Multiple sequence alignment - TraesCS1D01G118900

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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 TraesCS1D01G118900 chr1D 100.000 3050 0 0 1 3050 114645813 114642764 0.000000e+00 5633.0
1 TraesCS1D01G118900 chr1D 96.970 165 4 1 2887 3050 114633371 114633207 3.000000e-70 276.0
2 TraesCS1D01G118900 chr1A 93.764 1732 66 18 724 2452 125148168 125146476 0.000000e+00 2562.0
3 TraesCS1D01G118900 chr1A 86.292 445 23 7 1 408 125150346 125149903 1.670000e-122 449.0
4 TraesCS1D01G118900 chr1A 76.970 495 98 13 1319 1809 545648874 545648392 5.010000e-68 268.0
5 TraesCS1D01G118900 chr1A 82.072 251 8 15 456 703 125148371 125148155 2.420000e-41 180.0
6 TraesCS1D01G118900 chr1A 92.982 57 4 0 2 58 569255751 569255695 1.950000e-12 84.2
7 TraesCS1D01G118900 chr1B 92.142 1769 83 25 456 2211 175660611 175658886 0.000000e+00 2446.0
8 TraesCS1D01G118900 chr1B 88.489 417 15 6 1 384 175661211 175660795 9.900000e-130 473.0
9 TraesCS1D01G118900 chr1B 91.463 246 15 2 2207 2452 175658618 175658379 1.750000e-87 333.0
10 TraesCS1D01G118900 chr1B 90.909 55 4 1 2445 2498 207853750 207853804 4.220000e-09 73.1
11 TraesCS1D01G118900 chr1B 97.222 36 0 1 376 411 175660747 175660713 3.280000e-05 60.2
12 TraesCS1D01G118900 chr4D 90.575 435 40 1 2453 2887 197769832 197769399 2.640000e-160 575.0
13 TraesCS1D01G118900 chr4D 89.908 436 42 2 2452 2887 418436057 418435624 7.380000e-156 560.0
14 TraesCS1D01G118900 chr7B 90.976 410 36 1 2453 2862 407605803 407605395 4.440000e-153 551.0
15 TraesCS1D01G118900 chr7B 92.800 125 9 0 2476 2600 407606161 407606037 6.720000e-42 182.0
16 TraesCS1D01G118900 chr6A 89.703 437 37 5 2452 2887 26758141 26757712 4.440000e-153 551.0
17 TraesCS1D01G118900 chr5B 90.777 412 36 2 2452 2862 588689484 588689074 1.600000e-152 549.0
18 TraesCS1D01G118900 chr5B 85.657 251 28 4 2610 2860 469210151 469210393 1.090000e-64 257.0
19 TraesCS1D01G118900 chr5B 90.909 88 6 2 2800 2887 469210384 469210469 1.920000e-22 117.0
20 TraesCS1D01G118900 chr2B 86.344 454 35 5 2451 2887 2135922 2135479 1.280000e-128 470.0
21 TraesCS1D01G118900 chr7D 87.714 350 35 2 2545 2887 92421356 92421704 4.740000e-108 401.0
22 TraesCS1D01G118900 chr7D 91.667 48 4 0 2453 2500 608083702 608083749 1.960000e-07 67.6
23 TraesCS1D01G118900 chr5D 86.234 385 30 3 2503 2887 550165930 550166291 2.200000e-106 396.0
24 TraesCS1D01G118900 chr5D 96.970 165 4 1 2887 3050 390633878 390634042 3.000000e-70 276.0
25 TraesCS1D01G118900 chr5D 96.970 165 4 1 2887 3050 438392387 438392223 3.000000e-70 276.0
26 TraesCS1D01G118900 chr5D 96.364 165 5 1 2887 3050 67917477 67917641 1.390000e-68 270.0
27 TraesCS1D01G118900 chr3B 77.890 493 91 13 1317 1804 462866640 462867119 1.070000e-74 291.0
28 TraesCS1D01G118900 chr3D 96.450 169 5 1 2883 3050 12308053 12307885 8.330000e-71 278.0
29 TraesCS1D01G118900 chr3D 96.970 165 4 1 2887 3050 209459251 209459087 3.000000e-70 276.0
30 TraesCS1D01G118900 chr2D 96.970 165 4 1 2887 3050 109709291 109709127 3.000000e-70 276.0
31 TraesCS1D01G118900 chr2D 96.970 165 4 1 2887 3050 423300877 423301041 3.000000e-70 276.0
32 TraesCS1D01G118900 chr6D 96.364 165 5 1 2887 3050 466258487 466258323 1.390000e-68 270.0
33 TraesCS1D01G118900 chr4A 94.444 54 3 0 2 55 624834562 624834615 1.950000e-12 84.2
34 TraesCS1D01G118900 chr6B 87.692 65 6 2 2452 2515 715311509 715311446 1.170000e-09 75.0


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 TraesCS1D01G118900 chr1D 114642764 114645813 3049 True 5633.000000 5633 100.000 1 3050 1 chr1D.!!$R2 3049
1 TraesCS1D01G118900 chr1A 125146476 125150346 3870 True 1063.666667 2562 87.376 1 2452 3 chr1A.!!$R3 2451
2 TraesCS1D01G118900 chr1B 175658379 175661211 2832 True 828.050000 2446 92.329 1 2452 4 chr1B.!!$R1 2451
3 TraesCS1D01G118900 chr7B 407605395 407606161 766 True 366.500000 551 91.888 2453 2862 2 chr7B.!!$R1 409

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
414 1973 0.248215 GCCGTTTCAATCAGGATGCG 60.248 55.0 0.0 0.0 34.76 4.73 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2203 3826 0.108585 ACACACCCTGCCTTGTACAG 59.891 55.0 0.0 0.0 34.82 2.74 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
64 65 3.576356 GCGCCATGTCCATGTCCG 61.576 66.667 0.00 9.14 37.11 4.79
122 130 3.857665 GCATGTCATATATGTACCCGTCG 59.142 47.826 12.42 0.00 0.00 5.12
133 141 0.461135 TACCCGTCGGAGGTTAATGC 59.539 55.000 14.39 0.00 38.89 3.56
134 142 1.523032 CCCGTCGGAGGTTAATGCC 60.523 63.158 14.39 0.00 0.00 4.40
135 143 1.219664 CCGTCGGAGGTTAATGCCA 59.780 57.895 4.91 0.00 0.00 4.92
357 399 2.899044 GCGTTTGTGCCAGGCGTTA 61.899 57.895 7.03 0.00 0.00 3.18
414 1973 0.248215 GCCGTTTCAATCAGGATGCG 60.248 55.000 0.00 0.00 34.76 4.73
436 1995 4.681978 GACCGGCACCACTCGCTT 62.682 66.667 0.00 0.00 0.00 4.68
478 2059 5.779241 TGAAAGGAGGAATAATGTGGTCT 57.221 39.130 0.00 0.00 0.00 3.85
504 2085 1.847818 TGTGTCCTCGTTGTTTCTCG 58.152 50.000 0.00 0.00 0.00 4.04
537 2118 0.682532 TGCTGGCACTTGTTTCACCA 60.683 50.000 0.00 0.00 0.00 4.17
538 2119 0.675633 GCTGGCACTTGTTTCACCAT 59.324 50.000 0.00 0.00 0.00 3.55
573 2159 3.751518 ACAGGTGGATGACTAACCAAAC 58.248 45.455 0.00 0.00 37.94 2.93
581 2168 4.814771 GGATGACTAACCAAACCCTAATCG 59.185 45.833 0.00 0.00 0.00 3.34
635 2222 8.219105 CCTATTAAACTCGAAGTTTACACACAC 58.781 37.037 15.30 0.00 46.72 3.82
636 2223 4.509915 AAACTCGAAGTTTACACACACG 57.490 40.909 10.11 0.00 45.75 4.49
638 2225 3.772932 ACTCGAAGTTTACACACACGAA 58.227 40.909 0.00 0.00 31.16 3.85
700 2287 4.987408 CACAACATGCATATGGAAGGAA 57.013 40.909 14.21 0.00 38.66 3.36
701 2288 5.327616 CACAACATGCATATGGAAGGAAA 57.672 39.130 14.21 0.00 38.66 3.13
702 2289 5.722263 CACAACATGCATATGGAAGGAAAA 58.278 37.500 14.21 0.00 38.66 2.29
703 2290 5.577945 CACAACATGCATATGGAAGGAAAAC 59.422 40.000 14.21 0.00 38.66 2.43
704 2291 5.111293 CAACATGCATATGGAAGGAAAACC 58.889 41.667 0.00 0.00 38.66 3.27
705 2292 4.613437 ACATGCATATGGAAGGAAAACCT 58.387 39.130 0.00 0.00 38.66 3.50
706 2293 4.646492 ACATGCATATGGAAGGAAAACCTC 59.354 41.667 0.00 0.00 38.66 3.85
707 2294 4.591321 TGCATATGGAAGGAAAACCTCT 57.409 40.909 4.56 0.00 0.00 3.69
708 2295 4.272489 TGCATATGGAAGGAAAACCTCTG 58.728 43.478 4.56 0.00 0.00 3.35
709 2296 3.067320 GCATATGGAAGGAAAACCTCTGC 59.933 47.826 4.56 0.00 0.00 4.26
710 2297 2.978156 ATGGAAGGAAAACCTCTGCA 57.022 45.000 0.00 0.00 0.00 4.41
711 2298 1.981256 TGGAAGGAAAACCTCTGCAC 58.019 50.000 0.00 0.00 0.00 4.57
712 2299 1.494721 TGGAAGGAAAACCTCTGCACT 59.505 47.619 0.00 0.00 0.00 4.40
713 2300 1.882623 GGAAGGAAAACCTCTGCACTG 59.117 52.381 0.00 0.00 0.00 3.66
714 2301 2.576615 GAAGGAAAACCTCTGCACTGT 58.423 47.619 0.00 0.00 0.00 3.55
715 2302 1.972872 AGGAAAACCTCTGCACTGTG 58.027 50.000 2.76 2.76 0.00 3.66
716 2303 1.212935 AGGAAAACCTCTGCACTGTGT 59.787 47.619 9.86 0.00 0.00 3.72
717 2304 2.024414 GGAAAACCTCTGCACTGTGTT 58.976 47.619 9.86 0.00 0.00 3.32
718 2305 2.033424 GGAAAACCTCTGCACTGTGTTC 59.967 50.000 9.86 2.66 0.00 3.18
719 2306 2.418368 AAACCTCTGCACTGTGTTCA 57.582 45.000 9.86 0.00 0.00 3.18
720 2307 2.418368 AACCTCTGCACTGTGTTCAA 57.582 45.000 9.86 0.00 0.00 2.69
721 2308 2.418368 ACCTCTGCACTGTGTTCAAA 57.582 45.000 9.86 0.00 0.00 2.69
722 2309 2.722094 ACCTCTGCACTGTGTTCAAAA 58.278 42.857 9.86 0.00 0.00 2.44
723 2310 3.088532 ACCTCTGCACTGTGTTCAAAAA 58.911 40.909 9.86 0.00 0.00 1.94
724 2311 3.701040 ACCTCTGCACTGTGTTCAAAAAT 59.299 39.130 9.86 0.00 0.00 1.82
737 2324 8.655651 TGTGTTCAAAAATATGGAAGGAAAAC 57.344 30.769 0.00 0.00 0.00 2.43
748 2368 4.874199 TGGAAGGAAAACCTGGTTAAACT 58.126 39.130 13.37 8.14 0.00 2.66
860 2480 2.283173 CCTGCCCCCTTTCACACC 60.283 66.667 0.00 0.00 0.00 4.16
969 2589 4.808414 TTCCCAACACACAAACATGAAA 57.192 36.364 0.00 0.00 0.00 2.69
976 2596 3.256879 ACACACAAACATGAAACACACCA 59.743 39.130 0.00 0.00 0.00 4.17
1839 3459 3.690460 GCCAATCAAGAAAGAGGAGGAA 58.310 45.455 0.00 0.00 0.00 3.36
1869 3489 1.065928 GCGTACATGGGAGTCTCCG 59.934 63.158 12.91 1.81 37.43 4.63
1983 3603 1.450531 GCAGGATCAGGGAATTGGCG 61.451 60.000 0.00 0.00 0.00 5.69
2050 3670 3.319137 TCGAAGTCTGCAGCTGTTAAT 57.681 42.857 16.64 0.00 0.00 1.40
2088 3708 5.227908 GTGTTCAGTCAAATAAGGACTCGA 58.772 41.667 0.00 0.00 43.47 4.04
2089 3709 5.694910 GTGTTCAGTCAAATAAGGACTCGAA 59.305 40.000 0.00 0.00 43.47 3.71
2092 3712 4.921515 TCAGTCAAATAAGGACTCGAAACG 59.078 41.667 0.00 0.00 43.47 3.60
2103 3723 0.528684 CTCGAAACGGAGGCTGGATC 60.529 60.000 0.00 0.00 0.00 3.36
2151 3771 0.456221 ATGTCGTTAGGCAGTCCTCG 59.544 55.000 0.00 0.00 43.06 4.63
2167 3790 6.030849 CAGTCCTCGAGATTTTGTAGTACAG 58.969 44.000 15.71 0.00 0.00 2.74
2168 3791 5.944599 AGTCCTCGAGATTTTGTAGTACAGA 59.055 40.000 15.71 0.00 0.00 3.41
2169 3792 6.094325 AGTCCTCGAGATTTTGTAGTACAGAG 59.906 42.308 15.71 5.00 0.00 3.35
2170 3793 5.038033 CCTCGAGATTTTGTAGTACAGAGC 58.962 45.833 15.71 0.00 0.00 4.09
2171 3794 5.393135 CCTCGAGATTTTGTAGTACAGAGCA 60.393 44.000 15.71 0.00 0.00 4.26
2172 3795 5.641709 TCGAGATTTTGTAGTACAGAGCAG 58.358 41.667 2.68 0.00 0.00 4.24
2203 3826 1.407258 AGCCGAGCTCTTCAGTGATAC 59.593 52.381 12.85 0.00 30.62 2.24
2251 4144 4.107127 AGGGTCAGTAGCTATAGGAGTG 57.893 50.000 0.00 0.00 0.00 3.51
2252 4145 3.722627 AGGGTCAGTAGCTATAGGAGTGA 59.277 47.826 0.00 0.00 0.00 3.41
2264 4157 4.775058 ATAGGAGTGATGCGTAGTGATC 57.225 45.455 0.00 0.00 0.00 2.92
2332 4225 9.459640 CCAGCTTTGATATAATTGTGAAGAATG 57.540 33.333 0.00 0.00 0.00 2.67
2362 4256 6.478512 AAGTAGAAGGCTTAGATTGAGAGG 57.521 41.667 0.00 0.00 0.00 3.69
2402 4296 7.338703 TCTCCCTCAGATTTTCATGATTTTCTG 59.661 37.037 17.08 17.08 33.55 3.02
2406 4300 6.627243 TCAGATTTTCATGATTTTCTGCTGG 58.373 36.000 17.86 3.00 32.57 4.85
2427 4321 2.046700 TTTTGCCTACCTCCGCCG 60.047 61.111 0.00 0.00 0.00 6.46
2443 4337 2.252260 CGCGAAGTTGCAACCAGG 59.748 61.111 25.62 15.33 34.15 4.45
2452 4346 5.163854 CGAAGTTGCAACCAGGATAAACTAG 60.164 44.000 25.62 0.00 0.00 2.57
2453 4347 4.589908 AGTTGCAACCAGGATAAACTAGG 58.410 43.478 25.62 0.00 0.00 3.02
2454 4348 2.999331 TGCAACCAGGATAAACTAGGC 58.001 47.619 0.00 0.00 0.00 3.93
2455 4349 2.298610 GCAACCAGGATAAACTAGGCC 58.701 52.381 0.00 0.00 0.00 5.19
2456 4350 2.356741 GCAACCAGGATAAACTAGGCCA 60.357 50.000 5.01 0.00 0.00 5.36
2457 4351 3.279434 CAACCAGGATAAACTAGGCCAC 58.721 50.000 5.01 0.00 0.00 5.01
2487 4381 3.111442 GTGCGCCGGCCAAAATTG 61.111 61.111 23.46 5.76 38.85 2.32
2495 4389 4.371590 GCCAAAATTGCGGCCGGT 62.372 61.111 29.38 0.00 42.82 5.28
2543 4437 8.801882 ACTATTTTAATCCCGTCTGATTGAAA 57.198 30.769 10.01 10.01 41.48 2.69
2559 4453 9.300681 TCTGATTGAAATGGTGAGATAAAAAGT 57.699 29.630 0.00 0.00 0.00 2.66
2568 4462 4.070009 GTGAGATAAAAAGTTGTCCGGGT 58.930 43.478 0.00 0.00 0.00 5.28
2569 4463 5.240121 GTGAGATAAAAAGTTGTCCGGGTA 58.760 41.667 0.00 0.00 0.00 3.69
2573 4467 6.301486 AGATAAAAAGTTGTCCGGGTAGTTT 58.699 36.000 0.00 0.00 0.00 2.66
2623 4517 1.514678 GCTTGTCCCACGTGCATCAA 61.515 55.000 10.91 12.70 0.00 2.57
2631 4525 2.577644 CGTGCATCAACGCCATGC 60.578 61.111 6.83 6.83 45.92 4.06
2656 4550 0.665068 ATGCTGCATGTTGTTGCGTG 60.665 50.000 15.44 0.00 45.77 5.34
2693 4587 4.380550 CCAACGATGCTACACTTCTCACTA 60.381 45.833 0.00 0.00 0.00 2.74
2728 4622 6.990349 CAGGGAGTCTGTAGTTGTTTTTAGAA 59.010 38.462 0.00 0.00 38.64 2.10
2751 4645 5.984233 TGTATCATCTATGTCGGCAAAAC 57.016 39.130 0.00 0.00 0.00 2.43
2756 4650 5.185454 TCATCTATGTCGGCAAAACTTCAT 58.815 37.500 0.00 0.00 0.00 2.57
2778 4672 8.810652 TCATAACAAAACCTACAAATCAAAGC 57.189 30.769 0.00 0.00 0.00 3.51
2839 4733 4.130286 ACCGAAACCATGAAAGCAAAAA 57.870 36.364 0.00 0.00 0.00 1.94
2862 4756 6.639632 ATGGTGTATGTTTCCAGCATATTC 57.360 37.500 2.79 0.00 45.17 1.75
2863 4757 4.887071 TGGTGTATGTTTCCAGCATATTCC 59.113 41.667 0.00 0.00 34.43 3.01
2864 4758 4.278419 GGTGTATGTTTCCAGCATATTCCC 59.722 45.833 0.00 0.00 32.32 3.97
2865 4759 4.278419 GTGTATGTTTCCAGCATATTCCCC 59.722 45.833 0.00 0.00 32.32 4.81
2866 4760 3.686227 ATGTTTCCAGCATATTCCCCA 57.314 42.857 0.00 0.00 0.00 4.96
2867 4761 3.686227 TGTTTCCAGCATATTCCCCAT 57.314 42.857 0.00 0.00 0.00 4.00
2868 4762 4.805140 TGTTTCCAGCATATTCCCCATA 57.195 40.909 0.00 0.00 0.00 2.74
2869 4763 5.337956 TGTTTCCAGCATATTCCCCATAT 57.662 39.130 0.00 0.00 0.00 1.78
2870 4764 5.714863 TGTTTCCAGCATATTCCCCATATT 58.285 37.500 0.00 0.00 0.00 1.28
2871 4765 6.142498 TGTTTCCAGCATATTCCCCATATTT 58.858 36.000 0.00 0.00 0.00 1.40
2872 4766 6.267471 TGTTTCCAGCATATTCCCCATATTTC 59.733 38.462 0.00 0.00 0.00 2.17
2873 4767 5.865977 TCCAGCATATTCCCCATATTTCT 57.134 39.130 0.00 0.00 0.00 2.52
2874 4768 6.968400 TCCAGCATATTCCCCATATTTCTA 57.032 37.500 0.00 0.00 0.00 2.10
2875 4769 6.721318 TCCAGCATATTCCCCATATTTCTAC 58.279 40.000 0.00 0.00 0.00 2.59
2876 4770 6.274436 TCCAGCATATTCCCCATATTTCTACA 59.726 38.462 0.00 0.00 0.00 2.74
2877 4771 6.947733 CCAGCATATTCCCCATATTTCTACAA 59.052 38.462 0.00 0.00 0.00 2.41
2878 4772 7.094205 CCAGCATATTCCCCATATTTCTACAAC 60.094 40.741 0.00 0.00 0.00 3.32
2879 4773 7.667219 CAGCATATTCCCCATATTTCTACAACT 59.333 37.037 0.00 0.00 0.00 3.16
2880 4774 7.667219 AGCATATTCCCCATATTTCTACAACTG 59.333 37.037 0.00 0.00 0.00 3.16
2881 4775 7.665559 GCATATTCCCCATATTTCTACAACTGA 59.334 37.037 0.00 0.00 0.00 3.41
2882 4776 9.573166 CATATTCCCCATATTTCTACAACTGAA 57.427 33.333 0.00 0.00 0.00 3.02
2884 4778 8.893563 ATTCCCCATATTTCTACAACTGAAAA 57.106 30.769 0.00 0.00 37.05 2.29
2885 4779 8.713708 TTCCCCATATTTCTACAACTGAAAAA 57.286 30.769 0.00 0.00 37.05 1.94
2886 4780 8.348285 TCCCCATATTTCTACAACTGAAAAAG 57.652 34.615 0.00 0.00 37.05 2.27
2887 4781 7.947890 TCCCCATATTTCTACAACTGAAAAAGT 59.052 33.333 0.00 0.00 42.60 2.66
2888 4782 8.028938 CCCCATATTTCTACAACTGAAAAAGTG 58.971 37.037 0.00 0.00 39.81 3.16
2889 4783 8.576442 CCCATATTTCTACAACTGAAAAAGTGT 58.424 33.333 0.00 0.00 39.81 3.55
2890 4784 9.965824 CCATATTTCTACAACTGAAAAAGTGTT 57.034 29.630 0.00 0.00 39.81 3.32
2894 4788 8.736751 TTTCTACAACTGAAAAAGTGTTGAAC 57.263 30.769 11.30 0.00 42.35 3.18
2895 4789 7.441890 TCTACAACTGAAAAAGTGTTGAACA 57.558 32.000 11.30 0.00 42.35 3.18
2896 4790 8.050778 TCTACAACTGAAAAAGTGTTGAACAT 57.949 30.769 0.00 0.00 42.35 2.71
2897 4791 6.949578 ACAACTGAAAAAGTGTTGAACATG 57.050 33.333 0.00 0.00 42.35 3.21
2898 4792 6.454795 ACAACTGAAAAAGTGTTGAACATGT 58.545 32.000 0.00 0.00 42.35 3.21
2899 4793 6.365789 ACAACTGAAAAAGTGTTGAACATGTG 59.634 34.615 0.00 0.00 42.35 3.21
2900 4794 6.024552 ACTGAAAAAGTGTTGAACATGTGT 57.975 33.333 0.00 0.00 37.88 3.72
2901 4795 7.151999 ACTGAAAAAGTGTTGAACATGTGTA 57.848 32.000 0.00 0.00 37.88 2.90
2902 4796 7.027161 ACTGAAAAAGTGTTGAACATGTGTAC 58.973 34.615 0.00 0.00 37.88 2.90
2903 4797 6.914259 TGAAAAAGTGTTGAACATGTGTACA 58.086 32.000 0.00 1.19 0.00 2.90
2904 4798 7.542890 TGAAAAAGTGTTGAACATGTGTACAT 58.457 30.769 0.00 0.00 36.96 2.29
2905 4799 8.678199 TGAAAAAGTGTTGAACATGTGTACATA 58.322 29.630 0.00 0.00 34.26 2.29
2906 4800 9.677567 GAAAAAGTGTTGAACATGTGTACATAT 57.322 29.630 0.00 0.00 34.26 1.78
2909 4803 7.520119 AGTGTTGAACATGTGTACATATACG 57.480 36.000 4.64 0.00 34.26 3.06
2910 4804 7.094631 AGTGTTGAACATGTGTACATATACGT 58.905 34.615 4.64 0.00 34.26 3.57
2911 4805 8.245491 AGTGTTGAACATGTGTACATATACGTA 58.755 33.333 4.64 0.00 34.26 3.57
2912 4806 8.529102 GTGTTGAACATGTGTACATATACGTAG 58.471 37.037 4.64 0.00 34.26 3.51
2913 4807 7.703197 TGTTGAACATGTGTACATATACGTAGG 59.297 37.037 4.64 0.00 34.26 3.18
2914 4808 7.337480 TGAACATGTGTACATATACGTAGGT 57.663 36.000 4.64 2.06 34.26 3.08
2915 4809 7.420002 TGAACATGTGTACATATACGTAGGTC 58.580 38.462 4.64 1.86 34.26 3.85
2916 4810 7.283807 TGAACATGTGTACATATACGTAGGTCT 59.716 37.037 4.64 0.00 34.26 3.85
2917 4811 6.967135 ACATGTGTACATATACGTAGGTCTG 58.033 40.000 4.64 0.00 34.26 3.51
2918 4812 6.016527 ACATGTGTACATATACGTAGGTCTGG 60.017 42.308 4.64 0.00 34.26 3.86
2919 4813 4.823442 TGTGTACATATACGTAGGTCTGGG 59.177 45.833 0.00 0.00 33.60 4.45
2920 4814 4.823989 GTGTACATATACGTAGGTCTGGGT 59.176 45.833 0.00 0.00 33.60 4.51
2921 4815 5.300286 GTGTACATATACGTAGGTCTGGGTT 59.700 44.000 0.00 0.00 33.60 4.11
2922 4816 5.532406 TGTACATATACGTAGGTCTGGGTTC 59.468 44.000 0.08 0.00 33.60 3.62
2923 4817 4.801164 ACATATACGTAGGTCTGGGTTCT 58.199 43.478 0.08 0.00 0.00 3.01
2924 4818 4.583489 ACATATACGTAGGTCTGGGTTCTG 59.417 45.833 0.08 0.00 0.00 3.02
2925 4819 2.592102 TACGTAGGTCTGGGTTCTGT 57.408 50.000 0.00 0.00 0.00 3.41
2926 4820 2.592102 ACGTAGGTCTGGGTTCTGTA 57.408 50.000 0.00 0.00 0.00 2.74
2927 4821 3.097342 ACGTAGGTCTGGGTTCTGTAT 57.903 47.619 0.00 0.00 0.00 2.29
2928 4822 2.758979 ACGTAGGTCTGGGTTCTGTATG 59.241 50.000 0.00 0.00 0.00 2.39
2929 4823 2.481449 CGTAGGTCTGGGTTCTGTATGC 60.481 54.545 0.00 0.00 0.00 3.14
2930 4824 1.656587 AGGTCTGGGTTCTGTATGCA 58.343 50.000 0.00 0.00 0.00 3.96
2931 4825 1.556911 AGGTCTGGGTTCTGTATGCAG 59.443 52.381 4.14 4.14 43.87 4.41
2932 4826 1.279271 GGTCTGGGTTCTGTATGCAGT 59.721 52.381 10.80 0.00 43.05 4.40
2933 4827 2.500098 GGTCTGGGTTCTGTATGCAGTA 59.500 50.000 10.80 0.00 43.05 2.74
2934 4828 3.522553 GTCTGGGTTCTGTATGCAGTAC 58.477 50.000 10.80 11.08 43.05 2.73
2941 4835 5.326200 GTTCTGTATGCAGTACCTGTAGT 57.674 43.478 10.80 0.00 43.05 2.73
2942 4836 6.446781 GTTCTGTATGCAGTACCTGTAGTA 57.553 41.667 10.80 0.00 43.05 1.82
2943 4837 7.040473 GTTCTGTATGCAGTACCTGTAGTAT 57.960 40.000 10.80 0.00 43.05 2.12
2944 4838 6.879276 TCTGTATGCAGTACCTGTAGTATC 57.121 41.667 10.80 0.00 43.05 2.24
2945 4839 6.602278 TCTGTATGCAGTACCTGTAGTATCT 58.398 40.000 10.80 0.00 43.05 1.98
2946 4840 6.486993 TCTGTATGCAGTACCTGTAGTATCTG 59.513 42.308 10.80 0.00 43.05 2.90
2947 4841 6.127101 TGTATGCAGTACCTGTAGTATCTGT 58.873 40.000 0.00 0.00 34.87 3.41
2948 4842 5.776173 ATGCAGTACCTGTAGTATCTGTC 57.224 43.478 0.00 0.00 34.87 3.51
2949 4843 4.856509 TGCAGTACCTGTAGTATCTGTCT 58.143 43.478 0.00 0.00 34.87 3.41
2950 4844 4.882427 TGCAGTACCTGTAGTATCTGTCTC 59.118 45.833 0.00 0.00 34.87 3.36
2951 4845 4.276431 GCAGTACCTGTAGTATCTGTCTCC 59.724 50.000 0.00 0.00 34.87 3.71
2952 4846 4.822896 CAGTACCTGTAGTATCTGTCTCCC 59.177 50.000 0.00 0.00 32.28 4.30
2953 4847 4.727841 AGTACCTGTAGTATCTGTCTCCCT 59.272 45.833 0.00 0.00 32.28 4.20
2954 4848 4.173290 ACCTGTAGTATCTGTCTCCCTC 57.827 50.000 0.00 0.00 0.00 4.30
2955 4849 3.789274 ACCTGTAGTATCTGTCTCCCTCT 59.211 47.826 0.00 0.00 0.00 3.69
2956 4850 4.141287 CCTGTAGTATCTGTCTCCCTCTG 58.859 52.174 0.00 0.00 0.00 3.35
2957 4851 4.385865 CCTGTAGTATCTGTCTCCCTCTGT 60.386 50.000 0.00 0.00 0.00 3.41
2958 4852 5.163184 CCTGTAGTATCTGTCTCCCTCTGTA 60.163 48.000 0.00 0.00 0.00 2.74
2959 4853 6.466615 CCTGTAGTATCTGTCTCCCTCTGTAT 60.467 46.154 0.00 0.00 0.00 2.29
2960 4854 6.299922 TGTAGTATCTGTCTCCCTCTGTATG 58.700 44.000 0.00 0.00 0.00 2.39
2961 4855 5.396057 AGTATCTGTCTCCCTCTGTATGT 57.604 43.478 0.00 0.00 0.00 2.29
2962 4856 6.517013 AGTATCTGTCTCCCTCTGTATGTA 57.483 41.667 0.00 0.00 0.00 2.29
2963 4857 6.300703 AGTATCTGTCTCCCTCTGTATGTAC 58.699 44.000 0.00 0.00 0.00 2.90
2964 4858 3.542648 TCTGTCTCCCTCTGTATGTACG 58.457 50.000 0.00 0.00 0.00 3.67
2965 4859 3.054582 TCTGTCTCCCTCTGTATGTACGT 60.055 47.826 0.00 0.00 0.00 3.57
2966 4860 3.014623 TGTCTCCCTCTGTATGTACGTG 58.985 50.000 0.00 0.00 0.00 4.49
2967 4861 3.015327 GTCTCCCTCTGTATGTACGTGT 58.985 50.000 0.00 0.00 0.00 4.49
2968 4862 4.194640 GTCTCCCTCTGTATGTACGTGTA 58.805 47.826 0.00 0.00 0.00 2.90
2969 4863 4.820716 GTCTCCCTCTGTATGTACGTGTAT 59.179 45.833 0.00 0.00 0.00 2.29
2970 4864 5.049543 GTCTCCCTCTGTATGTACGTGTATC 60.050 48.000 0.00 0.00 0.00 2.24
2971 4865 5.045012 TCCCTCTGTATGTACGTGTATCT 57.955 43.478 0.00 0.00 0.00 1.98
2972 4866 6.042437 TCTCCCTCTGTATGTACGTGTATCTA 59.958 42.308 0.00 0.00 0.00 1.98
2973 4867 6.594744 TCCCTCTGTATGTACGTGTATCTAA 58.405 40.000 0.00 0.00 0.00 2.10
2974 4868 6.709397 TCCCTCTGTATGTACGTGTATCTAAG 59.291 42.308 0.00 0.00 0.00 2.18
2975 4869 6.709397 CCCTCTGTATGTACGTGTATCTAAGA 59.291 42.308 0.00 0.00 0.00 2.10
2976 4870 7.228108 CCCTCTGTATGTACGTGTATCTAAGAA 59.772 40.741 0.00 0.00 0.00 2.52
2977 4871 8.283992 CCTCTGTATGTACGTGTATCTAAGAAG 58.716 40.741 0.00 0.00 0.00 2.85
2978 4872 8.953368 TCTGTATGTACGTGTATCTAAGAAGA 57.047 34.615 0.00 0.00 35.80 2.87
2979 4873 8.824781 TCTGTATGTACGTGTATCTAAGAAGAC 58.175 37.037 0.00 0.00 33.57 3.01
2980 4874 8.496707 TGTATGTACGTGTATCTAAGAAGACA 57.503 34.615 0.00 0.00 33.57 3.41
2981 4875 8.949177 TGTATGTACGTGTATCTAAGAAGACAA 58.051 33.333 0.00 0.00 33.57 3.18
2982 4876 9.435802 GTATGTACGTGTATCTAAGAAGACAAG 57.564 37.037 0.00 0.00 33.57 3.16
2983 4877 7.677454 TGTACGTGTATCTAAGAAGACAAGA 57.323 36.000 0.00 0.00 33.57 3.02
2984 4878 8.277490 TGTACGTGTATCTAAGAAGACAAGAT 57.723 34.615 0.00 0.00 33.57 2.40
2985 4879 9.387257 TGTACGTGTATCTAAGAAGACAAGATA 57.613 33.333 0.00 0.00 33.57 1.98
2986 4880 9.649024 GTACGTGTATCTAAGAAGACAAGATAC 57.351 37.037 12.58 12.58 46.43 2.24
2991 4885 5.481200 TCTAAGAAGACAAGATACGGTCG 57.519 43.478 0.00 0.00 39.01 4.79
2992 4886 2.563471 AGAAGACAAGATACGGTCGC 57.437 50.000 0.00 0.00 39.01 5.19
2993 4887 1.816835 AGAAGACAAGATACGGTCGCA 59.183 47.619 0.00 0.00 39.01 5.10
2994 4888 1.918609 GAAGACAAGATACGGTCGCAC 59.081 52.381 0.00 0.00 39.01 5.34
2995 4889 0.172803 AGACAAGATACGGTCGCACC 59.827 55.000 0.00 0.00 39.01 5.01
2996 4890 0.804933 GACAAGATACGGTCGCACCC 60.805 60.000 0.00 0.00 33.75 4.61
2997 4891 1.520787 CAAGATACGGTCGCACCCC 60.521 63.158 0.00 0.00 33.75 4.95
2998 4892 1.684734 AAGATACGGTCGCACCCCT 60.685 57.895 0.00 0.00 33.75 4.79
2999 4893 1.262640 AAGATACGGTCGCACCCCTT 61.263 55.000 0.00 0.00 33.75 3.95
3000 4894 1.520787 GATACGGTCGCACCCCTTG 60.521 63.158 0.00 0.00 33.75 3.61
3001 4895 2.234913 GATACGGTCGCACCCCTTGT 62.235 60.000 0.00 0.00 33.75 3.16
3002 4896 0.971959 ATACGGTCGCACCCCTTGTA 60.972 55.000 0.00 0.00 33.75 2.41
3003 4897 1.876497 TACGGTCGCACCCCTTGTAC 61.876 60.000 0.00 0.00 33.75 2.90
3004 4898 2.046604 GGTCGCACCCCTTGTACC 60.047 66.667 0.00 0.00 30.04 3.34
3005 4899 2.590114 GGTCGCACCCCTTGTACCT 61.590 63.158 0.00 0.00 33.04 3.08
3006 4900 1.259840 GGTCGCACCCCTTGTACCTA 61.260 60.000 0.00 0.00 33.04 3.08
3007 4901 0.828677 GTCGCACCCCTTGTACCTAT 59.171 55.000 0.00 0.00 0.00 2.57
3008 4902 2.034124 GTCGCACCCCTTGTACCTATA 58.966 52.381 0.00 0.00 0.00 1.31
3009 4903 2.631545 GTCGCACCCCTTGTACCTATAT 59.368 50.000 0.00 0.00 0.00 0.86
3010 4904 3.828451 GTCGCACCCCTTGTACCTATATA 59.172 47.826 0.00 0.00 0.00 0.86
3011 4905 4.465305 GTCGCACCCCTTGTACCTATATAT 59.535 45.833 0.00 0.00 0.00 0.86
3012 4906 5.653769 GTCGCACCCCTTGTACCTATATATA 59.346 44.000 0.00 0.00 0.00 0.86
3013 4907 6.323225 GTCGCACCCCTTGTACCTATATATAT 59.677 42.308 0.00 0.00 0.00 0.86
3014 4908 6.322969 TCGCACCCCTTGTACCTATATATATG 59.677 42.308 5.44 0.00 0.00 1.78
3015 4909 6.097839 CGCACCCCTTGTACCTATATATATGT 59.902 42.308 5.44 6.03 0.00 2.29
3016 4910 7.286087 CGCACCCCTTGTACCTATATATATGTA 59.714 40.741 5.44 4.33 0.00 2.29
3017 4911 8.419442 GCACCCCTTGTACCTATATATATGTAC 58.581 40.741 22.02 22.02 35.94 2.90
3018 4912 8.921205 CACCCCTTGTACCTATATATATGTACC 58.079 40.741 24.13 13.54 35.10 3.34
3019 4913 8.864154 ACCCCTTGTACCTATATATATGTACCT 58.136 37.037 24.13 7.37 35.10 3.08
3027 4921 8.447924 ACCTATATATATGTACCTAGTGCACG 57.552 38.462 12.01 0.00 29.98 5.34
3028 4922 8.270030 ACCTATATATATGTACCTAGTGCACGA 58.730 37.037 12.01 5.11 29.98 4.35
3029 4923 9.286170 CCTATATATATGTACCTAGTGCACGAT 57.714 37.037 12.01 0.00 29.98 3.73
3031 4925 8.747538 ATATATATGTACCTAGTGCACGATCA 57.252 34.615 12.01 6.90 29.98 2.92
3032 4926 5.784578 ATATGTACCTAGTGCACGATCAA 57.215 39.130 12.01 0.00 29.98 2.57
3033 4927 4.672587 ATGTACCTAGTGCACGATCAAT 57.327 40.909 12.01 0.00 29.98 2.57
3034 4928 4.041740 TGTACCTAGTGCACGATCAATC 57.958 45.455 12.01 1.83 0.00 2.67
3035 4929 3.445805 TGTACCTAGTGCACGATCAATCA 59.554 43.478 12.01 4.47 0.00 2.57
3036 4930 3.610040 ACCTAGTGCACGATCAATCAA 57.390 42.857 12.01 0.00 0.00 2.57
3037 4931 4.142609 ACCTAGTGCACGATCAATCAAT 57.857 40.909 12.01 0.00 0.00 2.57
3038 4932 4.517285 ACCTAGTGCACGATCAATCAATT 58.483 39.130 12.01 0.00 0.00 2.32
3039 4933 5.670485 ACCTAGTGCACGATCAATCAATTA 58.330 37.500 12.01 0.00 0.00 1.40
3040 4934 6.291377 ACCTAGTGCACGATCAATCAATTAT 58.709 36.000 12.01 0.00 0.00 1.28
3041 4935 6.425114 ACCTAGTGCACGATCAATCAATTATC 59.575 38.462 12.01 0.00 0.00 1.75
3042 4936 5.334435 AGTGCACGATCAATCAATTATCG 57.666 39.130 12.01 6.10 46.02 2.92
3043 4937 5.049828 AGTGCACGATCAATCAATTATCGA 58.950 37.500 12.01 0.00 43.96 3.59
3044 4938 5.698089 AGTGCACGATCAATCAATTATCGAT 59.302 36.000 12.01 2.16 43.96 3.59
3045 4939 5.787062 GTGCACGATCAATCAATTATCGATG 59.213 40.000 8.54 9.06 43.96 3.84
3046 4940 4.785055 GCACGATCAATCAATTATCGATGC 59.215 41.667 8.54 13.54 43.96 3.91
3047 4941 5.615325 GCACGATCAATCAATTATCGATGCA 60.615 40.000 8.54 0.00 43.96 3.96
3048 4942 5.787062 CACGATCAATCAATTATCGATGCAC 59.213 40.000 8.54 0.00 43.96 4.57
3049 4943 5.106948 ACGATCAATCAATTATCGATGCACC 60.107 40.000 8.54 0.00 43.96 5.01
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
100 101 3.857665 CGACGGGTACATATATGACATGC 59.142 47.826 19.63 0.79 0.00 4.06
122 130 2.825532 TGCTTCTTTGGCATTAACCTCC 59.174 45.455 0.00 0.00 34.56 4.30
133 141 2.005451 CACCTCGAGATGCTTCTTTGG 58.995 52.381 15.71 8.74 30.30 3.28
134 142 1.396301 GCACCTCGAGATGCTTCTTTG 59.604 52.381 25.04 0.21 38.84 2.77
135 143 1.002430 TGCACCTCGAGATGCTTCTTT 59.998 47.619 31.15 0.00 42.55 2.52
229 256 3.541831 CGCGCTAATGCACGTCGT 61.542 61.111 5.56 0.00 39.56 4.34
239 266 3.454587 AATCCCATCCGCGCGCTAA 62.455 57.895 30.48 17.40 0.00 3.09
240 267 3.923864 AATCCCATCCGCGCGCTA 61.924 61.111 30.48 17.82 0.00 4.26
357 399 0.654160 CGCATGCGTCATCACAGAAT 59.346 50.000 31.33 0.00 34.35 2.40
414 1973 1.668151 GAGTGGTGCCGGTCACTTC 60.668 63.158 22.54 16.76 43.41 3.01
478 2059 4.330944 AACAACGAGGACACAAGATGTA 57.669 40.909 0.00 0.00 43.56 2.29
504 2085 1.743996 CCAGCAGGGAAAGTAGAAGC 58.256 55.000 0.00 0.00 40.01 3.86
537 2118 9.997172 TCATCCACCTGTTGAGTCTATATATAT 57.003 33.333 0.00 0.00 0.00 0.86
538 2119 9.244292 GTCATCCACCTGTTGAGTCTATATATA 57.756 37.037 0.00 0.00 0.00 0.86
638 2225 3.373849 GGTAAATGGAACGCGTGTTTTT 58.626 40.909 14.98 14.41 38.78 1.94
699 2286 2.722094 TGAACACAGTGCAGAGGTTTT 58.278 42.857 0.00 0.00 0.00 2.43
700 2287 2.418368 TGAACACAGTGCAGAGGTTT 57.582 45.000 0.00 0.00 0.00 3.27
701 2288 2.418368 TTGAACACAGTGCAGAGGTT 57.582 45.000 0.00 0.00 0.00 3.50
702 2289 2.418368 TTTGAACACAGTGCAGAGGT 57.582 45.000 0.00 0.00 0.00 3.85
703 2290 3.781079 TTTTTGAACACAGTGCAGAGG 57.219 42.857 0.00 0.00 0.00 3.69
704 2291 5.860182 CCATATTTTTGAACACAGTGCAGAG 59.140 40.000 0.00 0.00 0.00 3.35
705 2292 5.534278 TCCATATTTTTGAACACAGTGCAGA 59.466 36.000 0.00 0.00 0.00 4.26
706 2293 5.771469 TCCATATTTTTGAACACAGTGCAG 58.229 37.500 0.00 0.00 0.00 4.41
707 2294 5.781210 TCCATATTTTTGAACACAGTGCA 57.219 34.783 0.00 0.00 0.00 4.57
708 2295 5.634859 CCTTCCATATTTTTGAACACAGTGC 59.365 40.000 0.00 0.00 0.00 4.40
709 2296 6.980593 TCCTTCCATATTTTTGAACACAGTG 58.019 36.000 0.00 0.00 0.00 3.66
710 2297 7.595819 TTCCTTCCATATTTTTGAACACAGT 57.404 32.000 0.00 0.00 0.00 3.55
711 2298 8.764287 GTTTTCCTTCCATATTTTTGAACACAG 58.236 33.333 0.00 0.00 0.00 3.66
712 2299 7.713073 GGTTTTCCTTCCATATTTTTGAACACA 59.287 33.333 0.00 0.00 36.94 3.72
713 2300 8.083462 GGTTTTCCTTCCATATTTTTGAACAC 57.917 34.615 0.00 0.00 36.94 3.32
737 2324 3.562182 AGGGAACACAAGTTTAACCAGG 58.438 45.455 0.00 0.00 38.30 4.45
748 2368 5.887754 AGCTTATTTAGGAAGGGAACACAA 58.112 37.500 0.00 0.00 0.00 3.33
894 2514 2.036733 CGGAAGGTATTCATAGCGGGAA 59.963 50.000 0.00 0.00 37.15 3.97
1065 2685 0.040514 CGAGAGATACAGCAGCTCCG 60.041 60.000 0.00 0.00 40.77 4.63
1068 2688 1.358402 CGCGAGAGATACAGCAGCT 59.642 57.895 0.00 0.00 0.00 4.24
1155 2775 1.893335 CATGATGCCCCATTCGCGA 60.893 57.895 3.71 3.71 0.00 5.87
1297 2917 1.372623 GGTGACAACCTCCGTCGTC 60.373 63.158 0.00 0.00 43.84 4.20
1394 3014 4.415150 CCCCGTGCACCATGAGCT 62.415 66.667 12.15 0.00 0.00 4.09
1523 3143 2.438434 CCTCGGGTGCCATGAACC 60.438 66.667 8.60 8.60 36.94 3.62
1690 3310 2.283529 ACTGTGGCACCTCCGGTAG 61.284 63.158 16.26 6.25 37.80 3.18
1839 3459 0.246635 ATGTACGCTTCTTCACCGCT 59.753 50.000 0.00 0.00 0.00 5.52
2013 3633 1.796796 GATCCAGCCTTGTTCGTGC 59.203 57.895 0.00 0.00 0.00 5.34
2015 3635 0.320374 TTCGATCCAGCCTTGTTCGT 59.680 50.000 0.00 0.00 32.81 3.85
2019 3639 1.066573 CAGACTTCGATCCAGCCTTGT 60.067 52.381 0.00 0.00 0.00 3.16
2050 3670 4.759693 ACTGAACACGCTAAAATCCATCAA 59.240 37.500 0.00 0.00 0.00 2.57
2088 3708 2.584608 CCGATCCAGCCTCCGTTT 59.415 61.111 0.00 0.00 0.00 3.60
2089 3709 4.162690 GCCGATCCAGCCTCCGTT 62.163 66.667 0.00 0.00 0.00 4.44
2092 3712 3.581687 GATCGCCGATCCAGCCTCC 62.582 68.421 16.12 0.00 33.37 4.30
2151 3771 5.171476 TGCTGCTCTGTACTACAAAATCTC 58.829 41.667 0.00 0.00 0.00 2.75
2203 3826 0.108585 ACACACCCTGCCTTGTACAG 59.891 55.000 0.00 0.00 34.82 2.74
2251 4144 3.039405 CGTTCTGAGATCACTACGCATC 58.961 50.000 0.00 0.00 0.00 3.91
2252 4145 2.796383 GCGTTCTGAGATCACTACGCAT 60.796 50.000 19.89 0.00 45.21 4.73
2340 4233 5.772004 TCCTCTCAATCTAAGCCTTCTACT 58.228 41.667 0.00 0.00 0.00 2.57
2341 4234 6.472686 TTCCTCTCAATCTAAGCCTTCTAC 57.527 41.667 0.00 0.00 0.00 2.59
2342 4235 7.496346 TTTTCCTCTCAATCTAAGCCTTCTA 57.504 36.000 0.00 0.00 0.00 2.10
2343 4236 6.380079 TTTTCCTCTCAATCTAAGCCTTCT 57.620 37.500 0.00 0.00 0.00 2.85
2362 4256 6.231211 TCTGAGGGAGACAACAACTATTTTC 58.769 40.000 0.00 0.00 0.00 2.29
2402 4296 2.293170 GAGGTAGGCAAAAGATCCAGC 58.707 52.381 0.00 0.00 0.00 4.85
2406 4300 1.300481 GCGGAGGTAGGCAAAAGATC 58.700 55.000 0.00 0.00 0.00 2.75
2427 4321 1.448985 TATCCTGGTTGCAACTTCGC 58.551 50.000 27.64 12.57 0.00 4.70
2429 4323 5.123979 CCTAGTTTATCCTGGTTGCAACTTC 59.876 44.000 27.64 13.64 0.00 3.01
2438 4332 2.505819 CAGTGGCCTAGTTTATCCTGGT 59.494 50.000 3.32 0.00 0.00 4.00
2443 4337 4.570930 GCCTATCAGTGGCCTAGTTTATC 58.429 47.826 3.32 0.00 44.32 1.75
2454 4348 3.849951 ACCGGCGCCTATCAGTGG 61.850 66.667 26.68 18.69 0.00 4.00
2455 4349 2.586079 CACCGGCGCCTATCAGTG 60.586 66.667 26.68 18.72 0.00 3.66
2456 4350 4.530857 GCACCGGCGCCTATCAGT 62.531 66.667 26.68 10.93 0.00 3.41
2500 4394 0.643310 GTCAAATCGTATGTGCGCGA 59.357 50.000 12.10 0.00 41.50 5.87
2543 4437 4.700213 CCGGACAACTTTTTATCTCACCAT 59.300 41.667 0.00 0.00 0.00 3.55
2559 4453 4.426736 AAGAAAGAAACTACCCGGACAA 57.573 40.909 0.73 0.00 0.00 3.18
2568 4462 6.347402 GCGTACATGAGCAAAGAAAGAAACTA 60.347 38.462 0.00 0.00 0.00 2.24
2569 4463 5.560953 GCGTACATGAGCAAAGAAAGAAACT 60.561 40.000 0.00 0.00 0.00 2.66
2573 4467 3.186409 GTGCGTACATGAGCAAAGAAAGA 59.814 43.478 14.50 0.00 45.61 2.52
2639 4533 2.651137 GCACGCAACAACATGCAGC 61.651 57.895 0.00 0.00 46.76 5.25
2642 4536 2.353376 ACGCACGCAACAACATGC 60.353 55.556 0.00 0.00 42.94 4.06
2664 4558 1.451387 GTAGCATCGTTGGGGTGGG 60.451 63.158 0.00 0.00 0.00 4.61
2674 4568 4.624336 AGTAGTGAGAAGTGTAGCATCG 57.376 45.455 0.00 0.00 0.00 3.84
2728 4622 6.291377 AGTTTTGCCGACATAGATGATACAT 58.709 36.000 0.00 0.00 0.00 2.29
2736 4630 5.935206 TGTTATGAAGTTTTGCCGACATAGA 59.065 36.000 0.00 0.00 0.00 1.98
2756 4650 9.436957 TTTTGCTTTGATTTGTAGGTTTTGTTA 57.563 25.926 0.00 0.00 0.00 2.41
2820 4714 4.511082 ACCATTTTTGCTTTCATGGTTTCG 59.489 37.500 5.63 0.00 46.00 3.46
2821 4715 5.296531 ACACCATTTTTGCTTTCATGGTTTC 59.703 36.000 8.07 0.00 46.00 2.78
2826 4720 7.424227 AACATACACCATTTTTGCTTTCATG 57.576 32.000 0.00 0.00 0.00 3.07
2839 4733 5.536161 GGAATATGCTGGAAACATACACCAT 59.464 40.000 0.00 0.00 41.51 3.55
2862 4756 8.028938 CACTTTTTCAGTTGTAGAAATATGGGG 58.971 37.037 0.00 0.00 35.17 4.96
2863 4757 8.576442 ACACTTTTTCAGTTGTAGAAATATGGG 58.424 33.333 0.00 0.00 35.17 4.00
2864 4758 9.965824 AACACTTTTTCAGTTGTAGAAATATGG 57.034 29.630 0.00 0.00 35.17 2.74
2868 4762 9.353999 GTTCAACACTTTTTCAGTTGTAGAAAT 57.646 29.630 0.00 0.00 42.33 2.17
2869 4763 8.353684 TGTTCAACACTTTTTCAGTTGTAGAAA 58.646 29.630 0.00 0.00 42.33 2.52
2870 4764 7.877003 TGTTCAACACTTTTTCAGTTGTAGAA 58.123 30.769 0.00 0.00 42.33 2.10
2871 4765 7.441890 TGTTCAACACTTTTTCAGTTGTAGA 57.558 32.000 0.00 0.00 42.33 2.59
2872 4766 7.754924 ACATGTTCAACACTTTTTCAGTTGTAG 59.245 33.333 0.00 0.00 42.33 2.74
2873 4767 7.540400 CACATGTTCAACACTTTTTCAGTTGTA 59.460 33.333 0.00 0.00 42.33 2.41
2874 4768 6.365789 CACATGTTCAACACTTTTTCAGTTGT 59.634 34.615 0.00 0.00 42.33 3.32
2875 4769 6.365789 ACACATGTTCAACACTTTTTCAGTTG 59.634 34.615 0.00 0.00 42.90 3.16
2876 4770 6.454795 ACACATGTTCAACACTTTTTCAGTT 58.545 32.000 0.00 0.00 30.92 3.16
2877 4771 6.024552 ACACATGTTCAACACTTTTTCAGT 57.975 33.333 0.00 0.00 35.35 3.41
2878 4772 7.026562 TGTACACATGTTCAACACTTTTTCAG 58.973 34.615 0.00 0.00 0.00 3.02
2879 4773 6.914259 TGTACACATGTTCAACACTTTTTCA 58.086 32.000 0.00 0.00 0.00 2.69
2880 4774 7.985634 ATGTACACATGTTCAACACTTTTTC 57.014 32.000 0.00 0.00 34.83 2.29
2883 4777 8.440059 CGTATATGTACACATGTTCAACACTTT 58.560 33.333 0.00 0.00 37.15 2.66
2884 4778 7.601130 ACGTATATGTACACATGTTCAACACTT 59.399 33.333 0.00 0.00 37.15 3.16
2885 4779 7.094631 ACGTATATGTACACATGTTCAACACT 58.905 34.615 0.00 0.00 37.15 3.55
2886 4780 7.285783 ACGTATATGTACACATGTTCAACAC 57.714 36.000 0.00 0.00 37.15 3.32
2887 4781 7.703197 CCTACGTATATGTACACATGTTCAACA 59.297 37.037 0.00 0.97 37.15 3.33
2888 4782 7.703621 ACCTACGTATATGTACACATGTTCAAC 59.296 37.037 0.00 0.00 37.15 3.18
2889 4783 7.774134 ACCTACGTATATGTACACATGTTCAA 58.226 34.615 0.00 0.00 37.15 2.69
2890 4784 7.283807 AGACCTACGTATATGTACACATGTTCA 59.716 37.037 0.00 0.00 37.15 3.18
2891 4785 7.590322 CAGACCTACGTATATGTACACATGTTC 59.410 40.741 0.00 0.00 37.15 3.18
2892 4786 7.423199 CAGACCTACGTATATGTACACATGTT 58.577 38.462 0.00 0.00 37.15 2.71
2893 4787 6.016527 CCAGACCTACGTATATGTACACATGT 60.017 42.308 0.00 0.00 37.15 3.21
2894 4788 6.379386 CCAGACCTACGTATATGTACACATG 58.621 44.000 0.00 0.00 37.15 3.21
2895 4789 5.475909 CCCAGACCTACGTATATGTACACAT 59.524 44.000 0.00 0.00 40.22 3.21
2896 4790 4.823442 CCCAGACCTACGTATATGTACACA 59.177 45.833 0.00 0.00 0.00 3.72
2897 4791 4.823989 ACCCAGACCTACGTATATGTACAC 59.176 45.833 0.00 0.00 0.00 2.90
2898 4792 5.052693 ACCCAGACCTACGTATATGTACA 57.947 43.478 0.00 0.00 0.00 2.90
2899 4793 5.767168 AGAACCCAGACCTACGTATATGTAC 59.233 44.000 0.00 0.00 0.00 2.90
2900 4794 5.766670 CAGAACCCAGACCTACGTATATGTA 59.233 44.000 4.75 4.75 0.00 2.29
2901 4795 4.583489 CAGAACCCAGACCTACGTATATGT 59.417 45.833 2.56 2.56 0.00 2.29
2902 4796 4.583489 ACAGAACCCAGACCTACGTATATG 59.417 45.833 0.00 0.00 0.00 1.78
2903 4797 4.801164 ACAGAACCCAGACCTACGTATAT 58.199 43.478 0.00 0.00 0.00 0.86
2904 4798 4.240881 ACAGAACCCAGACCTACGTATA 57.759 45.455 0.00 0.00 0.00 1.47
2905 4799 3.097342 ACAGAACCCAGACCTACGTAT 57.903 47.619 0.00 0.00 0.00 3.06
2906 4800 2.592102 ACAGAACCCAGACCTACGTA 57.408 50.000 0.00 0.00 0.00 3.57
2907 4801 2.592102 TACAGAACCCAGACCTACGT 57.408 50.000 0.00 0.00 0.00 3.57
2908 4802 2.481449 GCATACAGAACCCAGACCTACG 60.481 54.545 0.00 0.00 0.00 3.51
2909 4803 2.500098 TGCATACAGAACCCAGACCTAC 59.500 50.000 0.00 0.00 0.00 3.18
2910 4804 2.827755 TGCATACAGAACCCAGACCTA 58.172 47.619 0.00 0.00 0.00 3.08
2911 4805 1.656587 TGCATACAGAACCCAGACCT 58.343 50.000 0.00 0.00 0.00 3.85
2930 4824 4.727841 AGGGAGACAGATACTACAGGTACT 59.272 45.833 0.00 0.00 43.88 2.73
2931 4825 5.051409 AGGGAGACAGATACTACAGGTAC 57.949 47.826 0.00 0.00 32.72 3.34
2932 4826 4.976442 AGAGGGAGACAGATACTACAGGTA 59.024 45.833 0.00 0.00 34.62 3.08
2933 4827 3.789274 AGAGGGAGACAGATACTACAGGT 59.211 47.826 0.00 0.00 0.00 4.00
2934 4828 4.141287 CAGAGGGAGACAGATACTACAGG 58.859 52.174 0.00 0.00 0.00 4.00
2935 4829 4.787551 ACAGAGGGAGACAGATACTACAG 58.212 47.826 0.00 0.00 0.00 2.74
2936 4830 4.864483 ACAGAGGGAGACAGATACTACA 57.136 45.455 0.00 0.00 0.00 2.74
2937 4831 6.300703 ACATACAGAGGGAGACAGATACTAC 58.699 44.000 0.00 0.00 0.00 2.73
2938 4832 6.517013 ACATACAGAGGGAGACAGATACTA 57.483 41.667 0.00 0.00 0.00 1.82
2939 4833 5.396057 ACATACAGAGGGAGACAGATACT 57.604 43.478 0.00 0.00 0.00 2.12
2940 4834 5.179742 CGTACATACAGAGGGAGACAGATAC 59.820 48.000 0.00 0.00 0.00 2.24
2941 4835 5.163227 ACGTACATACAGAGGGAGACAGATA 60.163 44.000 0.00 0.00 0.00 1.98
2942 4836 4.138290 CGTACATACAGAGGGAGACAGAT 58.862 47.826 0.00 0.00 0.00 2.90
2943 4837 3.054582 ACGTACATACAGAGGGAGACAGA 60.055 47.826 0.00 0.00 0.00 3.41
2944 4838 3.065510 CACGTACATACAGAGGGAGACAG 59.934 52.174 0.00 0.00 0.00 3.51
2945 4839 3.014623 CACGTACATACAGAGGGAGACA 58.985 50.000 0.00 0.00 0.00 3.41
2946 4840 3.015327 ACACGTACATACAGAGGGAGAC 58.985 50.000 0.00 0.00 0.00 3.36
2947 4841 3.361281 ACACGTACATACAGAGGGAGA 57.639 47.619 0.00 0.00 0.00 3.71
2948 4842 5.064558 AGATACACGTACATACAGAGGGAG 58.935 45.833 0.00 0.00 0.00 4.30
2949 4843 5.045012 AGATACACGTACATACAGAGGGA 57.955 43.478 0.00 0.00 0.00 4.20
2950 4844 6.709397 TCTTAGATACACGTACATACAGAGGG 59.291 42.308 0.00 0.00 0.00 4.30
2951 4845 7.725818 TCTTAGATACACGTACATACAGAGG 57.274 40.000 0.00 0.00 0.00 3.69
2952 4846 9.043079 TCTTCTTAGATACACGTACATACAGAG 57.957 37.037 0.00 0.00 0.00 3.35
2953 4847 8.824781 GTCTTCTTAGATACACGTACATACAGA 58.175 37.037 0.00 0.00 31.86 3.41
2954 4848 8.610035 TGTCTTCTTAGATACACGTACATACAG 58.390 37.037 0.00 0.00 31.86 2.74
2955 4849 8.496707 TGTCTTCTTAGATACACGTACATACA 57.503 34.615 0.00 0.00 31.86 2.29
2956 4850 9.435802 CTTGTCTTCTTAGATACACGTACATAC 57.564 37.037 0.00 0.00 31.86 2.39
2957 4851 9.387257 TCTTGTCTTCTTAGATACACGTACATA 57.613 33.333 0.00 0.00 31.86 2.29
2958 4852 8.277490 TCTTGTCTTCTTAGATACACGTACAT 57.723 34.615 0.00 0.00 31.86 2.29
2959 4853 7.677454 TCTTGTCTTCTTAGATACACGTACA 57.323 36.000 0.00 0.00 31.86 2.90
2960 4854 9.649024 GTATCTTGTCTTCTTAGATACACGTAC 57.351 37.037 13.69 0.00 45.06 3.67
2961 4855 8.546244 CGTATCTTGTCTTCTTAGATACACGTA 58.454 37.037 16.98 0.00 45.58 3.57
2962 4856 7.408123 CGTATCTTGTCTTCTTAGATACACGT 58.592 38.462 16.98 0.00 45.58 4.49
2963 4857 6.851837 CCGTATCTTGTCTTCTTAGATACACG 59.148 42.308 16.98 9.61 45.58 4.49
2964 4858 7.705214 ACCGTATCTTGTCTTCTTAGATACAC 58.295 38.462 16.98 0.33 45.58 2.90
2965 4859 7.254692 CGACCGTATCTTGTCTTCTTAGATACA 60.255 40.741 16.98 0.00 45.58 2.29
2966 4860 7.070798 CGACCGTATCTTGTCTTCTTAGATAC 58.929 42.308 0.00 0.00 43.52 2.24
2967 4861 6.293298 GCGACCGTATCTTGTCTTCTTAGATA 60.293 42.308 0.00 0.00 31.86 1.98
2968 4862 5.505985 GCGACCGTATCTTGTCTTCTTAGAT 60.506 44.000 0.00 0.00 31.86 1.98
2969 4863 4.201891 GCGACCGTATCTTGTCTTCTTAGA 60.202 45.833 0.00 0.00 0.00 2.10
2970 4864 4.036352 GCGACCGTATCTTGTCTTCTTAG 58.964 47.826 0.00 0.00 0.00 2.18
2971 4865 3.441222 TGCGACCGTATCTTGTCTTCTTA 59.559 43.478 0.00 0.00 0.00 2.10
2972 4866 2.230508 TGCGACCGTATCTTGTCTTCTT 59.769 45.455 0.00 0.00 0.00 2.52
2973 4867 1.816835 TGCGACCGTATCTTGTCTTCT 59.183 47.619 0.00 0.00 0.00 2.85
2974 4868 1.918609 GTGCGACCGTATCTTGTCTTC 59.081 52.381 0.00 0.00 0.00 2.87
2975 4869 1.403780 GGTGCGACCGTATCTTGTCTT 60.404 52.381 0.00 0.00 0.00 3.01
2976 4870 0.172803 GGTGCGACCGTATCTTGTCT 59.827 55.000 0.00 0.00 0.00 3.41
2977 4871 0.804933 GGGTGCGACCGTATCTTGTC 60.805 60.000 0.00 0.00 39.83 3.18
2978 4872 1.217244 GGGTGCGACCGTATCTTGT 59.783 57.895 0.00 0.00 39.83 3.16
2979 4873 1.520787 GGGGTGCGACCGTATCTTG 60.521 63.158 0.00 0.00 39.83 3.02
2980 4874 1.262640 AAGGGGTGCGACCGTATCTT 61.263 55.000 0.00 0.00 39.83 2.40
2981 4875 1.684734 AAGGGGTGCGACCGTATCT 60.685 57.895 0.00 0.00 39.83 1.98
2982 4876 1.520787 CAAGGGGTGCGACCGTATC 60.521 63.158 0.00 0.00 39.83 2.24
2983 4877 0.971959 TACAAGGGGTGCGACCGTAT 60.972 55.000 0.00 0.00 39.83 3.06
2984 4878 1.606025 TACAAGGGGTGCGACCGTA 60.606 57.895 0.00 0.00 39.83 4.02
2985 4879 2.918802 TACAAGGGGTGCGACCGT 60.919 61.111 0.00 0.00 39.83 4.83
2986 4880 2.433664 GTACAAGGGGTGCGACCG 60.434 66.667 0.00 0.00 39.83 4.79
2987 4881 1.259840 TAGGTACAAGGGGTGCGACC 61.260 60.000 0.00 0.00 36.98 4.79
2988 4882 0.828677 ATAGGTACAAGGGGTGCGAC 59.171 55.000 0.00 0.00 32.16 5.19
2989 4883 2.457813 TATAGGTACAAGGGGTGCGA 57.542 50.000 0.00 0.00 32.16 5.10
2990 4884 6.097839 ACATATATATAGGTACAAGGGGTGCG 59.902 42.308 8.25 0.00 32.16 5.34
2991 4885 7.433537 ACATATATATAGGTACAAGGGGTGC 57.566 40.000 8.25 0.00 0.00 5.01
2992 4886 8.921205 GGTACATATATATAGGTACAAGGGGTG 58.079 40.741 32.59 12.53 46.55 4.61
2993 4887 8.864154 AGGTACATATATATAGGTACAAGGGGT 58.136 37.037 32.59 16.51 46.55 4.95
3001 4895 9.551734 CGTGCACTAGGTACATATATATAGGTA 57.448 37.037 16.19 12.14 31.67 3.08
3002 4896 8.270030 TCGTGCACTAGGTACATATATATAGGT 58.730 37.037 16.19 14.03 31.67 3.08
3003 4897 8.672823 TCGTGCACTAGGTACATATATATAGG 57.327 38.462 16.19 2.88 31.67 2.57
3005 4899 9.841295 TGATCGTGCACTAGGTACATATATATA 57.159 33.333 16.19 0.00 31.67 0.86
3006 4900 8.747538 TGATCGTGCACTAGGTACATATATAT 57.252 34.615 16.19 0.00 31.67 0.86
3007 4901 8.570068 TTGATCGTGCACTAGGTACATATATA 57.430 34.615 16.19 0.00 31.67 0.86
3008 4902 7.462571 TTGATCGTGCACTAGGTACATATAT 57.537 36.000 16.19 0.00 31.67 0.86
3009 4903 6.887626 TTGATCGTGCACTAGGTACATATA 57.112 37.500 16.19 0.00 31.67 0.86
3010 4904 5.784578 TTGATCGTGCACTAGGTACATAT 57.215 39.130 16.19 0.00 31.67 1.78
3011 4905 5.300792 TGATTGATCGTGCACTAGGTACATA 59.699 40.000 16.19 0.00 31.67 2.29
3012 4906 4.099419 TGATTGATCGTGCACTAGGTACAT 59.901 41.667 16.19 0.00 31.67 2.29
3013 4907 3.445805 TGATTGATCGTGCACTAGGTACA 59.554 43.478 16.19 4.45 31.67 2.90
3014 4908 4.041740 TGATTGATCGTGCACTAGGTAC 57.958 45.455 16.19 1.84 0.00 3.34
3015 4909 4.729227 TTGATTGATCGTGCACTAGGTA 57.271 40.909 16.19 0.00 0.00 3.08
3016 4910 3.610040 TTGATTGATCGTGCACTAGGT 57.390 42.857 16.19 0.00 0.00 3.08
3017 4911 6.400409 CGATAATTGATTGATCGTGCACTAGG 60.400 42.308 16.19 0.00 38.10 3.02
3018 4912 6.363357 TCGATAATTGATTGATCGTGCACTAG 59.637 38.462 16.19 0.00 42.37 2.57
3019 4913 6.212955 TCGATAATTGATTGATCGTGCACTA 58.787 36.000 16.19 3.92 42.37 2.74
3020 4914 5.049828 TCGATAATTGATTGATCGTGCACT 58.950 37.500 16.19 0.00 42.37 4.40
3021 4915 5.328886 TCGATAATTGATTGATCGTGCAC 57.671 39.130 6.82 6.82 42.37 4.57
3022 4916 5.615325 GCATCGATAATTGATTGATCGTGCA 60.615 40.000 19.03 0.00 42.67 4.57
3023 4917 4.785055 GCATCGATAATTGATTGATCGTGC 59.215 41.667 0.00 13.84 42.37 5.34
3024 4918 5.787062 GTGCATCGATAATTGATTGATCGTG 59.213 40.000 0.00 6.61 42.37 4.35
3025 4919 5.106948 GGTGCATCGATAATTGATTGATCGT 60.107 40.000 0.00 0.00 42.37 3.73
3026 4920 5.319139 GGTGCATCGATAATTGATTGATCG 58.681 41.667 0.00 1.88 42.96 3.69


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

AutoCloner maintained by Alex Coulton.