Multiple sequence alignment - TraesCS5A01G475900

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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 TraesCS5A01G475900 chr5A 100.000 3599 0 0 1 3599 650670032 650673630 0.000000e+00 6647.0
1 TraesCS5A01G475900 chr5D 88.833 3161 214 64 48 3135 524480101 524483195 0.000000e+00 3753.0
2 TraesCS5A01G475900 chr5D 91.500 200 13 3 3203 3401 524483303 524483499 4.580000e-69 272.0
3 TraesCS5A01G475900 chr5D 97.222 36 1 0 3417 3452 524483539 524483574 1.080000e-05 62.1
4 TraesCS5A01G475900 chr5B 89.974 2743 186 50 1 2726 659028229 659030899 0.000000e+00 3459.0
5 TraesCS5A01G475900 chr5B 83.920 199 12 10 3203 3399 659031426 659031606 4.780000e-39 172.0
6 TraesCS5A01G475900 chr5B 97.222 36 1 0 3417 3452 659031655 659031690 1.080000e-05 62.1
7 TraesCS5A01G475900 chr2B 87.546 1638 183 11 981 2605 635704931 635703302 0.000000e+00 1875.0
8 TraesCS5A01G475900 chr2B 87.097 93 7 2 3455 3547 230293602 230293515 2.290000e-17 100.0
9 TraesCS5A01G475900 chr2A 87.333 1642 187 11 981 2609 678018400 678016767 0.000000e+00 1860.0
10 TraesCS5A01G475900 chr2A 85.294 102 6 6 3445 3546 428902065 428902157 2.960000e-16 97.1
11 TraesCS5A01G475900 chr2D 88.287 1366 142 11 1252 2605 534492443 534491084 0.000000e+00 1620.0
12 TraesCS5A01G475900 chr1D 76.667 270 33 17 1305 1566 452336674 452336427 4.880000e-24 122.0
13 TraesCS5A01G475900 chr1D 76.779 267 32 17 1305 1563 452351679 452351923 4.880000e-24 122.0
14 TraesCS5A01G475900 chr1A 87.629 97 7 2 3453 3549 307866759 307866668 1.370000e-19 108.0
15 TraesCS5A01G475900 chr1A 85.714 98 8 3 3454 3551 560378112 560378203 8.220000e-17 99.0
16 TraesCS5A01G475900 chr6A 85.000 100 12 3 1470 1566 261507852 261507951 8.220000e-17 99.0
17 TraesCS5A01G475900 chr7D 85.000 100 9 4 3446 3545 178614043 178613950 2.960000e-16 97.1
18 TraesCS5A01G475900 chr4B 86.170 94 8 2 3454 3547 538676150 538676062 2.960000e-16 97.1
19 TraesCS5A01G475900 chr6B 85.567 97 4 5 3449 3545 532238255 532238341 3.830000e-15 93.5
20 TraesCS5A01G475900 chr1B 85.870 92 8 3 3455 3546 4339070 4339156 3.830000e-15 93.5
21 TraesCS5A01G475900 chr1B 82.051 117 13 5 3432 3546 513248525 513248415 3.830000e-15 93.5


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 TraesCS5A01G475900 chr5A 650670032 650673630 3598 False 6647.000000 6647 100.000000 1 3599 1 chr5A.!!$F1 3598
1 TraesCS5A01G475900 chr5D 524480101 524483574 3473 False 1362.366667 3753 92.518333 48 3452 3 chr5D.!!$F1 3404
2 TraesCS5A01G475900 chr5B 659028229 659031690 3461 False 1231.033333 3459 90.372000 1 3452 3 chr5B.!!$F1 3451
3 TraesCS5A01G475900 chr2B 635703302 635704931 1629 True 1875.000000 1875 87.546000 981 2605 1 chr2B.!!$R2 1624
4 TraesCS5A01G475900 chr2A 678016767 678018400 1633 True 1860.000000 1860 87.333000 981 2609 1 chr2A.!!$R1 1628
5 TraesCS5A01G475900 chr2D 534491084 534492443 1359 True 1620.000000 1620 88.287000 1252 2605 1 chr2D.!!$R1 1353


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
227 228 0.037697 TGGGTCCGATCTTTCACACG 60.038 55.0 0.0 0.0 0.0 4.49 F
1155 1177 0.395036 TCTCTTCCTCCCTCTCGCAG 60.395 60.0 0.0 0.0 0.0 5.18 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1573 1601 0.402121 GACTCCTTGGCCAAGAACCT 59.598 55.0 41.1 22.49 40.79 3.50 R
2774 2817 0.032952 GGGTTCACGCACACTGACTA 59.967 55.0 0.0 0.00 0.00 2.59 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
22 23 5.728637 CAGGAAGTTTTCTTAAAGCCCAT 57.271 39.130 0.00 0.00 40.61 4.00
29 30 2.717639 TCTTAAAGCCCATCTCTGCC 57.282 50.000 0.00 0.00 0.00 4.85
32 33 0.107017 TAAAGCCCATCTCTGCCAGC 60.107 55.000 0.00 0.00 0.00 4.85
41 42 1.769026 TCTCTGCCAGCGAGTATTCT 58.231 50.000 9.98 0.00 0.00 2.40
42 43 1.406898 TCTCTGCCAGCGAGTATTCTG 59.593 52.381 9.98 0.00 0.00 3.02
66 67 3.330701 AGCAACTCTCCCAATTAAGACCA 59.669 43.478 0.00 0.00 0.00 4.02
85 86 3.259123 ACCAAATGATTCACTTGCCCTTC 59.741 43.478 2.35 0.00 0.00 3.46
103 104 3.438087 CCTTCGCCATGGACATTATCATC 59.562 47.826 18.40 0.00 0.00 2.92
134 135 1.356624 GCCATTTGGAATCCTCGCG 59.643 57.895 0.00 0.00 37.39 5.87
137 138 1.064060 CCATTTGGAATCCTCGCGAAC 59.936 52.381 11.33 0.00 37.39 3.95
147 148 1.135373 TCCTCGCGAACAGTTCATCTC 60.135 52.381 11.33 0.00 0.00 2.75
150 151 1.000394 TCGCGAACAGTTCATCTCCAA 60.000 47.619 6.20 0.00 0.00 3.53
152 153 2.159787 CGCGAACAGTTCATCTCCAAAG 60.160 50.000 13.82 0.00 0.00 2.77
178 179 1.520600 CGCCCAACCTGGTTTACACC 61.521 60.000 9.90 0.00 44.56 4.16
218 219 1.757118 TCTGTCAGAATGGGTCCGATC 59.243 52.381 0.00 0.00 36.16 3.69
224 225 2.939103 CAGAATGGGTCCGATCTTTCAC 59.061 50.000 0.00 0.00 0.00 3.18
227 228 0.037697 TGGGTCCGATCTTTCACACG 60.038 55.000 0.00 0.00 0.00 4.49
272 273 4.904154 CGTTGTTGTCGAAAATTTCCTCTC 59.096 41.667 0.00 0.00 0.00 3.20
318 319 4.080393 CACATTTTGTTTTTGTGTGTGCG 58.920 39.130 0.00 0.00 36.77 5.34
321 322 2.440539 TTGTTTTTGTGTGTGCGGTT 57.559 40.000 0.00 0.00 0.00 4.44
356 357 6.128138 AGTTTTAGACCATAGCTCCTTGTT 57.872 37.500 0.00 0.00 0.00 2.83
420 424 9.765795 AATACTCTATTGGAAGAAATTCCTACG 57.234 33.333 8.40 0.00 41.65 3.51
427 431 3.864003 GGAAGAAATTCCTACGAGTTCGG 59.136 47.826 6.48 0.00 39.73 4.30
428 432 4.492611 GAAGAAATTCCTACGAGTTCGGT 58.507 43.478 6.48 0.00 44.95 4.69
429 433 4.107363 AGAAATTCCTACGAGTTCGGTC 57.893 45.455 6.48 0.00 44.95 4.79
430 434 3.508793 AGAAATTCCTACGAGTTCGGTCA 59.491 43.478 6.48 0.00 44.95 4.02
431 435 3.505464 AATTCCTACGAGTTCGGTCAG 57.495 47.619 6.48 0.58 44.95 3.51
432 436 2.189594 TTCCTACGAGTTCGGTCAGA 57.810 50.000 6.48 0.00 44.95 3.27
480 484 1.720852 GCAACTTAAATGCGGTGCAAG 59.279 47.619 0.00 0.00 43.62 4.01
497 501 2.737679 GCAAGCATCCATCAAAGAAGGC 60.738 50.000 0.00 0.00 0.00 4.35
498 502 2.494471 CAAGCATCCATCAAAGAAGGCA 59.506 45.455 0.00 0.00 0.00 4.75
499 503 3.028094 AGCATCCATCAAAGAAGGCAT 57.972 42.857 0.00 0.00 0.00 4.40
542 548 7.619050 AGCTTTCACTGATAATTCTTCTCTCA 58.381 34.615 0.00 0.00 0.00 3.27
543 549 7.548780 AGCTTTCACTGATAATTCTTCTCTCAC 59.451 37.037 0.00 0.00 0.00 3.51
623 633 3.047796 CACTTGCATGAAGTTCACAAGC 58.952 45.455 25.14 20.80 42.70 4.01
628 638 2.351157 GCATGAAGTTCACAAGCTGGAC 60.351 50.000 7.96 0.00 0.00 4.02
631 641 1.795286 GAAGTTCACAAGCTGGACTCG 59.205 52.381 0.00 0.00 0.00 4.18
700 715 4.904251 TCCATGACCAATCCCTTTGAAAAA 59.096 37.500 0.00 0.00 37.53 1.94
711 726 7.669089 ATCCCTTTGAAAAACTCAACCTTTA 57.331 32.000 0.00 0.00 43.90 1.85
757 772 4.487714 TGGTCACTTCTCTCACTTGTTT 57.512 40.909 0.00 0.00 0.00 2.83
758 773 4.442706 TGGTCACTTCTCTCACTTGTTTC 58.557 43.478 0.00 0.00 0.00 2.78
820 840 2.166907 TGGTGTTGACCCAACCAATT 57.833 45.000 7.29 0.00 42.96 2.32
831 851 3.319689 ACCCAACCAATTTTAGGTCGTTG 59.680 43.478 0.00 0.00 38.76 4.10
832 852 3.305744 CCCAACCAATTTTAGGTCGTTGG 60.306 47.826 9.32 9.32 46.32 3.77
841 861 0.599558 TAGGTCGTTGGTTGAGGACG 59.400 55.000 0.00 0.00 35.77 4.79
856 876 3.358076 GACGTCTTCTCGGGCAGGG 62.358 68.421 8.70 0.00 34.94 4.45
869 889 2.335712 GCAGGGGCAGTTGTAGCAC 61.336 63.158 0.00 0.00 40.72 4.40
900 920 2.685999 GGGCAGCCTTCCCTGATT 59.314 61.111 12.43 0.00 40.66 2.57
932 952 1.719600 GAACAGCATCAGTTCGAGCT 58.280 50.000 0.00 0.00 36.40 4.09
977 997 5.221904 CCATTTTGTCTCCCTTCCCATTTTT 60.222 40.000 0.00 0.00 0.00 1.94
1092 1114 3.793144 GCAGCTTTGTCTCCGGCG 61.793 66.667 0.00 0.00 0.00 6.46
1140 1162 1.812093 CTCCGTCTCGTCGCTCTCT 60.812 63.158 0.00 0.00 0.00 3.10
1141 1163 1.363145 CTCCGTCTCGTCGCTCTCTT 61.363 60.000 0.00 0.00 0.00 2.85
1152 1174 1.444119 CGCTCTCTTCCTCCCTCTCG 61.444 65.000 0.00 0.00 0.00 4.04
1155 1177 0.395036 TCTCTTCCTCCCTCTCGCAG 60.395 60.000 0.00 0.00 0.00 5.18
1230 1252 0.529833 CTCTCATGTCCGTCTGCAGT 59.470 55.000 14.67 0.00 0.00 4.40
1368 1396 4.742649 TCCGACGGCCTGCTCTCT 62.743 66.667 9.66 0.00 0.00 3.10
1462 1490 3.691342 CGGGGTCGTGCTCTTCCA 61.691 66.667 0.00 0.00 0.00 3.53
1503 1531 3.200887 GATGCTCGACTCCGGCGAT 62.201 63.158 9.30 0.00 37.13 4.58
1509 1537 2.482333 CGACTCCGGCGATCTCCTT 61.482 63.158 9.30 0.00 0.00 3.36
1573 1601 4.020617 CCTCCGAGGCCACTTGCA 62.021 66.667 5.01 0.00 43.89 4.08
1585 1613 1.108727 CACTTGCAGGTTCTTGGCCA 61.109 55.000 0.00 0.00 0.00 5.36
1722 1750 2.910479 ACTGTGTCGGCTCGTGGA 60.910 61.111 0.00 0.00 0.00 4.02
1977 2005 2.027625 CAAGGTCGAGGCGTTCCAC 61.028 63.158 0.00 0.00 33.74 4.02
2083 2111 3.976701 AACATGGCCTCCTTCCGCG 62.977 63.158 3.32 0.00 0.00 6.46
2124 2152 2.679716 GCCACCTTCCTCAGCCAT 59.320 61.111 0.00 0.00 0.00 4.40
2127 2155 0.679002 CCACCTTCCTCAGCCATGTG 60.679 60.000 0.00 0.00 0.00 3.21
2268 2299 2.821366 GTGTGGATGCTGGAGGCG 60.821 66.667 0.00 0.00 45.43 5.52
2376 2407 0.467384 AGGAGATGGGCATCGTGAAG 59.533 55.000 0.00 0.00 42.48 3.02
2623 2654 2.663188 GCGATCCATCCGACCTGC 60.663 66.667 0.00 0.00 0.00 4.85
2624 2655 2.355126 CGATCCATCCGACCTGCG 60.355 66.667 0.00 0.00 40.47 5.18
2625 2656 2.845550 CGATCCATCCGACCTGCGA 61.846 63.158 0.00 0.00 44.57 5.10
2626 2657 1.300233 GATCCATCCGACCTGCGAC 60.300 63.158 0.00 0.00 44.57 5.19
2627 2658 1.739338 GATCCATCCGACCTGCGACT 61.739 60.000 0.00 0.00 44.57 4.18
2637 2675 0.179000 ACCTGCGACTTGGATCATCC 59.821 55.000 0.00 0.00 36.96 3.51
2654 2692 2.113860 TCCATCTTGCCTTGTACAGC 57.886 50.000 0.00 0.00 0.00 4.40
2656 2694 2.025981 TCCATCTTGCCTTGTACAGCAT 60.026 45.455 10.26 0.00 39.11 3.79
2675 2713 1.375908 GTGCCACGGATTCAGCTCA 60.376 57.895 0.00 0.00 0.00 4.26
2676 2714 1.078918 TGCCACGGATTCAGCTCAG 60.079 57.895 0.00 0.00 0.00 3.35
2678 2716 1.086634 GCCACGGATTCAGCTCAGTC 61.087 60.000 0.00 0.00 0.00 3.51
2679 2717 0.460987 CCACGGATTCAGCTCAGTCC 60.461 60.000 0.00 0.00 0.00 3.85
2680 2718 0.247460 CACGGATTCAGCTCAGTCCA 59.753 55.000 0.00 0.00 0.00 4.02
2681 2719 0.534412 ACGGATTCAGCTCAGTCCAG 59.466 55.000 0.00 0.00 0.00 3.86
2682 2720 0.179089 CGGATTCAGCTCAGTCCAGG 60.179 60.000 0.00 0.00 0.00 4.45
2686 2724 0.035725 TTCAGCTCAGTCCAGGCATG 60.036 55.000 0.00 0.00 0.00 4.06
2700 2738 3.128242 CCAGGCATGCTTTTTCTCTGTAG 59.872 47.826 18.92 0.00 0.00 2.74
2717 2755 8.116651 TCTCTGTAGGAATCTCTGTATATTGC 57.883 38.462 0.00 0.00 0.00 3.56
2740 2783 3.676172 TGTTTTTCATACGAGTGGTAGCG 59.324 43.478 0.00 0.00 33.84 4.26
2770 2813 7.525688 TTAGATGACGATGATGAGTGTTTTC 57.474 36.000 0.00 0.00 0.00 2.29
2771 2814 4.872691 AGATGACGATGATGAGTGTTTTCC 59.127 41.667 0.00 0.00 0.00 3.13
2772 2815 4.271696 TGACGATGATGAGTGTTTTCCT 57.728 40.909 0.00 0.00 0.00 3.36
2773 2816 4.641396 TGACGATGATGAGTGTTTTCCTT 58.359 39.130 0.00 0.00 0.00 3.36
2774 2817 5.063204 TGACGATGATGAGTGTTTTCCTTT 58.937 37.500 0.00 0.00 0.00 3.11
2802 2845 2.811431 TGTGCGTGAACCCAATAAGAAG 59.189 45.455 0.00 0.00 0.00 2.85
2807 2850 3.007635 GTGAACCCAATAAGAAGACGGG 58.992 50.000 0.00 0.00 43.02 5.28
2847 2898 7.845066 TCTCTGATGTGAAGAAATCAATCTG 57.155 36.000 0.00 0.00 40.50 2.90
2851 2902 6.792326 TGATGTGAAGAAATCAATCTGCATC 58.208 36.000 0.00 0.00 40.50 3.91
2855 2906 5.011586 TGAAGAAATCAATCTGCATCCACA 58.988 37.500 0.00 0.00 34.30 4.17
2865 2916 0.107643 TGCATCCACAGTCGAACCAA 59.892 50.000 0.00 0.00 0.00 3.67
2910 2970 3.137913 AGATGTTGAGAATATGGCCTGCT 59.862 43.478 3.32 0.00 0.00 4.24
2913 2973 2.245159 TGAGAATATGGCCTGCTTCG 57.755 50.000 3.32 0.00 0.00 3.79
2922 2982 2.345244 CCTGCTTCGGCTCACTGT 59.655 61.111 0.00 0.00 42.37 3.55
2923 2983 1.739562 CCTGCTTCGGCTCACTGTC 60.740 63.158 0.00 0.00 42.37 3.51
2924 2984 1.005748 CTGCTTCGGCTCACTGTCA 60.006 57.895 0.00 0.00 42.37 3.58
2925 2985 0.390866 CTGCTTCGGCTCACTGTCAT 60.391 55.000 0.00 0.00 42.37 3.06
2928 2988 1.800805 CTTCGGCTCACTGTCATTGT 58.199 50.000 0.00 0.00 0.00 2.71
2929 2989 1.462283 CTTCGGCTCACTGTCATTGTG 59.538 52.381 0.00 0.00 36.82 3.33
2943 3015 3.927142 GTCATTGTGTGTCTAGGTGCTAC 59.073 47.826 0.00 0.00 0.00 3.58
2958 3030 2.499197 TGCTACCGCATCAAACTGAAA 58.501 42.857 0.00 0.00 42.25 2.69
2998 3073 4.082274 TGCGACGTCTCGAGTTAATTAA 57.918 40.909 14.70 0.00 43.06 1.40
2999 3074 4.093514 TGCGACGTCTCGAGTTAATTAAG 58.906 43.478 14.70 0.00 43.06 1.85
3000 3075 3.061994 GCGACGTCTCGAGTTAATTAAGC 60.062 47.826 14.70 5.81 43.06 3.09
3001 3076 4.341099 CGACGTCTCGAGTTAATTAAGCT 58.659 43.478 14.70 0.00 43.06 3.74
3016 3117 0.759346 AAGCTCGTCTTGTTGGAGGT 59.241 50.000 0.00 0.00 39.97 3.85
3072 3173 2.124529 GCTGGTTGCTAGGGAGGC 60.125 66.667 0.00 0.00 38.95 4.70
3101 3214 4.802999 CACTTTCTCTGAAAGGAAATGCC 58.197 43.478 19.86 0.00 34.31 4.40
3118 3231 1.875963 CCACAGGTTGGCAACGATC 59.124 57.895 22.95 10.35 39.07 3.69
3149 3262 2.321719 GGAATACCCACTCTCTCCCTC 58.678 57.143 0.00 0.00 34.14 4.30
3150 3263 2.359355 GGAATACCCACTCTCTCCCTCA 60.359 54.545 0.00 0.00 34.14 3.86
3151 3264 2.765689 ATACCCACTCTCTCCCTCAG 57.234 55.000 0.00 0.00 0.00 3.35
3152 3265 0.631753 TACCCACTCTCTCCCTCAGG 59.368 60.000 0.00 0.00 0.00 3.86
3153 3266 1.382420 CCCACTCTCTCCCTCAGGG 60.382 68.421 1.80 1.80 46.11 4.45
3154 3267 2.063378 CCACTCTCTCCCTCAGGGC 61.063 68.421 4.08 0.00 43.94 5.19
3158 3300 0.756442 CTCTCTCCCTCAGGGCTCAG 60.756 65.000 4.08 0.00 43.94 3.35
3160 3302 3.478274 CTCCCTCAGGGCTCAGGC 61.478 72.222 4.08 0.00 43.94 4.85
3171 3313 0.905357 GGCTCAGGCTACTCTTTCCA 59.095 55.000 0.00 0.00 38.73 3.53
3267 3430 2.679837 CGTCAGATTCAGATTTGGGTGG 59.320 50.000 0.00 0.00 0.00 4.61
3294 3457 2.098770 GCATTGCATCTGAAGAACCCTC 59.901 50.000 3.15 0.00 0.00 4.30
3305 3468 3.511146 TGAAGAACCCTCCATGCATTTTC 59.489 43.478 0.00 0.00 0.00 2.29
3306 3469 3.463048 AGAACCCTCCATGCATTTTCT 57.537 42.857 0.00 0.00 0.00 2.52
3309 3472 4.221482 AGAACCCTCCATGCATTTTCTTTC 59.779 41.667 0.00 0.00 0.00 2.62
3316 3479 4.281435 TCCATGCATTTTCTTTCTCTTGCA 59.719 37.500 0.00 0.00 43.42 4.08
3325 3488 5.652744 TTCTTTCTCTTGCAACGACTAAC 57.347 39.130 0.00 0.00 0.00 2.34
3327 3490 3.462483 TTCTCTTGCAACGACTAACCA 57.538 42.857 0.00 0.00 0.00 3.67
3334 3497 1.135689 GCAACGACTAACCATGCAAGG 60.136 52.381 6.39 6.39 37.00 3.61
3401 3571 7.549134 GGTCAACTGTTGATAATCATGTACTCA 59.451 37.037 24.44 0.00 42.47 3.41
3402 3572 8.935844 GTCAACTGTTGATAATCATGTACTCAA 58.064 33.333 24.44 0.00 42.47 3.02
3403 3573 9.154847 TCAACTGTTGATAATCATGTACTCAAG 57.845 33.333 18.69 0.00 34.08 3.02
3404 3574 8.393366 CAACTGTTGATAATCATGTACTCAAGG 58.607 37.037 15.26 0.00 0.00 3.61
3405 3575 7.050377 ACTGTTGATAATCATGTACTCAAGGG 58.950 38.462 0.00 0.00 0.00 3.95
3467 3661 7.503549 GTACAAATGTACTACTTCCTTCGTC 57.496 40.000 14.84 0.00 45.47 4.20
3468 3662 5.476614 ACAAATGTACTACTTCCTTCGTCC 58.523 41.667 0.00 0.00 0.00 4.79
3469 3663 4.732672 AATGTACTACTTCCTTCGTCCC 57.267 45.455 0.00 0.00 0.00 4.46
3470 3664 3.159213 TGTACTACTTCCTTCGTCCCA 57.841 47.619 0.00 0.00 0.00 4.37
3471 3665 3.705051 TGTACTACTTCCTTCGTCCCAT 58.295 45.455 0.00 0.00 0.00 4.00
3472 3666 4.858850 TGTACTACTTCCTTCGTCCCATA 58.141 43.478 0.00 0.00 0.00 2.74
3473 3667 5.263599 TGTACTACTTCCTTCGTCCCATAA 58.736 41.667 0.00 0.00 0.00 1.90
3474 3668 5.895534 TGTACTACTTCCTTCGTCCCATAAT 59.104 40.000 0.00 0.00 0.00 1.28
3475 3669 7.062322 TGTACTACTTCCTTCGTCCCATAATA 58.938 38.462 0.00 0.00 0.00 0.98
3476 3670 7.727186 TGTACTACTTCCTTCGTCCCATAATAT 59.273 37.037 0.00 0.00 0.00 1.28
3477 3671 9.236006 GTACTACTTCCTTCGTCCCATAATATA 57.764 37.037 0.00 0.00 0.00 0.86
3478 3672 8.716674 ACTACTTCCTTCGTCCCATAATATAA 57.283 34.615 0.00 0.00 0.00 0.98
3479 3673 8.804204 ACTACTTCCTTCGTCCCATAATATAAG 58.196 37.037 0.00 0.00 0.00 1.73
3480 3674 7.850935 ACTTCCTTCGTCCCATAATATAAGA 57.149 36.000 0.00 0.00 0.00 2.10
3481 3675 8.258850 ACTTCCTTCGTCCCATAATATAAGAA 57.741 34.615 0.00 0.00 0.00 2.52
3482 3676 8.881262 ACTTCCTTCGTCCCATAATATAAGAAT 58.119 33.333 0.00 0.00 0.00 2.40
3483 3677 9.155975 CTTCCTTCGTCCCATAATATAAGAATG 57.844 37.037 0.00 0.00 0.00 2.67
3484 3678 8.202461 TCCTTCGTCCCATAATATAAGAATGT 57.798 34.615 0.00 0.00 0.00 2.71
3485 3679 8.656806 TCCTTCGTCCCATAATATAAGAATGTT 58.343 33.333 0.00 0.00 0.00 2.71
3486 3680 9.284968 CCTTCGTCCCATAATATAAGAATGTTT 57.715 33.333 0.00 0.00 0.00 2.83
3502 3696 8.603242 AAGAATGTTTTTGACACGAGTATAGT 57.397 30.769 0.00 0.00 42.04 2.12
3503 3697 9.701098 AAGAATGTTTTTGACACGAGTATAGTA 57.299 29.630 0.00 0.00 42.04 1.82
3504 3698 9.136952 AGAATGTTTTTGACACGAGTATAGTAC 57.863 33.333 0.00 0.00 42.04 2.73
3505 3699 8.821147 AATGTTTTTGACACGAGTATAGTACA 57.179 30.769 0.00 0.00 42.04 2.90
3506 3700 7.862741 TGTTTTTGACACGAGTATAGTACAG 57.137 36.000 0.00 0.00 32.00 2.74
3507 3701 7.428020 TGTTTTTGACACGAGTATAGTACAGT 58.572 34.615 0.00 0.00 32.00 3.55
3508 3702 7.380333 TGTTTTTGACACGAGTATAGTACAGTG 59.620 37.037 0.00 11.47 41.80 3.66
3510 3704 6.564709 TTGACACGAGTATAGTACAGTGTT 57.435 37.500 0.00 0.00 45.66 3.32
3511 3705 7.671495 TTGACACGAGTATAGTACAGTGTTA 57.329 36.000 0.00 12.40 45.66 2.41
3512 3706 7.065216 TGACACGAGTATAGTACAGTGTTAC 57.935 40.000 0.00 0.00 45.66 2.50
3513 3707 6.650390 TGACACGAGTATAGTACAGTGTTACA 59.350 38.462 0.00 11.23 45.66 2.41
3514 3708 7.173047 TGACACGAGTATAGTACAGTGTTACAA 59.827 37.037 0.00 0.00 45.66 2.41
3515 3709 7.874940 ACACGAGTATAGTACAGTGTTACAAA 58.125 34.615 0.00 0.00 44.40 2.83
3516 3710 8.517878 ACACGAGTATAGTACAGTGTTACAAAT 58.482 33.333 0.00 0.00 44.40 2.32
3517 3711 8.795341 CACGAGTATAGTACAGTGTTACAAATG 58.205 37.037 0.00 0.00 35.96 2.32
3518 3712 8.517878 ACGAGTATAGTACAGTGTTACAAATGT 58.482 33.333 0.00 9.03 0.00 2.71
3519 3713 9.350357 CGAGTATAGTACAGTGTTACAAATGTT 57.650 33.333 0.00 0.00 0.00 2.71
3541 3735 9.753674 ATGTTTTTATATTTTGAGACAGAGGGA 57.246 29.630 0.00 0.00 0.00 4.20
3542 3736 9.231297 TGTTTTTATATTTTGAGACAGAGGGAG 57.769 33.333 0.00 0.00 0.00 4.30
3543 3737 9.232473 GTTTTTATATTTTGAGACAGAGGGAGT 57.768 33.333 0.00 0.00 0.00 3.85
3546 3740 9.488762 TTTATATTTTGAGACAGAGGGAGTAGA 57.511 33.333 0.00 0.00 0.00 2.59
3547 3741 7.979786 ATATTTTGAGACAGAGGGAGTAGAA 57.020 36.000 0.00 0.00 0.00 2.10
3548 3742 6.882768 ATTTTGAGACAGAGGGAGTAGAAT 57.117 37.500 0.00 0.00 0.00 2.40
3549 3743 5.667539 TTTGAGACAGAGGGAGTAGAATG 57.332 43.478 0.00 0.00 0.00 2.67
3550 3744 4.592997 TGAGACAGAGGGAGTAGAATGA 57.407 45.455 0.00 0.00 0.00 2.57
3551 3745 4.274147 TGAGACAGAGGGAGTAGAATGAC 58.726 47.826 0.00 0.00 0.00 3.06
3552 3746 4.263949 TGAGACAGAGGGAGTAGAATGACA 60.264 45.833 0.00 0.00 0.00 3.58
3553 3747 4.277476 AGACAGAGGGAGTAGAATGACAG 58.723 47.826 0.00 0.00 0.00 3.51
3554 3748 4.017958 AGACAGAGGGAGTAGAATGACAGA 60.018 45.833 0.00 0.00 0.00 3.41
3555 3749 4.277476 ACAGAGGGAGTAGAATGACAGAG 58.723 47.826 0.00 0.00 0.00 3.35
3556 3750 3.636300 CAGAGGGAGTAGAATGACAGAGG 59.364 52.174 0.00 0.00 0.00 3.69
3557 3751 2.962421 GAGGGAGTAGAATGACAGAGGG 59.038 54.545 0.00 0.00 0.00 4.30
3558 3752 1.414550 GGGAGTAGAATGACAGAGGGC 59.585 57.143 0.00 0.00 0.00 5.19
3559 3753 1.067821 GGAGTAGAATGACAGAGGGCG 59.932 57.143 0.00 0.00 0.00 6.13
3560 3754 1.067821 GAGTAGAATGACAGAGGGCGG 59.932 57.143 0.00 0.00 0.00 6.13
3561 3755 0.105039 GTAGAATGACAGAGGGCGGG 59.895 60.000 0.00 0.00 0.00 6.13
3562 3756 0.032515 TAGAATGACAGAGGGCGGGA 60.033 55.000 0.00 0.00 0.00 5.14
3563 3757 0.909610 AGAATGACAGAGGGCGGGAA 60.910 55.000 0.00 0.00 0.00 3.97
3564 3758 0.744771 GAATGACAGAGGGCGGGAAC 60.745 60.000 0.00 0.00 0.00 3.62
3565 3759 1.488705 AATGACAGAGGGCGGGAACA 61.489 55.000 0.00 0.00 0.00 3.18
3566 3760 1.903877 ATGACAGAGGGCGGGAACAG 61.904 60.000 0.00 0.00 0.00 3.16
3567 3761 3.959991 GACAGAGGGCGGGAACAGC 62.960 68.421 0.00 0.00 0.00 4.40
3578 3772 4.465512 GAACAGCGGCATGGCGTG 62.466 66.667 37.28 32.45 38.18 5.34
3586 3780 2.202650 GCATGGCGTGGCATGTTC 60.203 61.111 29.50 15.50 0.00 3.18
3587 3781 2.703798 GCATGGCGTGGCATGTTCT 61.704 57.895 29.50 0.00 0.00 3.01
3588 3782 1.430632 CATGGCGTGGCATGTTCTC 59.569 57.895 23.71 0.00 0.00 2.87
3589 3783 1.750399 ATGGCGTGGCATGTTCTCC 60.750 57.895 8.23 1.32 0.00 3.71
3590 3784 3.134127 GGCGTGGCATGTTCTCCC 61.134 66.667 8.75 0.00 0.00 4.30
3591 3785 2.045926 GCGTGGCATGTTCTCCCT 60.046 61.111 8.75 0.00 0.00 4.20
3592 3786 2.401766 GCGTGGCATGTTCTCCCTG 61.402 63.158 8.75 0.00 0.00 4.45
3593 3787 1.296392 CGTGGCATGTTCTCCCTGA 59.704 57.895 0.00 0.00 0.00 3.86
3594 3788 1.021390 CGTGGCATGTTCTCCCTGAC 61.021 60.000 0.00 0.00 0.00 3.51
3595 3789 0.678048 GTGGCATGTTCTCCCTGACC 60.678 60.000 0.00 0.00 0.00 4.02
3596 3790 0.842030 TGGCATGTTCTCCCTGACCT 60.842 55.000 0.00 0.00 0.00 3.85
3597 3791 0.393537 GGCATGTTCTCCCTGACCTG 60.394 60.000 0.00 0.00 0.00 4.00
3598 3792 0.393537 GCATGTTCTCCCTGACCTGG 60.394 60.000 0.00 0.00 0.00 4.45
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
4 5 5.047731 GCAGAGATGGGCTTTAAGAAAACTT 60.048 40.000 0.00 0.00 0.00 2.66
11 12 2.295885 CTGGCAGAGATGGGCTTTAAG 58.704 52.381 9.42 0.00 0.00 1.85
13 14 0.107017 GCTGGCAGAGATGGGCTTTA 60.107 55.000 20.86 0.00 0.00 1.85
16 17 4.172512 CGCTGGCAGAGATGGGCT 62.173 66.667 20.86 0.00 0.00 5.19
17 18 4.166888 TCGCTGGCAGAGATGGGC 62.167 66.667 20.86 0.00 0.00 5.36
18 19 1.395045 TACTCGCTGGCAGAGATGGG 61.395 60.000 21.25 12.33 38.97 4.00
19 20 0.678395 ATACTCGCTGGCAGAGATGG 59.322 55.000 21.25 13.04 38.97 3.51
22 23 1.406898 CAGAATACTCGCTGGCAGAGA 59.593 52.381 20.86 20.31 38.97 3.10
29 30 1.929836 GTTGCTCCAGAATACTCGCTG 59.070 52.381 0.00 0.00 0.00 5.18
32 33 3.701241 GAGAGTTGCTCCAGAATACTCG 58.299 50.000 0.00 0.00 40.03 4.18
46 47 6.434028 TCATTTGGTCTTAATTGGGAGAGTTG 59.566 38.462 0.00 0.00 0.00 3.16
60 61 3.259123 GGGCAAGTGAATCATTTGGTCTT 59.741 43.478 17.99 0.00 32.85 3.01
64 65 3.674138 CGAAGGGCAAGTGAATCATTTGG 60.674 47.826 17.99 2.96 32.85 3.28
66 67 2.094545 GCGAAGGGCAAGTGAATCATTT 60.095 45.455 0.00 0.00 42.87 2.32
85 86 4.067192 TCAAGATGATAATGTCCATGGCG 58.933 43.478 6.96 0.00 0.00 5.69
103 104 4.217510 TCCAAATGGCCCAAGATATCAAG 58.782 43.478 0.00 0.00 34.44 3.02
147 148 0.879090 GTTGGGCGTAACTCCTTTGG 59.121 55.000 0.00 0.00 0.00 3.28
150 151 0.036306 CAGGTTGGGCGTAACTCCTT 59.964 55.000 3.76 0.00 0.00 3.36
152 153 1.376812 CCAGGTTGGGCGTAACTCC 60.377 63.158 3.76 0.00 32.67 3.85
160 161 0.468400 TGGTGTAAACCAGGTTGGGC 60.468 55.000 5.30 0.00 43.37 5.36
178 179 5.021033 AGAGCAACATATGAGTTCCTCTG 57.979 43.478 10.38 0.00 43.22 3.35
194 195 1.003580 GGACCCATTCTGACAGAGCAA 59.996 52.381 5.10 0.00 0.00 3.91
196 197 0.460987 CGGACCCATTCTGACAGAGC 60.461 60.000 5.10 0.00 31.20 4.09
218 219 4.214980 AGTTGCAAAGATCGTGTGAAAG 57.785 40.909 0.00 0.00 0.00 2.62
224 225 3.257393 AGCTCTAGTTGCAAAGATCGTG 58.743 45.455 0.00 0.00 0.00 4.35
227 228 4.267452 CGAAGAGCTCTAGTTGCAAAGATC 59.733 45.833 18.59 3.00 0.00 2.75
272 273 0.107945 GGCTGCCTAGTCACCTCTTG 60.108 60.000 12.43 0.00 0.00 3.02
318 319 9.609346 TGGTCTAAAACTATGAGCTAAATAACC 57.391 33.333 0.00 0.00 0.00 2.85
473 477 1.820519 TCTTTGATGGATGCTTGCACC 59.179 47.619 0.00 2.63 0.00 5.01
474 478 3.508762 CTTCTTTGATGGATGCTTGCAC 58.491 45.455 0.00 0.00 0.00 4.57
475 479 2.494471 CCTTCTTTGATGGATGCTTGCA 59.506 45.455 0.00 0.00 0.00 4.08
476 480 2.737679 GCCTTCTTTGATGGATGCTTGC 60.738 50.000 4.02 0.00 0.00 4.01
477 481 2.494471 TGCCTTCTTTGATGGATGCTTG 59.506 45.455 4.02 0.00 0.00 4.01
480 484 3.814005 AATGCCTTCTTTGATGGATGC 57.186 42.857 4.02 0.00 0.00 3.91
542 548 2.143122 CGTATCTGGTTGCACTTGTGT 58.857 47.619 2.61 0.00 0.00 3.72
543 549 2.096268 CACGTATCTGGTTGCACTTGTG 60.096 50.000 0.00 0.00 0.00 3.33
623 633 6.545298 AGGTAGTAGTAATTTACCGAGTCCAG 59.455 42.308 2.92 0.00 41.34 3.86
628 638 6.909357 CGTTGAGGTAGTAGTAATTTACCGAG 59.091 42.308 2.92 0.00 41.34 4.63
631 641 7.699812 CACTCGTTGAGGTAGTAGTAATTTACC 59.300 40.741 2.92 0.00 37.66 2.85
700 715 6.002653 AGGTCAAAACTCTAAAGGTTGAGT 57.997 37.500 0.00 0.00 44.40 3.41
711 726 4.823989 CCAGTGAATGAAGGTCAAAACTCT 59.176 41.667 0.00 0.00 0.00 3.24
768 788 1.134098 CACAAGGGAGACAAGTGGTGT 60.134 52.381 0.00 0.00 45.74 4.16
820 840 2.546373 CGTCCTCAACCAACGACCTAAA 60.546 50.000 0.00 0.00 38.65 1.85
831 851 0.109226 CCGAGAAGACGTCCTCAACC 60.109 60.000 16.22 4.43 0.00 3.77
832 852 0.109226 CCCGAGAAGACGTCCTCAAC 60.109 60.000 16.22 8.70 0.00 3.18
833 853 1.874345 GCCCGAGAAGACGTCCTCAA 61.874 60.000 16.22 0.00 0.00 3.02
834 854 2.341101 GCCCGAGAAGACGTCCTCA 61.341 63.158 16.22 0.00 0.00 3.86
841 861 4.475135 GCCCCTGCCCGAGAAGAC 62.475 72.222 0.00 0.00 0.00 3.01
856 876 2.380410 CCGTCGTGCTACAACTGCC 61.380 63.158 0.00 0.00 0.00 4.85
932 952 0.178981 AAGAGGAGCAAAGCCAAGCA 60.179 50.000 0.00 0.00 0.00 3.91
977 997 1.076014 TGGTACTGGAGCGGAGACA 59.924 57.895 0.00 0.00 0.00 3.41
1140 1162 3.077556 GGCTGCGAGAGGGAGGAA 61.078 66.667 0.00 0.00 34.11 3.36
1462 1490 2.029666 GACCGCAGACACAGCAGT 59.970 61.111 0.00 0.00 0.00 4.40
1569 1597 1.114722 CCTTGGCCAAGAACCTGCAA 61.115 55.000 41.10 6.66 40.79 4.08
1573 1601 0.402121 GACTCCTTGGCCAAGAACCT 59.598 55.000 41.10 22.49 40.79 3.50
2083 2111 4.561731 GGCTATCTCGGCGATGAC 57.438 61.111 11.27 0.00 33.48 3.06
2151 2179 4.920112 TCCGTGCGGGTGTTGGTG 62.920 66.667 10.94 0.00 37.00 4.17
2152 2180 4.619227 CTCCGTGCGGGTGTTGGT 62.619 66.667 10.94 0.00 37.00 3.67
2187 2215 3.175240 CCGACGTTGCAGAGCTCG 61.175 66.667 8.37 4.60 34.45 5.03
2215 2246 4.124943 CCCGACCTCCTCCCTCGA 62.125 72.222 0.00 0.00 0.00 4.04
2570 2601 3.195698 GGAACACGCCGAGCATCC 61.196 66.667 0.00 0.00 0.00 3.51
2637 2675 2.751259 ACATGCTGTACAAGGCAAGATG 59.249 45.455 16.35 11.66 41.90 2.90
2654 2692 1.028330 AGCTGAATCCGTGGCACATG 61.028 55.000 19.09 8.15 44.52 3.21
2656 2694 1.375908 GAGCTGAATCCGTGGCACA 60.376 57.895 19.09 0.00 0.00 4.57
2659 2697 1.078848 ACTGAGCTGAATCCGTGGC 60.079 57.895 0.00 0.00 0.00 5.01
2675 2713 2.165998 GAGAAAAAGCATGCCTGGACT 58.834 47.619 15.66 9.02 0.00 3.85
2676 2714 2.094854 CAGAGAAAAAGCATGCCTGGAC 60.095 50.000 15.66 3.83 0.00 4.02
2678 2716 1.891150 ACAGAGAAAAAGCATGCCTGG 59.109 47.619 15.66 1.20 0.00 4.45
2679 2717 3.128242 CCTACAGAGAAAAAGCATGCCTG 59.872 47.826 15.66 14.65 0.00 4.85
2680 2718 3.009473 TCCTACAGAGAAAAAGCATGCCT 59.991 43.478 15.66 3.13 0.00 4.75
2681 2719 3.347216 TCCTACAGAGAAAAAGCATGCC 58.653 45.455 15.66 0.00 0.00 4.40
2682 2720 5.356470 AGATTCCTACAGAGAAAAAGCATGC 59.644 40.000 10.51 10.51 0.00 4.06
2686 2724 6.169800 ACAGAGATTCCTACAGAGAAAAAGC 58.830 40.000 0.00 0.00 0.00 3.51
2700 2738 8.677300 TGAAAAACAGCAATATACAGAGATTCC 58.323 33.333 0.00 0.00 0.00 3.01
2717 2755 4.201589 CGCTACCACTCGTATGAAAAACAG 60.202 45.833 0.00 0.00 0.00 3.16
2740 2783 8.079203 ACACTCATCATCGTCATCTAAATCTAC 58.921 37.037 0.00 0.00 0.00 2.59
2770 2813 2.148916 TCACGCACACTGACTAAAGG 57.851 50.000 0.00 0.00 0.00 3.11
2771 2814 2.221055 GGTTCACGCACACTGACTAAAG 59.779 50.000 0.00 0.00 0.00 1.85
2772 2815 2.206750 GGTTCACGCACACTGACTAAA 58.793 47.619 0.00 0.00 0.00 1.85
2773 2816 1.539496 GGGTTCACGCACACTGACTAA 60.539 52.381 0.00 0.00 0.00 2.24
2774 2817 0.032952 GGGTTCACGCACACTGACTA 59.967 55.000 0.00 0.00 0.00 2.59
2802 2845 8.552034 CAGAGATTAATTACAATCTTTCCCGTC 58.448 37.037 5.20 0.00 43.66 4.79
2847 2898 1.398390 GATTGGTTCGACTGTGGATGC 59.602 52.381 0.00 0.00 0.00 3.91
2886 2946 4.340381 GCAGGCCATATTCTCAACATCTTT 59.660 41.667 5.01 0.00 0.00 2.52
2910 2970 1.202639 ACACAATGACAGTGAGCCGAA 60.203 47.619 10.34 0.00 40.16 4.30
2913 2973 1.532868 GACACACAATGACAGTGAGCC 59.467 52.381 10.34 0.00 40.16 4.70
2920 2980 2.368548 AGCACCTAGACACACAATGACA 59.631 45.455 0.00 0.00 0.00 3.58
2922 2982 3.056107 GGTAGCACCTAGACACACAATGA 60.056 47.826 0.00 0.00 34.73 2.57
2923 2983 3.262420 GGTAGCACCTAGACACACAATG 58.738 50.000 0.00 0.00 34.73 2.82
2924 2984 2.094182 CGGTAGCACCTAGACACACAAT 60.094 50.000 0.00 0.00 35.66 2.71
2925 2985 1.271379 CGGTAGCACCTAGACACACAA 59.729 52.381 0.00 0.00 35.66 3.33
2928 2988 1.888018 GCGGTAGCACCTAGACACA 59.112 57.895 0.00 0.00 44.35 3.72
2929 2989 4.808649 GCGGTAGCACCTAGACAC 57.191 61.111 0.00 0.00 44.35 3.67
2943 3015 7.306167 GCATTAATACATTTCAGTTTGATGCGG 60.306 37.037 0.00 0.00 0.00 5.69
2952 3024 3.951037 TGCCGGCATTAATACATTTCAGT 59.049 39.130 29.03 0.00 0.00 3.41
2954 3026 4.400884 AGTTGCCGGCATTAATACATTTCA 59.599 37.500 33.25 7.34 0.00 2.69
2955 3027 4.739716 CAGTTGCCGGCATTAATACATTTC 59.260 41.667 33.25 1.90 0.00 2.17
2958 3030 2.034558 GCAGTTGCCGGCATTAATACAT 59.965 45.455 33.25 11.73 34.31 2.29
2998 3073 0.318762 GACCTCCAACAAGACGAGCT 59.681 55.000 0.00 0.00 0.00 4.09
2999 3074 0.033504 TGACCTCCAACAAGACGAGC 59.966 55.000 0.00 0.00 0.00 5.03
3000 3075 1.341531 ACTGACCTCCAACAAGACGAG 59.658 52.381 0.00 0.00 0.00 4.18
3001 3076 1.340248 GACTGACCTCCAACAAGACGA 59.660 52.381 0.00 0.00 0.00 4.20
3003 3078 2.760374 CTGACTGACCTCCAACAAGAC 58.240 52.381 0.00 0.00 0.00 3.01
3016 3117 1.315981 CCTACTGCCGAGCTGACTGA 61.316 60.000 0.00 0.00 0.00 3.41
3072 3173 1.888215 TTCAGAGAAAGTGCCTGCTG 58.112 50.000 0.00 0.00 0.00 4.41
3101 3214 0.798776 GAGATCGTTGCCAACCTGTG 59.201 55.000 1.21 0.00 0.00 3.66
3135 3248 4.371699 CCTGAGGGAGAGAGTGGG 57.628 66.667 0.00 0.00 33.58 4.61
3146 3259 1.382420 AGTAGCCTGAGCCCTGAGG 60.382 63.158 0.00 0.00 41.25 3.86
3147 3260 0.396974 AGAGTAGCCTGAGCCCTGAG 60.397 60.000 0.00 0.00 41.25 3.35
3149 3262 0.908198 AAAGAGTAGCCTGAGCCCTG 59.092 55.000 0.00 0.00 41.25 4.45
3150 3263 1.199615 GAAAGAGTAGCCTGAGCCCT 58.800 55.000 0.00 0.00 41.25 5.19
3151 3264 0.179234 GGAAAGAGTAGCCTGAGCCC 59.821 60.000 0.00 0.00 41.25 5.19
3152 3265 0.905357 TGGAAAGAGTAGCCTGAGCC 59.095 55.000 0.00 0.00 41.25 4.70
3153 3266 1.827969 TCTGGAAAGAGTAGCCTGAGC 59.172 52.381 0.00 0.00 40.32 4.26
3154 3267 4.081198 ACAATCTGGAAAGAGTAGCCTGAG 60.081 45.833 0.00 0.00 33.94 3.35
3158 3300 4.837972 AGAACAATCTGGAAAGAGTAGCC 58.162 43.478 0.00 0.00 33.59 3.93
3160 3302 6.706295 AGGAAGAACAATCTGGAAAGAGTAG 58.294 40.000 0.00 0.00 35.59 2.57
3201 3346 0.747644 ATGCCGGTTCATGAATGCGA 60.748 50.000 12.12 6.76 0.00 5.10
3267 3430 3.273434 TCTTCAGATGCAATGCTACACC 58.727 45.455 6.82 0.00 0.00 4.16
3294 3457 4.562082 TGCAAGAGAAAGAAAATGCATGG 58.438 39.130 0.00 0.00 38.73 3.66
3305 3468 3.807622 TGGTTAGTCGTTGCAAGAGAAAG 59.192 43.478 0.00 0.00 0.00 2.62
3306 3469 3.799366 TGGTTAGTCGTTGCAAGAGAAA 58.201 40.909 0.00 0.00 0.00 2.52
3309 3472 2.159653 GCATGGTTAGTCGTTGCAAGAG 60.160 50.000 0.00 0.00 0.00 2.85
3316 3479 2.851263 TCCTTGCATGGTTAGTCGTT 57.149 45.000 17.54 0.00 0.00 3.85
3334 3497 4.213482 GGGTTACGGATAACAATGCAGATC 59.787 45.833 0.00 0.00 42.26 2.75
3401 3571 1.002257 TGACGCATCATGCACCCTT 60.002 52.632 11.00 0.00 45.36 3.95
3402 3572 1.746615 GTGACGCATCATGCACCCT 60.747 57.895 11.00 0.00 45.36 4.34
3403 3573 2.793946 GTGACGCATCATGCACCC 59.206 61.111 11.00 0.00 45.36 4.61
3404 3574 2.390599 ACGTGACGCATCATGCACC 61.391 57.895 11.00 0.53 45.36 5.01
3405 3575 1.225827 CACGTGACGCATCATGCAC 60.226 57.895 10.90 3.59 45.36 4.57
3446 3640 4.868734 GGGACGAAGGAAGTAGTACATTTG 59.131 45.833 2.52 0.00 0.00 2.32
3452 3646 9.812347 TTATATTATGGGACGAAGGAAGTAGTA 57.188 33.333 0.00 0.00 0.00 1.82
3453 3647 8.716674 TTATATTATGGGACGAAGGAAGTAGT 57.283 34.615 0.00 0.00 0.00 2.73
3454 3648 9.021807 TCTTATATTATGGGACGAAGGAAGTAG 57.978 37.037 0.00 0.00 0.00 2.57
3455 3649 8.945195 TCTTATATTATGGGACGAAGGAAGTA 57.055 34.615 0.00 0.00 0.00 2.24
3456 3650 7.850935 TCTTATATTATGGGACGAAGGAAGT 57.149 36.000 0.00 0.00 0.00 3.01
3457 3651 9.155975 CATTCTTATATTATGGGACGAAGGAAG 57.844 37.037 0.00 0.00 0.00 3.46
3458 3652 8.656806 ACATTCTTATATTATGGGACGAAGGAA 58.343 33.333 0.00 0.00 0.00 3.36
3459 3653 8.202461 ACATTCTTATATTATGGGACGAAGGA 57.798 34.615 0.00 0.00 0.00 3.36
3460 3654 8.848474 AACATTCTTATATTATGGGACGAAGG 57.152 34.615 0.00 0.00 0.00 3.46
3476 3670 9.701098 ACTATACTCGTGTCAAAAACATTCTTA 57.299 29.630 0.00 0.00 40.80 2.10
3477 3671 8.603242 ACTATACTCGTGTCAAAAACATTCTT 57.397 30.769 0.00 0.00 40.80 2.52
3478 3672 9.136952 GTACTATACTCGTGTCAAAAACATTCT 57.863 33.333 0.00 0.00 40.80 2.40
3479 3673 8.918658 TGTACTATACTCGTGTCAAAAACATTC 58.081 33.333 0.00 0.00 40.80 2.67
3480 3674 8.821147 TGTACTATACTCGTGTCAAAAACATT 57.179 30.769 0.00 0.00 40.80 2.71
3481 3675 8.086522 ACTGTACTATACTCGTGTCAAAAACAT 58.913 33.333 0.00 0.00 40.80 2.71
3482 3676 7.380333 CACTGTACTATACTCGTGTCAAAAACA 59.620 37.037 0.00 0.00 34.78 2.83
3483 3677 7.380602 ACACTGTACTATACTCGTGTCAAAAAC 59.619 37.037 0.00 0.00 38.60 2.43
3484 3678 7.428020 ACACTGTACTATACTCGTGTCAAAAA 58.572 34.615 0.00 0.00 38.60 1.94
3485 3679 6.973843 ACACTGTACTATACTCGTGTCAAAA 58.026 36.000 0.00 0.00 38.60 2.44
3486 3680 6.564709 ACACTGTACTATACTCGTGTCAAA 57.435 37.500 0.00 0.00 38.60 2.69
3487 3681 6.564709 AACACTGTACTATACTCGTGTCAA 57.435 37.500 11.99 0.00 40.44 3.18
3488 3682 6.650390 TGTAACACTGTACTATACTCGTGTCA 59.350 38.462 11.99 7.00 40.44 3.58
3489 3683 7.065216 TGTAACACTGTACTATACTCGTGTC 57.935 40.000 11.99 5.32 40.44 3.67
3490 3684 7.439157 TTGTAACACTGTACTATACTCGTGT 57.561 36.000 0.00 0.00 41.86 4.49
3491 3685 8.795341 CATTTGTAACACTGTACTATACTCGTG 58.205 37.037 0.00 0.00 37.07 4.35
3492 3686 8.517878 ACATTTGTAACACTGTACTATACTCGT 58.482 33.333 0.00 0.00 0.00 4.18
3493 3687 8.906636 ACATTTGTAACACTGTACTATACTCG 57.093 34.615 0.00 0.00 0.00 4.18
3515 3709 9.753674 TCCCTCTGTCTCAAAATATAAAAACAT 57.246 29.630 0.00 0.00 0.00 2.71
3516 3710 9.231297 CTCCCTCTGTCTCAAAATATAAAAACA 57.769 33.333 0.00 0.00 0.00 2.83
3517 3711 9.232473 ACTCCCTCTGTCTCAAAATATAAAAAC 57.768 33.333 0.00 0.00 0.00 2.43
3520 3714 9.488762 TCTACTCCCTCTGTCTCAAAATATAAA 57.511 33.333 0.00 0.00 0.00 1.40
3521 3715 9.488762 TTCTACTCCCTCTGTCTCAAAATATAA 57.511 33.333 0.00 0.00 0.00 0.98
3522 3716 9.661954 ATTCTACTCCCTCTGTCTCAAAATATA 57.338 33.333 0.00 0.00 0.00 0.86
3523 3717 7.979786 TTCTACTCCCTCTGTCTCAAAATAT 57.020 36.000 0.00 0.00 0.00 1.28
3524 3718 7.619698 TCATTCTACTCCCTCTGTCTCAAAATA 59.380 37.037 0.00 0.00 0.00 1.40
3525 3719 6.441924 TCATTCTACTCCCTCTGTCTCAAAAT 59.558 38.462 0.00 0.00 0.00 1.82
3526 3720 5.780282 TCATTCTACTCCCTCTGTCTCAAAA 59.220 40.000 0.00 0.00 0.00 2.44
3527 3721 5.186021 GTCATTCTACTCCCTCTGTCTCAAA 59.814 44.000 0.00 0.00 0.00 2.69
3528 3722 4.707448 GTCATTCTACTCCCTCTGTCTCAA 59.293 45.833 0.00 0.00 0.00 3.02
3529 3723 4.263949 TGTCATTCTACTCCCTCTGTCTCA 60.264 45.833 0.00 0.00 0.00 3.27
3530 3724 4.274147 TGTCATTCTACTCCCTCTGTCTC 58.726 47.826 0.00 0.00 0.00 3.36
3531 3725 4.017958 TCTGTCATTCTACTCCCTCTGTCT 60.018 45.833 0.00 0.00 0.00 3.41
3532 3726 4.274147 TCTGTCATTCTACTCCCTCTGTC 58.726 47.826 0.00 0.00 0.00 3.51
3533 3727 4.277476 CTCTGTCATTCTACTCCCTCTGT 58.723 47.826 0.00 0.00 0.00 3.41
3534 3728 3.636300 CCTCTGTCATTCTACTCCCTCTG 59.364 52.174 0.00 0.00 0.00 3.35
3535 3729 3.373658 CCCTCTGTCATTCTACTCCCTCT 60.374 52.174 0.00 0.00 0.00 3.69
3536 3730 2.962421 CCCTCTGTCATTCTACTCCCTC 59.038 54.545 0.00 0.00 0.00 4.30
3537 3731 2.957312 GCCCTCTGTCATTCTACTCCCT 60.957 54.545 0.00 0.00 0.00 4.20
3538 3732 1.414550 GCCCTCTGTCATTCTACTCCC 59.585 57.143 0.00 0.00 0.00 4.30
3539 3733 1.067821 CGCCCTCTGTCATTCTACTCC 59.932 57.143 0.00 0.00 0.00 3.85
3540 3734 1.067821 CCGCCCTCTGTCATTCTACTC 59.932 57.143 0.00 0.00 0.00 2.59
3541 3735 1.115467 CCGCCCTCTGTCATTCTACT 58.885 55.000 0.00 0.00 0.00 2.57
3542 3736 0.105039 CCCGCCCTCTGTCATTCTAC 59.895 60.000 0.00 0.00 0.00 2.59
3543 3737 0.032515 TCCCGCCCTCTGTCATTCTA 60.033 55.000 0.00 0.00 0.00 2.10
3544 3738 0.909610 TTCCCGCCCTCTGTCATTCT 60.910 55.000 0.00 0.00 0.00 2.40
3545 3739 0.744771 GTTCCCGCCCTCTGTCATTC 60.745 60.000 0.00 0.00 0.00 2.67
3546 3740 1.299976 GTTCCCGCCCTCTGTCATT 59.700 57.895 0.00 0.00 0.00 2.57
3547 3741 1.903877 CTGTTCCCGCCCTCTGTCAT 61.904 60.000 0.00 0.00 0.00 3.06
3548 3742 2.525629 TGTTCCCGCCCTCTGTCA 60.526 61.111 0.00 0.00 0.00 3.58
3549 3743 2.266055 CTGTTCCCGCCCTCTGTC 59.734 66.667 0.00 0.00 0.00 3.51
3550 3744 4.021925 GCTGTTCCCGCCCTCTGT 62.022 66.667 0.00 0.00 0.00 3.41
3561 3755 4.465512 CACGCCATGCCGCTGTTC 62.466 66.667 0.00 0.00 0.00 3.18
3568 3762 3.704908 GAACATGCCACGCCATGCC 62.705 63.158 10.19 1.63 44.98 4.40
3569 3763 2.202650 GAACATGCCACGCCATGC 60.203 61.111 10.19 0.00 44.98 4.06
3570 3764 1.430632 GAGAACATGCCACGCCATG 59.569 57.895 9.06 9.06 46.19 3.66
3571 3765 1.750399 GGAGAACATGCCACGCCAT 60.750 57.895 0.00 0.00 0.00 4.40
3572 3766 2.359850 GGAGAACATGCCACGCCA 60.360 61.111 0.00 0.00 0.00 5.69
3573 3767 3.134127 GGGAGAACATGCCACGCC 61.134 66.667 0.00 0.00 39.77 5.68
3574 3768 2.045926 AGGGAGAACATGCCACGC 60.046 61.111 0.00 0.00 43.31 5.34
3575 3769 1.021390 GTCAGGGAGAACATGCCACG 61.021 60.000 0.00 0.00 43.31 4.94
3576 3770 0.678048 GGTCAGGGAGAACATGCCAC 60.678 60.000 0.00 0.00 43.31 5.01
3577 3771 0.842030 AGGTCAGGGAGAACATGCCA 60.842 55.000 0.00 0.00 43.31 4.92
3578 3772 0.393537 CAGGTCAGGGAGAACATGCC 60.394 60.000 0.00 0.00 40.48 4.40
3579 3773 0.393537 CCAGGTCAGGGAGAACATGC 60.394 60.000 0.00 0.00 35.97 4.06
3580 3774 3.869623 CCAGGTCAGGGAGAACATG 57.130 57.895 0.00 0.00 35.97 3.21



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

AutoCloner maintained by Alex Coulton.