-17 99
39 TraesCS7D01G322600 chr3B 91.818 110 9 0 3383 3492 12102273 12102164 1.820000e-33 154
40 TraesCS7D01G322600 chr3B 90.541 74 7 0 3594 3667 26656461 26656388 8.640000e-17 99
41 TraesCS7D01G322600 chr1D 92.523 107 8 0 3383 3489 206955544 206955650 1.820000e-33 154


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 TraesCS7D01G322600 chr7D 412756201 412759979 3778 False 6979 6979 100.000000 1 3779 1 chr7D.!!$F3 3778
1 TraesCS7D01G322600 chr7B 426968654 426971179 2525 False 3746 3746 93.521000 841 3367 1 chr7B.!!$F1 2526
2 TraesCS7D01G322600 chr7A 473916890 473919576 2686 False 1164 3210 88.744667 777 3779 3 chr7A.!!$F1 3002
3 TraesCS7D01G322600 chr5B 487232357 487233032 675 False 926 926 91.496000 77 751 1 chr5B.!!$F3 674
4 TraesCS7D01G322600 chr1B 517097340 517098103 763 True 784 784 85.566000 1 751 1 chr1B.!!$R1 750

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
819 838 0.167470 CAAACGAGGTGCATGCAGAG 59.833 55.0 23.41 14.76 0.0 3.35 F
821 840 0.250467 AACGAGGTGCATGCAGAGTT 60.250 50.0 23.41 20.16 0.0 3.01 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2700 2767 1.602851 CTTACCATGAGCATGCAGAGC 59.397 52.381 21.98 6.69 37.49 4.09 R
2803 2870 2.705658 CCCCTACTGCACAATAGATCCA 59.294 50.000 0.00 0.00 0.00 3.41 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
18 19 1.589630 CCCACTCCATCGACGACAA 59.410 57.895 0.00 0.00 0.00 3.18
24 25 4.570772 CCACTCCATCGACGACAAAATAAT 59.429 41.667 0.00 0.00 0.00 1.28
27 28 5.749109 ACTCCATCGACGACAAAATAATCTC 59.251 40.000 0.00 0.00 0.00 2.75
55 56 4.019591 ACCAACTTAGGTGGATCAAGTACC 60.020 45.833 24.67 0.00 41.30 3.34
66 67 4.100963 TGGATCAAGTACCAGCGATGTTAT 59.899 41.667 0.00 0.00 0.00 1.89
149 150 2.120909 CCAAGGCGGCGGATCAAAT 61.121 57.895 9.78 0.00 0.00 2.32
169 170 0.819259 CCTGCACCATTACATCCCGG 60.819 60.000 0.00 0.00 0.00 5.73
180 181 1.452108 CATCCCGGCCTTCAAGGAC 60.452 63.158 7.98 2.14 41.17 3.85
282 285 2.372172 CCTGACACTTAAGGAGTTGGGT 59.628 50.000 7.53 0.00 36.10 4.51
307 310 3.867857 TGTCAATATACGCCAAGCTTGA 58.132 40.909 28.05 8.10 0.00 3.02
348 351 3.320626 TGAAGAGCTCAACATCGTGAAG 58.679 45.455 17.77 0.00 0.00 3.02
376 379 1.544759 CCACCGGCAAACTTAGGTCTT 60.545 52.381 0.00 0.00 34.25 3.01
433 436 1.428912 TCACCTTCTTTGCTTCCCCAT 59.571 47.619 0.00 0.00 0.00 4.00
442 445 5.939447 TCTTTGCTTCCCCATCAAAATTTT 58.061 33.333 0.00 0.00 30.47 1.82
444 447 4.970860 TGCTTCCCCATCAAAATTTTCA 57.029 36.364 0.00 0.00 0.00 2.69
500 503 3.073798 TGGGAGCTTAAAACAGGACATGA 59.926 43.478 0.00 0.00 0.00 3.07
515 518 6.655003 ACAGGACATGAAATAAACAGGTACAG 59.345 38.462 0.00 0.00 35.66 2.74
543 546 6.663093 TGGGCAACAGATTTTATGAGTACATT 59.337 34.615 0.00 0.00 36.69 2.71
581 584 0.407528 TAGCTTTGCCATCCAACCCA 59.592 50.000 0.00 0.00 31.97 4.51
598 601 2.175931 ACCCATTACCTTGTTCCACACA 59.824 45.455 0.00 0.00 0.00 3.72
599 602 3.181423 ACCCATTACCTTGTTCCACACAT 60.181 43.478 0.00 0.00 34.43 3.21
636 639 5.695851 ACTTGAAAGCACCATTCTTACTG 57.304 39.130 0.00 0.00 0.00 2.74
670 683 4.504864 CCGAGGGCATACCAAGATATTTCA 60.505 45.833 0.00 0.00 43.89 2.69
671 684 5.063204 CGAGGGCATACCAAGATATTTCAA 58.937 41.667 0.00 0.00 43.89 2.69
672 685 5.707298 CGAGGGCATACCAAGATATTTCAAT 59.293 40.000 0.00 0.00 43.89 2.57
674 687 5.776716 AGGGCATACCAAGATATTTCAATGG 59.223 40.000 6.50 6.50 43.89 3.16
677 696 6.925165 GGCATACCAAGATATTTCAATGGTTG 59.075 38.462 15.32 13.80 41.69 3.77
693 712 6.267242 TCAATGGTTGATTTGGAACATTGAGA 59.733 34.615 11.52 0.00 33.81 3.27
769 788 9.462606 AAATAGATAAAGGAAATCAAACGAGGT 57.537 29.630 0.00 0.00 0.00 3.85
770 789 9.462606 AATAGATAAAGGAAATCAAACGAGGTT 57.537 29.630 0.00 0.00 0.00 3.50
771 790 7.761038 AGATAAAGGAAATCAAACGAGGTTT 57.239 32.000 0.00 0.00 36.05 3.27
772 791 8.178313 AGATAAAGGAAATCAAACGAGGTTTT 57.822 30.769 0.00 0.00 33.10 2.43
773 792 8.638873 AGATAAAGGAAATCAAACGAGGTTTTT 58.361 29.630 0.00 0.00 33.10 1.94
813 832 2.795329 AGGAAATCAAACGAGGTGCAT 58.205 42.857 0.00 0.00 0.00 3.96
819 838 0.167470 CAAACGAGGTGCATGCAGAG 59.833 55.000 23.41 14.76 0.00 3.35
821 840 0.250467 AACGAGGTGCATGCAGAGTT 60.250 50.000 23.41 20.16 0.00 3.01
829 848 1.651240 GCATGCAGAGTTGGCACGAT 61.651 55.000 14.21 0.00 45.23 3.73
920 940 0.251916 TGTGGTCCCGAATTAGCAGG 59.748 55.000 0.00 0.00 0.00 4.85
969 989 1.911057 TGCAGAGAAAGGACGAGAGA 58.089 50.000 0.00 0.00 0.00 3.10
1179 1200 2.668550 GGCTTCTTCCACGCCGTT 60.669 61.111 0.00 0.00 33.64 4.44
1294 1315 1.300931 GCCGACTTCAGTGTGCTCA 60.301 57.895 0.00 0.00 0.00 4.26
1319 1340 1.207377 GACTAAATCGAGCCGACGCC 61.207 60.000 0.00 0.00 39.18 5.68
1451 1489 9.383519 TCATTCCTGTGAACTAGTAAATCAATC 57.616 33.333 0.00 0.00 32.13 2.67
1452 1490 9.166173 CATTCCTGTGAACTAGTAAATCAATCA 57.834 33.333 0.00 0.00 32.13 2.57
1456 1494 8.783093 CCTGTGAACTAGTAAATCAATCAAACA 58.217 33.333 0.00 0.00 0.00 2.83
1588 1634 5.570234 AACTCAGTAGCTAGTACTTCTGC 57.430 43.478 0.00 3.84 40.27 4.26
1640 1686 0.301687 CGCTGTATGTCGGTTCATGC 59.698 55.000 0.00 0.00 0.00 4.06
1641 1687 1.368641 GCTGTATGTCGGTTCATGCA 58.631 50.000 0.00 0.00 37.90 3.96
1766 1815 3.884895 TCGGCATGATAAGTTTCCATGT 58.115 40.909 14.60 0.00 39.69 3.21
1830 1879 6.716628 TCAATTTCCAACTTATCTTGTCAGCT 59.283 34.615 0.00 0.00 0.00 4.24
1858 1907 7.539712 ACATGTGAGTGTTATTTTCCTATCG 57.460 36.000 0.00 0.00 0.00 2.92
1860 1909 8.255206 ACATGTGAGTGTTATTTTCCTATCGTA 58.745 33.333 0.00 0.00 0.00 3.43
2034 2084 5.042463 TGTATTGTGTCTCCTTGAAACCA 57.958 39.130 0.00 0.00 31.90 3.67
2065 2115 1.265095 CACACTGCACATGTCAACTCC 59.735 52.381 0.00 0.00 0.00 3.85
2139 2189 9.859427 CATAAATGTTGGTTTAATCATGTCAGT 57.141 29.630 0.00 0.00 0.00 3.41
2243 2294 7.121907 TGCTATTGTGCCTGTTATTTTACATCA 59.878 33.333 0.00 0.00 0.00 3.07
2468 2520 3.078837 GGTGTATTCCTTGCCGAGAAAA 58.921 45.455 0.00 0.00 0.00 2.29
2639 2695 0.908198 GTCAGTCTGCATCCCCTTCT 59.092 55.000 0.00 0.00 0.00 2.85
2700 2767 2.317230 GGTGAACACCCTTGTGACG 58.683 57.895 12.42 0.00 45.76 4.35
2801 2868 2.338785 GCTGCCCTGCTCTTGAACC 61.339 63.158 0.00 0.00 0.00 3.62
2803 2870 2.032681 GCCCTGCTCTTGAACCGT 59.967 61.111 0.00 0.00 0.00 4.83
2810 2877 2.166459 CTGCTCTTGAACCGTGGATCTA 59.834 50.000 0.00 0.00 0.00 1.98
2817 2884 2.027653 TGAACCGTGGATCTATTGTGCA 60.028 45.455 0.00 0.00 0.00 4.57
2823 2890 3.733337 GTGGATCTATTGTGCAGTAGGG 58.267 50.000 0.00 0.00 0.00 3.53
2839 2906 3.718956 AGTAGGGGATTAAGCTGCTGATT 59.281 43.478 1.35 0.00 0.00 2.57
2885 2952 7.683437 ACAGTAAAGTGGAAGGTTAATTAGC 57.317 36.000 0.00 0.00 0.00 3.09
2907 2975 4.681512 GCCCTTGATTTTGATTGATGGTCC 60.682 45.833 0.00 0.00 0.00 4.46
2909 2977 4.467082 CCTTGATTTTGATTGATGGTCCCA 59.533 41.667 0.00 0.00 0.00 4.37
2913 2981 6.252233 TGATTTTGATTGATGGTCCCACTTA 58.748 36.000 0.00 0.00 0.00 2.24
3059 3128 5.558844 CGTCGTATATGCATTGCTTTGTCAT 60.559 40.000 3.54 0.00 0.00 3.06
3060 3129 5.848036 GTCGTATATGCATTGCTTTGTCATC 59.152 40.000 3.54 0.00 0.00 2.92
3061 3130 5.759763 TCGTATATGCATTGCTTTGTCATCT 59.240 36.000 3.54 0.00 0.00 2.90
3062 3131 6.928492 TCGTATATGCATTGCTTTGTCATCTA 59.072 34.615 3.54 0.00 0.00 1.98
3063 3132 7.603784 TCGTATATGCATTGCTTTGTCATCTAT 59.396 33.333 3.54 0.00 0.00 1.98
3064 3133 8.872845 CGTATATGCATTGCTTTGTCATCTATA 58.127 33.333 3.54 0.00 0.00 1.31
3070 3139 8.152898 TGCATTGCTTTGTCATCTATAGTCTAT 58.847 33.333 10.49 0.00 0.00 1.98
3115 3233 7.148255 CCTCGGTTTCATTTGTTCTATGATTGA 60.148 37.037 0.00 0.00 32.43 2.57
3129 3247 9.070149 GTTCTATGATTGATTCACTTTTTCAGC 57.930 33.333 0.00 0.00 37.11 4.26
3130 3248 8.571461 TCTATGATTGATTCACTTTTTCAGCT 57.429 30.769 0.00 0.00 37.11 4.24
3131 3249 9.671279 TCTATGATTGATTCACTTTTTCAGCTA 57.329 29.630 0.00 0.00 37.11 3.32
3132 3250 9.932699 CTATGATTGATTCACTTTTTCAGCTAG 57.067 33.333 0.00 0.00 37.11 3.42
3153 3271 2.457366 ACTTGAGACGGCAGTTTAGG 57.543 50.000 0.00 0.00 0.00 2.69
3159 3277 1.002087 AGACGGCAGTTTAGGTTGGAG 59.998 52.381 0.00 0.00 0.00 3.86
3164 3282 2.683362 GGCAGTTTAGGTTGGAGCATAC 59.317 50.000 0.00 0.00 0.00 2.39
3167 3286 3.941483 CAGTTTAGGTTGGAGCATACAGG 59.059 47.826 0.00 0.00 0.00 4.00
3235 3354 1.228657 GCACGTCACTCCACCCTTTC 61.229 60.000 0.00 0.00 0.00 2.62
3239 3358 2.143925 CGTCACTCCACCCTTTCTTTC 58.856 52.381 0.00 0.00 0.00 2.62
3247 3366 3.756434 TCCACCCTTTCTTTCTTTATGCG 59.244 43.478 0.00 0.00 0.00 4.73
3308 3427 3.839432 CGTCCTCGGGCCTCCTTC 61.839 72.222 0.84 0.00 0.00 3.46
3310 3429 3.684628 TCCTCGGGCCTCCTTCCT 61.685 66.667 0.84 0.00 0.00 3.36
3311 3430 3.157949 CCTCGGGCCTCCTTCCTC 61.158 72.222 0.84 0.00 0.00 3.71
3314 3433 4.806339 CGGGCCTCCTTCCTCCCT 62.806 72.222 0.84 0.00 36.61 4.20
3316 3435 2.684499 GGGCCTCCTTCCTCCCTTG 61.684 68.421 0.84 0.00 35.87 3.61
3317 3436 2.273776 GCCTCCTTCCTCCCTTGC 59.726 66.667 0.00 0.00 0.00 4.01
3359 3479 2.573462 CTCCTTTCCTCATCCCTTGTGA 59.427 50.000 0.00 0.00 0.00 3.58
3375 3507 1.978580 TGTGACCCCTTCTTTCTCCTC 59.021 52.381 0.00 0.00 0.00 3.71
3381 3513 3.110705 CCCCTTCTTTCTCCTCTGATCA 58.889 50.000 0.00 0.00 0.00 2.92
3382 3514 3.715834 CCCCTTCTTTCTCCTCTGATCAT 59.284 47.826 0.00 0.00 0.00 2.45
3383 3515 4.202346 CCCCTTCTTTCTCCTCTGATCATC 60.202 50.000 0.00 0.00 0.00 2.92
3384 3516 4.202346 CCCTTCTTTCTCCTCTGATCATCC 60.202 50.000 0.00 0.00 0.00 3.51
3385 3517 4.501229 CCTTCTTTCTCCTCTGATCATCCG 60.501 50.000 0.00 0.00 0.00 4.18
3386 3518 3.636679 TCTTTCTCCTCTGATCATCCGT 58.363 45.455 0.00 0.00 0.00 4.69
3387 3519 4.026744 TCTTTCTCCTCTGATCATCCGTT 58.973 43.478 0.00 0.00 0.00 4.44
3388 3520 4.467795 TCTTTCTCCTCTGATCATCCGTTT 59.532 41.667 0.00 0.00 0.00 3.60
3389 3521 4.392921 TTCTCCTCTGATCATCCGTTTC 57.607 45.455 0.00 0.00 0.00 2.78
3390 3522 3.636679 TCTCCTCTGATCATCCGTTTCT 58.363 45.455 0.00 0.00 0.00 2.52
3391 3523 4.793201 TCTCCTCTGATCATCCGTTTCTA 58.207 43.478 0.00 0.00 0.00 2.10
3392 3524 5.201243 TCTCCTCTGATCATCCGTTTCTAA 58.799 41.667 0.00 0.00 0.00 2.10
3393 3525 5.656859 TCTCCTCTGATCATCCGTTTCTAAA 59.343 40.000 0.00 0.00 0.00 1.85
3394 3526 6.325028 TCTCCTCTGATCATCCGTTTCTAAAT 59.675 38.462 0.00 0.00 0.00 1.40
3395 3527 6.283694 TCCTCTGATCATCCGTTTCTAAATG 58.716 40.000 0.00 0.00 0.00 2.32
3396 3528 6.051717 CCTCTGATCATCCGTTTCTAAATGT 58.948 40.000 0.00 0.00 0.00 2.71
3397 3529 6.540189 CCTCTGATCATCCGTTTCTAAATGTT 59.460 38.462 0.00 0.00 0.00 2.71
3398 3530 7.066284 CCTCTGATCATCCGTTTCTAAATGTTT 59.934 37.037 0.00 0.00 0.00 2.83
3399 3531 7.751732 TCTGATCATCCGTTTCTAAATGTTTG 58.248 34.615 0.00 0.00 0.00 2.93
3400 3532 7.390440 TCTGATCATCCGTTTCTAAATGTTTGT 59.610 33.333 0.00 0.00 0.00 2.83
3401 3533 7.526608 TGATCATCCGTTTCTAAATGTTTGTC 58.473 34.615 0.00 0.00 0.00 3.18
3402 3534 7.390440 TGATCATCCGTTTCTAAATGTTTGTCT 59.610 33.333 0.00 0.00 0.00 3.41
3403 3535 7.504924 TCATCCGTTTCTAAATGTTTGTCTT 57.495 32.000 0.00 0.00 0.00 3.01
3404 3536 7.936584 TCATCCGTTTCTAAATGTTTGTCTTT 58.063 30.769 0.00 0.00 0.00 2.52
3405 3537 8.410141 TCATCCGTTTCTAAATGTTTGTCTTTT 58.590 29.630 0.00 0.00 0.00 2.27
3406 3538 9.030301 CATCCGTTTCTAAATGTTTGTCTTTTT 57.970 29.630 0.00 0.00 0.00 1.94
3408 3540 9.724839 TCCGTTTCTAAATGTTTGTCTTTTTAG 57.275 29.630 0.00 0.00 0.00 1.85
3409 3541 9.724839 CCGTTTCTAAATGTTTGTCTTTTTAGA 57.275 29.630 0.00 0.00 0.00 2.10
3481 3613 7.138692 AGTGTAGATTCACTCATTTTGCTTC 57.861 36.000 0.00 0.00 44.07 3.86
3482 3614 6.712095 AGTGTAGATTCACTCATTTTGCTTCA 59.288 34.615 0.00 0.00 44.07 3.02
3483 3615 7.392673 AGTGTAGATTCACTCATTTTGCTTCAT 59.607 33.333 0.00 0.00 44.07 2.57
3484 3616 8.668353 GTGTAGATTCACTCATTTTGCTTCATA 58.332 33.333 0.00 0.00 35.68 2.15
3485 3617 9.399797 TGTAGATTCACTCATTTTGCTTCATAT 57.600 29.630 0.00 0.00 0.00 1.78
3486 3618 9.661187 GTAGATTCACTCATTTTGCTTCATATG 57.339 33.333 0.00 0.00 0.00 1.78
3487 3619 8.289939 AGATTCACTCATTTTGCTTCATATGT 57.710 30.769 1.90 0.00 0.00 2.29
3488 3620 9.399797 AGATTCACTCATTTTGCTTCATATGTA 57.600 29.630 1.90 0.00 0.00 2.29
3489 3621 9.443283 GATTCACTCATTTTGCTTCATATGTAC 57.557 33.333 1.90 0.00 0.00 2.90
3490 3622 8.565896 TTCACTCATTTTGCTTCATATGTACT 57.434 30.769 1.90 0.00 0.00 2.73
3491 3623 8.201554 TCACTCATTTTGCTTCATATGTACTC 57.798 34.615 1.90 0.00 0.00 2.59
3492 3624 7.280876 TCACTCATTTTGCTTCATATGTACTCC 59.719 37.037 1.90 0.00 0.00 3.85
3493 3625 7.066163 CACTCATTTTGCTTCATATGTACTCCA 59.934 37.037 1.90 0.00 0.00 3.86
3494 3626 7.776969 ACTCATTTTGCTTCATATGTACTCCAT 59.223 33.333 1.90 0.00 37.58 3.41
3495 3627 8.158169 TCATTTTGCTTCATATGTACTCCATC 57.842 34.615 1.90 0.00 34.86 3.51
3496 3628 6.942532 TTTTGCTTCATATGTACTCCATCC 57.057 37.500 1.90 0.00 34.86 3.51
3497 3629 4.257267 TGCTTCATATGTACTCCATCCG 57.743 45.455 1.90 0.00 34.86 4.18
3498 3630 3.641436 TGCTTCATATGTACTCCATCCGT 59.359 43.478 1.90 0.00 34.86 4.69
3499 3631 4.238514 GCTTCATATGTACTCCATCCGTC 58.761 47.826 1.90 0.00 34.86 4.79
3500 3632 4.810790 CTTCATATGTACTCCATCCGTCC 58.189 47.826 1.90 0.00 34.86 4.79
3501 3633 3.162666 TCATATGTACTCCATCCGTCCC 58.837 50.000 1.90 0.00 34.86 4.46
3502 3634 2.759839 TATGTACTCCATCCGTCCCA 57.240 50.000 0.00 0.00 34.86 4.37
3503 3635 1.874129 ATGTACTCCATCCGTCCCAA 58.126 50.000 0.00 0.00 0.00 4.12
3504 3636 1.646912 TGTACTCCATCCGTCCCAAA 58.353 50.000 0.00 0.00 0.00 3.28
3505 3637 2.193127 TGTACTCCATCCGTCCCAAAT 58.807 47.619 0.00 0.00 0.00 2.32
3506 3638 2.574369 TGTACTCCATCCGTCCCAAATT 59.426 45.455 0.00 0.00 0.00 1.82
3507 3639 2.899303 ACTCCATCCGTCCCAAATTT 57.101 45.000 0.00 0.00 0.00 1.82
3508 3640 3.169512 ACTCCATCCGTCCCAAATTTT 57.830 42.857 0.00 0.00 0.00 1.82
3509 3641 3.506398 ACTCCATCCGTCCCAAATTTTT 58.494 40.909 0.00 0.00 0.00 1.94
3589 3721 8.692710 ACATCCGTATCTGACTAATTTAAGACA 58.307 33.333 0.00 0.00 0.00 3.41
3590 3722 9.529325 CATCCGTATCTGACTAATTTAAGACAA 57.471 33.333 0.00 0.00 0.00 3.18
3591 3723 9.751542 ATCCGTATCTGACTAATTTAAGACAAG 57.248 33.333 0.00 0.00 0.00 3.16
3592 3724 8.963725 TCCGTATCTGACTAATTTAAGACAAGA 58.036 33.333 0.00 0.00 0.00 3.02
3593 3725 9.582431 CCGTATCTGACTAATTTAAGACAAGAA 57.418 33.333 0.00 0.00 0.00 2.52
3603 3735 9.341899 CTAATTTAAGACAAGAATTTTGGGACG 57.658 33.333 0.00 0.00 0.00 4.79
3604 3736 5.699097 TTAAGACAAGAATTTTGGGACGG 57.301 39.130 0.00 0.00 0.00 4.79
3605 3737 3.502123 AGACAAGAATTTTGGGACGGA 57.498 42.857 0.00 0.00 0.00 4.69
3606 3738 3.412386 AGACAAGAATTTTGGGACGGAG 58.588 45.455 0.00 0.00 0.00 4.63
3607 3739 2.488153 GACAAGAATTTTGGGACGGAGG 59.512 50.000 0.00 0.00 0.00 4.30
3608 3740 1.818674 CAAGAATTTTGGGACGGAGGG 59.181 52.381 0.00 0.00 0.00 4.30
3609 3741 1.368374 AGAATTTTGGGACGGAGGGA 58.632 50.000 0.00 0.00 0.00 4.20
3610 3742 1.708551 AGAATTTTGGGACGGAGGGAA 59.291 47.619 0.00 0.00 0.00 3.97
3611 3743 2.311841 AGAATTTTGGGACGGAGGGAAT 59.688 45.455 0.00 0.00 0.00 3.01
3612 3744 3.526019 AGAATTTTGGGACGGAGGGAATA 59.474 43.478 0.00 0.00 0.00 1.75
3613 3745 3.577805 ATTTTGGGACGGAGGGAATAG 57.422 47.619 0.00 0.00 0.00 1.73
3614 3746 1.961133 TTTGGGACGGAGGGAATAGT 58.039 50.000 0.00 0.00 0.00 2.12
3615 3747 1.492764 TTGGGACGGAGGGAATAGTC 58.507 55.000 0.00 0.00 0.00 2.59
3616 3748 0.337082 TGGGACGGAGGGAATAGTCA 59.663 55.000 0.00 0.00 35.49 3.41
3617 3749 0.751452 GGGACGGAGGGAATAGTCAC 59.249 60.000 0.00 0.00 35.49 3.67
3618 3750 1.688627 GGGACGGAGGGAATAGTCACT 60.689 57.143 0.00 0.00 41.60 3.41
3619 3751 2.108970 GGACGGAGGGAATAGTCACTT 58.891 52.381 0.00 0.00 37.77 3.16
3620 3752 2.159085 GGACGGAGGGAATAGTCACTTG 60.159 54.545 0.00 0.00 37.77 3.16
3621 3753 2.496470 GACGGAGGGAATAGTCACTTGT 59.504 50.000 0.00 0.00 37.77 3.16
3622 3754 2.904434 ACGGAGGGAATAGTCACTTGTT 59.096 45.455 0.00 0.00 37.77 2.83
3623 3755 3.262420 CGGAGGGAATAGTCACTTGTTG 58.738 50.000 0.00 0.00 37.77 3.33
3624 3756 3.056107 CGGAGGGAATAGTCACTTGTTGA 60.056 47.826 0.00 0.00 37.77 3.18
3625 3757 4.562757 CGGAGGGAATAGTCACTTGTTGAA 60.563 45.833 0.00 0.00 37.77 2.69
3626 3758 5.313712 GGAGGGAATAGTCACTTGTTGAAA 58.686 41.667 0.00 0.00 37.77 2.69
3627 3759 5.946377 GGAGGGAATAGTCACTTGTTGAAAT 59.054 40.000 0.00 0.00 37.77 2.17
3628 3760 6.094186 GGAGGGAATAGTCACTTGTTGAAATC 59.906 42.308 0.00 0.00 37.77 2.17
3629 3761 6.784031 AGGGAATAGTCACTTGTTGAAATCT 58.216 36.000 0.00 0.00 31.46 2.40
3630 3762 6.881602 AGGGAATAGTCACTTGTTGAAATCTC 59.118 38.462 0.00 0.00 31.46 2.75
3631 3763 6.881602 GGGAATAGTCACTTGTTGAAATCTCT 59.118 38.462 0.00 0.00 35.39 3.10
3632 3764 8.041323 GGGAATAGTCACTTGTTGAAATCTCTA 58.959 37.037 0.00 0.00 35.39 2.43
3633 3765 9.092876 GGAATAGTCACTTGTTGAAATCTCTAG 57.907 37.037 0.00 0.00 35.39 2.43
3634 3766 9.862371 GAATAGTCACTTGTTGAAATCTCTAGA 57.138 33.333 0.00 0.00 35.39 2.43
3637 3769 8.600449 AGTCACTTGTTGAAATCTCTAGAAAG 57.400 34.615 0.00 0.00 35.39 2.62
3638 3770 8.424918 AGTCACTTGTTGAAATCTCTAGAAAGA 58.575 33.333 0.00 0.00 35.39 2.52
3639 3771 8.491950 GTCACTTGTTGAAATCTCTAGAAAGAC 58.508 37.037 0.00 0.00 35.39 3.01
3640 3772 8.204160 TCACTTGTTGAAATCTCTAGAAAGACA 58.796 33.333 0.00 0.00 0.00 3.41
3641 3773 8.830580 CACTTGTTGAAATCTCTAGAAAGACAA 58.169 33.333 0.00 0.00 0.00 3.18
3642 3774 9.396022 ACTTGTTGAAATCTCTAGAAAGACAAA 57.604 29.630 0.00 0.00 0.00 2.83
3655 3787 9.595823 TCTAGAAAGACAAATATTTAGGAACGG 57.404 33.333 0.00 0.00 0.00 4.44
3656 3788 9.595823 CTAGAAAGACAAATATTTAGGAACGGA 57.404 33.333 0.00 0.00 0.00 4.69
3657 3789 8.494016 AGAAAGACAAATATTTAGGAACGGAG 57.506 34.615 0.00 0.00 0.00 4.63
3658 3790 7.553044 AGAAAGACAAATATTTAGGAACGGAGG 59.447 37.037 0.00 0.00 0.00 4.30
3659 3791 5.681639 AGACAAATATTTAGGAACGGAGGG 58.318 41.667 0.00 0.00 0.00 4.30
3660 3792 5.427481 AGACAAATATTTAGGAACGGAGGGA 59.573 40.000 0.00 0.00 0.00 4.20
3661 3793 5.681639 ACAAATATTTAGGAACGGAGGGAG 58.318 41.667 0.00 0.00 0.00 4.30
3666 3798 1.002069 TAGGAACGGAGGGAGTACCA 58.998 55.000 0.00 0.00 43.89 3.25
3671 3803 0.902531 ACGGAGGGAGTACCATTGTG 59.097 55.000 0.00 0.00 43.89 3.33
3679 3811 3.709653 GGGAGTACCATTGTGTCCTGATA 59.290 47.826 0.00 0.00 39.85 2.15
3682 3814 6.177610 GGAGTACCATTGTGTCCTGATAAAA 58.822 40.000 0.00 0.00 35.97 1.52
3692 3824 3.258372 TGTCCTGATAAAACTCTGCGACT 59.742 43.478 0.00 0.00 0.00 4.18
3694 3826 4.327627 GTCCTGATAAAACTCTGCGACTTC 59.672 45.833 0.00 0.00 0.00 3.01
3698 3834 2.510768 AAAACTCTGCGACTTCTCGT 57.489 45.000 0.00 0.00 42.33 4.18
3699 3835 2.053282 AAACTCTGCGACTTCTCGTC 57.947 50.000 0.00 0.00 42.33 4.20
3722 3858 3.433306 TGACCCTCCACCTTATTTGTG 57.567 47.619 0.00 0.00 0.00 3.33
3725 3861 2.290960 ACCCTCCACCTTATTTGTGAGC 60.291 50.000 0.00 0.00 35.74 4.26
3729 3865 1.474330 CACCTTATTTGTGAGCCCCC 58.526 55.000 0.00 0.00 35.74 5.40
3734 3870 1.213296 TATTTGTGAGCCCCCTCCTC 58.787 55.000 0.00 0.00 37.29 3.71
3735 3871 1.575447 ATTTGTGAGCCCCCTCCTCC 61.575 60.000 0.00 0.00 37.29 4.30
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
8 9 7.254455 GGTCAATGAGATTATTTTGTCGTCGAT 60.254 37.037 0.00 0.00 0.00 3.59
11 12 7.072177 TGGTCAATGAGATTATTTTGTCGTC 57.928 36.000 0.00 0.00 0.00 4.20
13 14 7.530010 AGTTGGTCAATGAGATTATTTTGTCG 58.470 34.615 0.00 0.00 0.00 4.35
18 19 8.960591 CACCTAAGTTGGTCAATGAGATTATTT 58.039 33.333 0.00 0.00 38.45 1.40
24 25 3.907474 TCCACCTAAGTTGGTCAATGAGA 59.093 43.478 0.00 0.00 38.45 3.27
27 28 4.588899 TGATCCACCTAAGTTGGTCAATG 58.411 43.478 0.00 0.00 38.45 2.82
74 75 1.909700 CTACCAAGGGTGCACAACAT 58.090 50.000 20.43 0.42 36.19 2.71
149 150 0.180171 CGGGATGTAATGGTGCAGGA 59.820 55.000 0.00 0.00 0.00 3.86
169 170 3.069778 AGGTCCGTCCTTGAAGGC 58.930 61.111 6.30 0.80 45.67 4.35
212 213 3.265791 ACTGAATTCTTCATGCCGAGTC 58.734 45.455 7.05 0.00 39.30 3.36
213 214 3.265791 GACTGAATTCTTCATGCCGAGT 58.734 45.455 7.05 0.00 39.30 4.18
282 285 4.513442 AGCTTGGCGTATATTGACAGAAA 58.487 39.130 0.00 0.00 0.00 2.52
339 342 2.600731 GTGGTCTCAGACTTCACGATG 58.399 52.381 4.40 0.00 32.47 3.84
348 351 1.070786 TTTGCCGGTGGTCTCAGAC 59.929 57.895 1.90 0.00 0.00 3.51
376 379 1.344438 GTGTCCTGGAGTGTGATGACA 59.656 52.381 0.00 0.00 0.00 3.58
515 518 2.760092 TCATAAAATCTGTTGCCCAGGC 59.240 45.455 0.38 0.38 41.83 4.85
543 546 4.898265 AGCTATTGTCAGCAGGAGATAAGA 59.102 41.667 0.00 0.00 44.35 2.10
548 551 3.603532 CAAAGCTATTGTCAGCAGGAGA 58.396 45.455 0.00 0.00 44.35 3.71
598 601 6.293462 GCTTTCAAGTTTCTCAAAGACCGTAT 60.293 38.462 0.00 0.00 0.00 3.06
599 602 5.007332 GCTTTCAAGTTTCTCAAAGACCGTA 59.993 40.000 0.00 0.00 0.00 4.02
670 683 6.268387 ACTCTCAATGTTCCAAATCAACCATT 59.732 34.615 0.00 0.00 0.00 3.16
671 684 5.776716 ACTCTCAATGTTCCAAATCAACCAT 59.223 36.000 0.00 0.00 0.00 3.55
672 685 5.009911 CACTCTCAATGTTCCAAATCAACCA 59.990 40.000 0.00 0.00 0.00 3.67
674 687 6.317789 TCACTCTCAATGTTCCAAATCAAC 57.682 37.500 0.00 0.00 0.00 3.18
677 696 6.998968 AGATCACTCTCAATGTTCCAAATC 57.001 37.500 0.00 0.00 0.00 2.17
693 712 7.605691 AGTTTGAAAGAATCGATCAAGATCACT 59.394 33.333 10.39 0.00 37.69 3.41
791 810 2.955660 TGCACCTCGTTTGATTTCCTTT 59.044 40.909 0.00 0.00 0.00 3.11
813 832 1.855213 GCAATCGTGCCAACTCTGCA 61.855 55.000 0.00 0.00 45.68 4.41
920 940 2.273179 GGCAAAAGGTCGTTCCCCC 61.273 63.158 0.00 0.00 36.75 5.40
969 989 3.132646 GTGATCTGATCTCCTCTGCACTT 59.867 47.826 17.82 0.00 0.00 3.16
1179 1200 0.468226 AAAGACGCACCTTCCAGTCA 59.532 50.000 0.00 0.00 36.18 3.41
1282 1303 2.135139 GTCGACAATGAGCACACTGAA 58.865 47.619 11.55 0.00 0.00 3.02
1313 1334 2.276430 GAAAAATCCGCGGCGTCG 60.276 61.111 23.51 4.29 39.81 5.12
1364 1385 4.833380 GCATAACTACCCAGACCATCTCTA 59.167 45.833 0.00 0.00 0.00 2.43
1367 1388 3.658725 AGCATAACTACCCAGACCATCT 58.341 45.455 0.00 0.00 0.00 2.90
1451 1489 2.353376 CAGCGCGGTGGTTGTTTG 60.353 61.111 29.65 1.57 0.00 2.93
1452 1490 4.264638 GCAGCGCGGTGGTTGTTT 62.265 61.111 35.99 0.00 0.00 2.83
1456 1494 2.796483 TTAGATGCAGCGCGGTGGTT 62.796 55.000 35.99 11.62 0.00 3.67
1588 1634 7.709182 TCAGGAAAACAATGGTATATGACTACG 59.291 37.037 0.00 0.00 0.00 3.51
1640 1686 9.169468 GGCGAAGTTGATTATTACACAATAATG 57.831 33.333 7.22 0.00 44.00 1.90
1641 1687 9.120538 AGGCGAAGTTGATTATTACACAATAAT 57.879 29.630 2.98 2.98 45.75 1.28
1684 1733 2.561419 TCAAGGTAAGAACAGGGACGAG 59.439 50.000 0.00 0.00 0.00 4.18
1766 1815 4.469586 TGATGGTTACCAGTAGCAGAATGA 59.530 41.667 10.74 0.00 35.44 2.57
1858 1907 6.090783 CGAAGGCCAAATAAAAAGGAACTAC 58.909 40.000 5.01 0.00 38.49 2.73
1860 1909 4.021456 CCGAAGGCCAAATAAAAAGGAACT 60.021 41.667 5.01 0.00 46.14 3.01
2034 2084 6.927416 ACATGTGCAGTGTGATTATTTTGAT 58.073 32.000 0.00 0.00 0.00 2.57
2065 2115 5.617187 CGCTGCAAATTAGATAAGCTTTACG 59.383 40.000 3.20 0.00 0.00 3.18
2107 2157 7.319646 TGATTAAACCAACATTTATGCAGGAC 58.680 34.615 0.00 0.00 0.00 3.85
2139 2189 1.617322 AACGCTACACTGAGACCTCA 58.383 50.000 0.00 0.00 38.06 3.86
2243 2294 7.771826 ACTACTTGTGTGGTTACATTTTACACT 59.228 33.333 0.00 0.00 41.50 3.55
2383 2435 7.212274 GGGGTAATCTAGCGTATTACAAAAGA 58.788 38.462 15.87 0.00 40.19 2.52
2468 2520 7.255001 CCAGTTTTGTCCTAAGAACGTGTTTAT 60.255 37.037 0.00 0.00 0.00 1.40
2639 2695 2.627945 CAGTTACGCATAAGGAAGGCA 58.372 47.619 0.00 0.00 0.00 4.75
2700 2767 1.602851 CTTACCATGAGCATGCAGAGC 59.397 52.381 21.98 6.69 37.49 4.09
2763 2830 2.744166 GCATCATCACTCCTGCTTGCTA 60.744 50.000 0.00 0.00 0.00 3.49
2801 2868 3.384668 CCTACTGCACAATAGATCCACG 58.615 50.000 0.00 0.00 0.00 4.94
2803 2870 2.705658 CCCCTACTGCACAATAGATCCA 59.294 50.000 0.00 0.00 0.00 3.41
2810 2877 3.203040 AGCTTAATCCCCTACTGCACAAT 59.797 43.478 0.00 0.00 0.00 2.71
2817 2884 2.764269 TCAGCAGCTTAATCCCCTACT 58.236 47.619 0.00 0.00 0.00 2.57
2823 2890 4.574828 TCCGTTAAATCAGCAGCTTAATCC 59.425 41.667 0.00 0.00 0.00 3.01
2839 2906 5.823570 TGTTCCAATCAAACTTCTCCGTTAA 59.176 36.000 0.00 0.00 0.00 2.01
2885 2952 4.141869 GGGACCATCAATCAAAATCAAGGG 60.142 45.833 0.00 0.00 0.00 3.95
2909 2977 4.160626 GCTTCAGTACCAGAGACCATAAGT 59.839 45.833 0.00 0.00 0.00 2.24
2913 2981 2.234908 GTGCTTCAGTACCAGAGACCAT 59.765 50.000 0.00 0.00 0.00 3.55
3065 3134 5.599999 TTTGGAGAGGCAAGTCTATAGAC 57.400 43.478 22.97 22.97 45.08 2.59
3070 3139 2.979678 AGGTTTTGGAGAGGCAAGTCTA 59.020 45.455 0.00 0.00 0.00 2.59
3074 3143 1.160137 CGAGGTTTTGGAGAGGCAAG 58.840 55.000 0.00 0.00 0.00 4.01
3115 3233 8.150945 TCTCAAGTACTAGCTGAAAAAGTGAAT 58.849 33.333 0.00 0.00 0.00 2.57
3126 3244 1.472878 TGCCGTCTCAAGTACTAGCTG 59.527 52.381 0.00 0.00 0.00 4.24
3127 3245 1.746220 CTGCCGTCTCAAGTACTAGCT 59.254 52.381 0.00 0.00 0.00 3.32
3128 3246 1.473278 ACTGCCGTCTCAAGTACTAGC 59.527 52.381 0.00 0.00 0.00 3.42
3129 3247 3.851976 AACTGCCGTCTCAAGTACTAG 57.148 47.619 0.00 0.00 0.00 2.57
3130 3248 4.157289 CCTAAACTGCCGTCTCAAGTACTA 59.843 45.833 0.00 0.00 0.00 1.82
3131 3249 3.056749 CCTAAACTGCCGTCTCAAGTACT 60.057 47.826 0.00 0.00 0.00 2.73
3132 3250 3.251571 CCTAAACTGCCGTCTCAAGTAC 58.748 50.000 0.00 0.00 0.00 2.73
3153 3271 2.689983 CCAAATCCCTGTATGCTCCAAC 59.310 50.000 0.00 0.00 0.00 3.77
3159 3277 3.763897 ACTCAAACCAAATCCCTGTATGC 59.236 43.478 0.00 0.00 0.00 3.14
3164 3282 4.281688 ACATCAACTCAAACCAAATCCCTG 59.718 41.667 0.00 0.00 0.00 4.45
3167 3286 4.448732 GCAACATCAACTCAAACCAAATCC 59.551 41.667 0.00 0.00 0.00 3.01
3235 3354 2.872858 GGTAGGGAGCGCATAAAGAAAG 59.127 50.000 11.47 0.00 0.00 2.62
3239 3358 1.689273 AGAGGTAGGGAGCGCATAAAG 59.311 52.381 11.47 0.00 0.00 1.85
3247 3366 1.762858 GGGGTGAGAGGTAGGGAGC 60.763 68.421 0.00 0.00 0.00 4.70
3271 3390 2.903855 CATGCATCACGAGGGGCC 60.904 66.667 0.00 0.00 0.00 5.80
3272 3391 2.903855 CCATGCATCACGAGGGGC 60.904 66.667 0.00 0.00 0.00 5.80
3273 3392 1.524621 GTCCATGCATCACGAGGGG 60.525 63.158 0.00 0.00 0.00 4.79
3308 3427 3.095347 GCTACTCGGGCAAGGGAGG 62.095 68.421 0.00 0.00 34.58 4.30
3310 3429 3.081409 GGCTACTCGGGCAAGGGA 61.081 66.667 0.00 0.00 0.00 4.20
3311 3430 2.666596 GATGGCTACTCGGGCAAGGG 62.667 65.000 0.00 0.00 44.59 3.95
3314 3433 1.689233 AGGATGGCTACTCGGGCAA 60.689 57.895 0.00 0.00 44.59 4.52
3316 3435 1.476007 ATCAGGATGGCTACTCGGGC 61.476 60.000 0.00 0.00 36.16 6.13
3317 3436 0.605589 GATCAGGATGGCTACTCGGG 59.394 60.000 0.00 0.00 36.16 5.14
3359 3479 2.723530 TCAGAGGAGAAAGAAGGGGT 57.276 50.000 0.00 0.00 0.00 4.95
3375 3507 7.530010 ACAAACATTTAGAAACGGATGATCAG 58.470 34.615 0.09 0.00 0.00 2.90
3382 3514 9.724839 CTAAAAAGACAAACATTTAGAAACGGA 57.275 29.630 0.00 0.00 37.48 4.69
3383 3515 9.724839 TCTAAAAAGACAAACATTTAGAAACGG 57.275 29.630 4.78 0.00 39.89 4.44
3458 3590 6.902341 TGAAGCAAAATGAGTGAATCTACAC 58.098 36.000 0.00 0.00 40.60 2.90
3459 3591 7.692460 ATGAAGCAAAATGAGTGAATCTACA 57.308 32.000 0.00 0.00 0.00 2.74
3460 3592 9.661187 CATATGAAGCAAAATGAGTGAATCTAC 57.339 33.333 0.00 0.00 0.00 2.59
3461 3593 9.399797 ACATATGAAGCAAAATGAGTGAATCTA 57.600 29.630 10.38 0.00 0.00 1.98
3462 3594 8.289939 ACATATGAAGCAAAATGAGTGAATCT 57.710 30.769 10.38 0.00 0.00 2.40
3463 3595 9.443283 GTACATATGAAGCAAAATGAGTGAATC 57.557 33.333 10.38 0.00 0.00 2.52
3464 3596 9.182214 AGTACATATGAAGCAAAATGAGTGAAT 57.818 29.630 10.38 0.00 0.00 2.57
3465 3597 8.565896 AGTACATATGAAGCAAAATGAGTGAA 57.434 30.769 10.38 0.00 0.00 3.18
3466 3598 7.280876 GGAGTACATATGAAGCAAAATGAGTGA 59.719 37.037 10.38 0.00 0.00 3.41
3467 3599 7.066163 TGGAGTACATATGAAGCAAAATGAGTG 59.934 37.037 10.38 0.00 0.00 3.51
3468 3600 7.112122 TGGAGTACATATGAAGCAAAATGAGT 58.888 34.615 10.38 0.00 0.00 3.41
3469 3601 7.558161 TGGAGTACATATGAAGCAAAATGAG 57.442 36.000 10.38 0.00 0.00 2.90
3470 3602 7.229306 GGATGGAGTACATATGAAGCAAAATGA 59.771 37.037 10.38 0.00 40.72 2.57
3471 3603 7.365741 GGATGGAGTACATATGAAGCAAAATG 58.634 38.462 10.38 0.00 40.72 2.32
3472 3604 6.205464 CGGATGGAGTACATATGAAGCAAAAT 59.795 38.462 10.38 0.00 40.72 1.82
3473 3605 5.527214 CGGATGGAGTACATATGAAGCAAAA 59.473 40.000 10.38 0.00 40.72 2.44
3474 3606 5.056480 CGGATGGAGTACATATGAAGCAAA 58.944 41.667 10.38 0.00 40.72 3.68
3475 3607 4.100963 ACGGATGGAGTACATATGAAGCAA 59.899 41.667 10.38 0.00 40.72 3.91
3476 3608 3.641436 ACGGATGGAGTACATATGAAGCA 59.359 43.478 10.38 0.00 40.72 3.91
3477 3609 4.238514 GACGGATGGAGTACATATGAAGC 58.761 47.826 10.38 0.00 40.72 3.86
3478 3610 4.322049 GGGACGGATGGAGTACATATGAAG 60.322 50.000 10.38 0.00 40.72 3.02
3479 3611 3.576982 GGGACGGATGGAGTACATATGAA 59.423 47.826 10.38 0.00 40.72 2.57
3480 3612 3.162666 GGGACGGATGGAGTACATATGA 58.837 50.000 10.38 0.00 40.72 2.15
3481 3613 2.897326 TGGGACGGATGGAGTACATATG 59.103 50.000 0.00 0.00 40.72 1.78
3482 3614 3.254093 TGGGACGGATGGAGTACATAT 57.746 47.619 0.00 0.00 40.72 1.78
3483 3615 2.759839 TGGGACGGATGGAGTACATA 57.240 50.000 0.00 0.00 40.72 2.29
3484 3616 1.874129 TTGGGACGGATGGAGTACAT 58.126 50.000 0.00 0.00 44.18 2.29
3485 3617 1.646912 TTTGGGACGGATGGAGTACA 58.353 50.000 0.00 0.00 0.00 2.90
3486 3618 3.277142 AATTTGGGACGGATGGAGTAC 57.723 47.619 0.00 0.00 0.00 2.73
3487 3619 4.310022 AAAATTTGGGACGGATGGAGTA 57.690 40.909 0.00 0.00 0.00 2.59
3488 3620 2.899303 AAATTTGGGACGGATGGAGT 57.101 45.000 0.00 0.00 0.00 3.85
3563 3695 8.692710 TGTCTTAAATTAGTCAGATACGGATGT 58.307 33.333 0.00 0.00 0.00 3.06
3564 3696 9.529325 TTGTCTTAAATTAGTCAGATACGGATG 57.471 33.333 0.00 0.00 0.00 3.51
3565 3697 9.751542 CTTGTCTTAAATTAGTCAGATACGGAT 57.248 33.333 0.00 0.00 0.00 4.18
3566 3698 8.963725 TCTTGTCTTAAATTAGTCAGATACGGA 58.036 33.333 0.00 0.00 0.00 4.69
3567 3699 9.582431 TTCTTGTCTTAAATTAGTCAGATACGG 57.418 33.333 0.00 0.00 0.00 4.02
3577 3709 9.341899 CGTCCCAAAATTCTTGTCTTAAATTAG 57.658 33.333 0.00 0.00 0.00 1.73
3578 3710 8.301002 CCGTCCCAAAATTCTTGTCTTAAATTA 58.699 33.333 0.00 0.00 0.00 1.40
3579 3711 7.014808 TCCGTCCCAAAATTCTTGTCTTAAATT 59.985 33.333 0.00 0.00 0.00 1.82
3580 3712 6.492087 TCCGTCCCAAAATTCTTGTCTTAAAT 59.508 34.615 0.00 0.00 0.00 1.40
3581 3713 5.828859 TCCGTCCCAAAATTCTTGTCTTAAA 59.171 36.000 0.00 0.00 0.00 1.52
3582 3714 5.378332 TCCGTCCCAAAATTCTTGTCTTAA 58.622 37.500 0.00 0.00 0.00 1.85
3583 3715 4.975631 TCCGTCCCAAAATTCTTGTCTTA 58.024 39.130 0.00 0.00 0.00 2.10
3584 3716 3.821033 CTCCGTCCCAAAATTCTTGTCTT 59.179 43.478 0.00 0.00 0.00 3.01
3585 3717 3.412386 CTCCGTCCCAAAATTCTTGTCT 58.588 45.455 0.00 0.00 0.00 3.41
3586 3718 2.488153 CCTCCGTCCCAAAATTCTTGTC 59.512 50.000 0.00 0.00 0.00 3.18
3587 3719 2.514803 CCTCCGTCCCAAAATTCTTGT 58.485 47.619 0.00 0.00 0.00 3.16
3588 3720 1.818674 CCCTCCGTCCCAAAATTCTTG 59.181 52.381 0.00 0.00 0.00 3.02
3589 3721 1.708551 TCCCTCCGTCCCAAAATTCTT 59.291 47.619 0.00 0.00 0.00 2.52
3590 3722 1.368374 TCCCTCCGTCCCAAAATTCT 58.632 50.000 0.00 0.00 0.00 2.40
3591 3723 2.209690 TTCCCTCCGTCCCAAAATTC 57.790 50.000 0.00 0.00 0.00 2.17
3592 3724 2.919772 ATTCCCTCCGTCCCAAAATT 57.080 45.000 0.00 0.00 0.00 1.82
3593 3725 2.850568 ACTATTCCCTCCGTCCCAAAAT 59.149 45.455 0.00 0.00 0.00 1.82
3594 3726 2.237893 GACTATTCCCTCCGTCCCAAAA 59.762 50.000 0.00 0.00 0.00 2.44
3595 3727 1.835531 GACTATTCCCTCCGTCCCAAA 59.164 52.381 0.00 0.00 0.00 3.28
3596 3728 1.273381 TGACTATTCCCTCCGTCCCAA 60.273 52.381 0.00 0.00 0.00 4.12
3597 3729 0.337082 TGACTATTCCCTCCGTCCCA 59.663 55.000 0.00 0.00 0.00 4.37
3598 3730 0.751452 GTGACTATTCCCTCCGTCCC 59.249 60.000 0.00 0.00 0.00 4.46
3599 3731 1.777941 AGTGACTATTCCCTCCGTCC 58.222 55.000 0.00 0.00 0.00 4.79
3600 3732 2.496470 ACAAGTGACTATTCCCTCCGTC 59.504 50.000 0.00 0.00 0.00 4.79
3601 3733 2.537143 ACAAGTGACTATTCCCTCCGT 58.463 47.619 0.00 0.00 0.00 4.69
3602 3734 3.056107 TCAACAAGTGACTATTCCCTCCG 60.056 47.826 0.00 0.00 0.00 4.63
3603 3735 4.553330 TCAACAAGTGACTATTCCCTCC 57.447 45.455 0.00 0.00 0.00 4.30
3604 3736 6.881602 AGATTTCAACAAGTGACTATTCCCTC 59.118 38.462 0.00 0.00 35.39 4.30
3605 3737 6.784031 AGATTTCAACAAGTGACTATTCCCT 58.216 36.000 0.00 0.00 35.39 4.20
3606 3738 6.881602 AGAGATTTCAACAAGTGACTATTCCC 59.118 38.462 0.00 0.00 35.39 3.97
3607 3739 7.913674 AGAGATTTCAACAAGTGACTATTCC 57.086 36.000 0.00 0.00 35.39 3.01
3608 3740 9.862371 TCTAGAGATTTCAACAAGTGACTATTC 57.138 33.333 0.00 0.00 35.39 1.75
3611 3743 9.698309 CTTTCTAGAGATTTCAACAAGTGACTA 57.302 33.333 0.00 0.00 35.39 2.59
3612 3744 8.424918 TCTTTCTAGAGATTTCAACAAGTGACT 58.575 33.333 0.00 0.00 35.39 3.41
3613 3745 8.491950 GTCTTTCTAGAGATTTCAACAAGTGAC 58.508 37.037 0.00 0.00 35.39 3.67
3614 3746 8.204160 TGTCTTTCTAGAGATTTCAACAAGTGA 58.796 33.333 0.00 0.00 0.00 3.41
3615 3747 8.370493 TGTCTTTCTAGAGATTTCAACAAGTG 57.630 34.615 0.00 0.00 0.00 3.16
3616 3748 8.964476 TTGTCTTTCTAGAGATTTCAACAAGT 57.036 30.769 0.00 0.00 0.00 3.16
3629 3761 9.595823 CCGTTCCTAAATATTTGTCTTTCTAGA 57.404 33.333 11.05 0.00 0.00 2.43
3630 3762 9.595823 TCCGTTCCTAAATATTTGTCTTTCTAG 57.404 33.333 11.05 0.00 0.00 2.43
3631 3763 9.595823 CTCCGTTCCTAAATATTTGTCTTTCTA 57.404 33.333 11.05 0.00 0.00 2.10
3632 3764 7.553044 CCTCCGTTCCTAAATATTTGTCTTTCT 59.447 37.037 11.05 0.00 0.00 2.52
3633 3765 7.201705 CCCTCCGTTCCTAAATATTTGTCTTTC 60.202 40.741 11.05 0.00 0.00 2.62
3634 3766 6.602009 CCCTCCGTTCCTAAATATTTGTCTTT 59.398 38.462 11.05 0.00 0.00 2.52
3635 3767 6.069847 TCCCTCCGTTCCTAAATATTTGTCTT 60.070 38.462 11.05 0.00 0.00 3.01
3636 3768 5.427481 TCCCTCCGTTCCTAAATATTTGTCT 59.573 40.000 11.05 0.00 0.00 3.41
3637 3769 5.677567 TCCCTCCGTTCCTAAATATTTGTC 58.322 41.667 11.05 0.00 0.00 3.18
3638 3770 5.191124 ACTCCCTCCGTTCCTAAATATTTGT 59.809 40.000 11.05 0.00 0.00 2.83
3639 3771 5.681639 ACTCCCTCCGTTCCTAAATATTTG 58.318 41.667 11.05 1.40 0.00 2.32
3640 3772 5.970501 ACTCCCTCCGTTCCTAAATATTT 57.029 39.130 5.89 5.89 0.00 1.40
3641 3773 5.306419 GGTACTCCCTCCGTTCCTAAATATT 59.694 44.000 0.00 0.00 0.00 1.28
3642 3774 4.837298 GGTACTCCCTCCGTTCCTAAATAT 59.163 45.833 0.00 0.00 0.00 1.28
3643 3775 4.218312 GGTACTCCCTCCGTTCCTAAATA 58.782 47.826 0.00 0.00 0.00 1.40
3644 3776 3.036819 GGTACTCCCTCCGTTCCTAAAT 58.963 50.000 0.00 0.00 0.00 1.40
3645 3777 2.225343 TGGTACTCCCTCCGTTCCTAAA 60.225 50.000 0.00 0.00 0.00 1.85
3646 3778 1.358787 TGGTACTCCCTCCGTTCCTAA 59.641 52.381 0.00 0.00 0.00 2.69
3647 3779 1.002069 TGGTACTCCCTCCGTTCCTA 58.998 55.000 0.00 0.00 0.00 2.94
3648 3780 0.338814 ATGGTACTCCCTCCGTTCCT 59.661 55.000 0.00 0.00 0.00 3.36
3649 3781 1.134491 CAATGGTACTCCCTCCGTTCC 60.134 57.143 0.00 0.00 31.49 3.62
3650 3782 1.553704 ACAATGGTACTCCCTCCGTTC 59.446 52.381 0.00 0.00 31.49 3.95
3651 3783 1.278127 CACAATGGTACTCCCTCCGTT 59.722 52.381 0.00 0.00 33.79 4.44
3652 3784 0.902531 CACAATGGTACTCCCTCCGT 59.097 55.000 0.00 0.00 0.00 4.69
3653 3785 0.902531 ACACAATGGTACTCCCTCCG 59.097 55.000 0.00 0.00 0.00 4.63
3654 3786 1.209747 GGACACAATGGTACTCCCTCC 59.790 57.143 0.00 0.00 0.00 4.30
3655 3787 2.093447 CAGGACACAATGGTACTCCCTC 60.093 54.545 0.00 0.00 26.18 4.30
3656 3788 1.909302 CAGGACACAATGGTACTCCCT 59.091 52.381 0.00 0.00 26.18 4.20
3657 3789 1.906574 TCAGGACACAATGGTACTCCC 59.093 52.381 0.00 0.00 26.18 4.30
3658 3790 3.914426 ATCAGGACACAATGGTACTCC 57.086 47.619 0.00 0.00 26.18 3.85
3659 3791 6.879458 AGTTTTATCAGGACACAATGGTACTC 59.121 38.462 0.00 0.00 26.18 2.59
3660 3792 6.779860 AGTTTTATCAGGACACAATGGTACT 58.220 36.000 0.00 0.00 29.93 2.73
3661 3793 6.879458 AGAGTTTTATCAGGACACAATGGTAC 59.121 38.462 0.00 0.00 0.00 3.34
3666 3798 4.393062 CGCAGAGTTTTATCAGGACACAAT 59.607 41.667 0.00 0.00 0.00 2.71
3671 3803 3.851098 AGTCGCAGAGTTTTATCAGGAC 58.149 45.455 0.00 0.00 36.34 3.85
3692 3824 1.275291 GTGGAGGGTCAATGACGAGAA 59.725 52.381 7.35 0.00 32.65 2.87
3694 3826 0.108138 GGTGGAGGGTCAATGACGAG 60.108 60.000 7.35 0.00 32.65 4.18
3698 3834 4.044065 ACAAATAAGGTGGAGGGTCAATGA 59.956 41.667 0.00 0.00 0.00 2.57
3699 3835 4.158394 CACAAATAAGGTGGAGGGTCAATG 59.842 45.833 0.00 0.00 32.65 2.82
3722 3858 3.339951 AAGGAGGAGGAGGGGGCTC 62.340 68.421 0.00 0.00 0.00 4.70
3725 3861 3.093172 GCAAGGAGGAGGAGGGGG 61.093 72.222 0.00 0.00 0.00 5.40
3729 3865 1.872773 AAGTAGGCAAGGAGGAGGAG 58.127 55.000 0.00 0.00 0.00 3.69
3734 3870 3.041946 AGTGGATAAGTAGGCAAGGAGG 58.958 50.000 0.00 0.00 0.00 4.30
3735 3871 3.742640 GCAGTGGATAAGTAGGCAAGGAG 60.743 52.174 0.00 0.00 0.00 3.69


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

AutoCloner maintained by Alex Coulton.