Multiple sequence alignment - TraesCS5D01G084900

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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 TraesCS5D01G084900 chr5D 100.000 5648 0 0 1 5648 89044200 89049847 0.000000e+00 10430.0
1 TraesCS5D01G084900 chr5D 96.963 461 12 2 5189 5648 332199337 332199796 0.000000e+00 773.0
2 TraesCS5D01G084900 chr5D 95.279 466 15 6 5186 5648 524423505 524423966 0.000000e+00 732.0
3 TraesCS5D01G084900 chr5B 93.684 4702 216 35 542 5187 95023945 95019269 0.000000e+00 6962.0
4 TraesCS5D01G084900 chr5B 90.200 500 46 2 1 498 95024688 95024190 0.000000e+00 649.0
5 TraesCS5D01G084900 chr5B 89.565 115 11 1 1 115 95024775 95024662 1.640000e-30 145.0
6 TraesCS5D01G084900 chr5A 90.843 3571 261 35 1659 5187 82982797 82986343 0.000000e+00 4723.0
7 TraesCS5D01G084900 chr5A 91.048 1698 110 20 1 1667 82981091 82982777 0.000000e+00 2255.0
8 TraesCS5D01G084900 chr6D 96.753 462 9 5 5189 5648 396455703 396456160 0.000000e+00 765.0
9 TraesCS5D01G084900 chr7D 96.529 461 13 3 5188 5648 425725299 425725756 0.000000e+00 760.0
10 TraesCS5D01G084900 chr2D 96.304 460 15 2 5189 5648 8517641 8518098 0.000000e+00 754.0
11 TraesCS5D01G084900 chr2D 95.464 463 15 6 5189 5648 637666285 637665826 0.000000e+00 734.0
12 TraesCS5D01G084900 chr3D 95.708 466 14 6 5186 5648 1909710 1910172 0.000000e+00 745.0
13 TraesCS5D01G084900 chr3D 95.896 463 14 5 5189 5648 614889766 614889306 0.000000e+00 745.0
14 TraesCS5D01G084900 chr4D 95.484 465 14 7 5187 5648 85853605 85854065 0.000000e+00 736.0
15 TraesCS5D01G084900 chr4D 82.689 543 81 8 1142 1680 50977625 50977092 2.380000e-128 470.0
16 TraesCS5D01G084900 chr4D 77.515 169 38 0 4434 4602 50975444 50975276 1.000000e-17 102.0
17 TraesCS5D01G084900 chr4A 83.395 542 79 9 1139 1677 546017795 546018328 5.080000e-135 492.0
18 TraesCS5D01G084900 chr4A 80.000 125 25 0 4475 4599 546020026 546020150 6.030000e-15 93.5
19 TraesCS5D01G084900 chr4B 78.125 128 28 0 4475 4602 75038337 75038210 1.300000e-11 82.4


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 TraesCS5D01G084900 chr5D 89044200 89049847 5647 False 10430.000000 10430 100.000000 1 5648 1 chr5D.!!$F1 5647
1 TraesCS5D01G084900 chr5B 95019269 95024775 5506 True 2585.333333 6962 91.149667 1 5187 3 chr5B.!!$R1 5186
2 TraesCS5D01G084900 chr5A 82981091 82986343 5252 False 3489.000000 4723 90.945500 1 5187 2 chr5A.!!$F1 5186
3 TraesCS5D01G084900 chr4D 50975276 50977625 2349 True 286.000000 470 80.102000 1142 4602 2 chr4D.!!$R1 3460
4 TraesCS5D01G084900 chr4A 546017795 546020150 2355 False 292.750000 492 81.697500 1139 4599 2 chr4A.!!$F1 3460

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
209 297 0.107268 CATGATGATGACCGGAGCCA 59.893 55.000 9.46 2.98 0.00 4.75 F
217 305 0.839277 TGACCGGAGCCATCATTCAT 59.161 50.000 9.46 0.00 0.00 2.57 F
529 620 1.452108 GGCAGGTGAGCGGCTAAAT 60.452 57.895 0.60 0.00 34.64 1.40 F
1431 1761 2.183811 CTCCTCGTGCAGCTCCTG 59.816 66.667 0.00 0.00 34.12 3.86 F
2310 2839 1.454539 GTGGTTAGGTGTGGCTGGT 59.545 57.895 0.00 0.00 0.00 4.00 F
2438 2969 0.523072 CTAGGCATTGTGTTGCGCTT 59.477 50.000 9.73 0.00 43.71 4.68 F
2640 3171 1.135112 CCACCGCTTAAAATTCCTGCC 60.135 52.381 0.00 0.00 0.00 4.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1709 2067 2.047061 TGTTTCAGCACCCTGTCTACT 58.953 47.619 0.00 0.0 40.09 2.57 R
1717 2075 3.412386 ACTATTCTGTGTTTCAGCACCC 58.588 45.455 0.00 0.0 43.32 4.61 R
2298 2827 0.252974 TACCCATACCAGCCACACCT 60.253 55.000 0.00 0.0 0.00 4.00 R
2422 2952 0.508213 GAAAAGCGCAACACAATGCC 59.492 50.000 11.47 0.0 43.47 4.40 R
3987 4642 3.041211 CCCTCCAGAGAATATGGTGTGA 58.959 50.000 0.00 0.0 39.01 3.58 R
4415 5085 2.040012 TGCATGGAAATGCCCAAACATT 59.960 40.909 8.13 0.0 46.43 2.71 R
4815 5487 3.308188 CCTGTAAATTTCCCTCCTTCCGT 60.308 47.826 0.00 0.0 0.00 4.69 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
112 200 1.026182 TGGTGAATGATGCGACCTGC 61.026 55.000 0.00 0.00 46.70 4.85
135 223 2.272447 CCGCCCCCGACAATTTTGT 61.272 57.895 0.00 0.00 45.65 2.83
168 256 1.687660 TGACACTTGTTACTACCGGCA 59.312 47.619 0.00 0.00 0.00 5.69
209 297 0.107268 CATGATGATGACCGGAGCCA 59.893 55.000 9.46 2.98 0.00 4.75
212 300 4.048696 TGATGACCGGAGCCATCA 57.951 55.556 24.17 24.17 44.66 3.07
217 305 0.839277 TGACCGGAGCCATCATTCAT 59.161 50.000 9.46 0.00 0.00 2.57
233 321 1.745232 TCATGGAAATCGGGGAAACG 58.255 50.000 0.00 0.00 0.00 3.60
342 430 1.795889 GCTACGAGGAGAACTTGCGAG 60.796 57.143 0.00 0.00 33.55 5.03
400 489 2.253452 CACCGCAAGCAAGAGCAC 59.747 61.111 0.00 0.00 45.49 4.40
406 495 1.962144 CAAGCAAGAGCACCAAGGG 59.038 57.895 0.00 0.00 45.49 3.95
407 496 1.905354 AAGCAAGAGCACCAAGGGC 60.905 57.895 0.00 0.00 45.49 5.19
408 497 2.282745 GCAAGAGCACCAAGGGCT 60.283 61.111 0.00 0.00 46.07 5.19
409 498 2.633509 GCAAGAGCACCAAGGGCTG 61.634 63.158 0.00 0.00 42.78 4.85
453 544 4.938756 TGGTGGGAAGGGGGTGCT 62.939 66.667 0.00 0.00 0.00 4.40
482 573 8.884124 TGATTTAAGGAAAAGGAAGATGTGAT 57.116 30.769 0.00 0.00 0.00 3.06
529 620 1.452108 GGCAGGTGAGCGGCTAAAT 60.452 57.895 0.60 0.00 34.64 1.40
556 848 6.917477 GCACAGTCAAAAGATTTTGTATCACA 59.083 34.615 15.58 0.00 45.77 3.58
621 922 2.745821 GCAGTTCCCTTACTAAAACCGG 59.254 50.000 0.00 0.00 0.00 5.28
640 941 9.683870 AAAACCGGTAGATATATTTTTACACCA 57.316 29.630 8.00 0.00 0.00 4.17
686 987 6.297582 TGGATCATGCTCCAAAAATTTGTTT 58.702 32.000 15.87 0.00 42.36 2.83
687 988 6.205076 TGGATCATGCTCCAAAAATTTGTTTG 59.795 34.615 15.87 0.00 42.36 2.93
707 1008 8.510243 TGTTTGAGACATGTGAATAGCATAAT 57.490 30.769 1.15 0.00 32.00 1.28
782 1104 3.791953 TTTCGGGGACAACCAATAGAA 57.208 42.857 0.00 0.00 42.91 2.10
793 1115 4.336433 ACAACCAATAGAAATCGCCTGATG 59.664 41.667 0.00 0.00 34.24 3.07
875 1204 8.876790 CGTACTACTATAAAAGGGTCCAAAAAG 58.123 37.037 0.00 0.00 0.00 2.27
1431 1761 2.183811 CTCCTCGTGCAGCTCCTG 59.816 66.667 0.00 0.00 34.12 3.86
1709 2067 6.821616 ATTTGCAATGGGGGTAATTTGATA 57.178 33.333 0.00 0.00 0.00 2.15
1717 2075 6.494666 TGGGGGTAATTTGATAGTAGACAG 57.505 41.667 0.00 0.00 0.00 3.51
1727 2085 4.093743 TGATAGTAGACAGGGTGCTGAAA 58.906 43.478 0.00 0.00 0.00 2.69
1996 2490 4.695455 ACGCTTGCTTTAATTCTCAGCTAA 59.305 37.500 0.00 0.00 34.42 3.09
2068 2562 3.873361 AGTGATGATGTACATTTGGCTCG 59.127 43.478 10.30 0.00 39.56 5.03
2128 2631 7.724305 TGTAGACATTTACCTTGACAAGAAC 57.276 36.000 16.99 0.00 0.00 3.01
2130 2633 5.070685 AGACATTTACCTTGACAAGAACCC 58.929 41.667 16.99 0.00 0.00 4.11
2131 2634 4.798882 ACATTTACCTTGACAAGAACCCA 58.201 39.130 16.99 0.00 0.00 4.51
2138 2641 5.205056 ACCTTGACAAGAACCCACAAAATA 58.795 37.500 16.99 0.00 0.00 1.40
2195 2703 8.534333 TTGTTTTCTACATAGCAACTACAGAG 57.466 34.615 0.00 0.00 36.44 3.35
2199 2707 8.803397 TTTCTACATAGCAACTACAGAGACTA 57.197 34.615 0.00 0.00 0.00 2.59
2200 2708 8.439993 TTCTACATAGCAACTACAGAGACTAG 57.560 38.462 0.00 0.00 0.00 2.57
2214 2722 7.644986 ACAGAGACTAGAATTTTCTGAAACG 57.355 36.000 1.58 0.00 38.81 3.60
2217 2725 9.193133 CAGAGACTAGAATTTTCTGAAACGTTA 57.807 33.333 0.00 0.00 37.96 3.18
2234 2742 7.279090 TGAAACGTTACAGTGAAAAGATCAGAA 59.721 33.333 0.00 0.00 39.19 3.02
2256 2764 9.340695 CAGAAAAGTTTGTTATGCGATTGATTA 57.659 29.630 0.00 0.00 0.00 1.75
2262 2770 5.657470 TGTTATGCGATTGATTAGCACTC 57.343 39.130 0.00 0.00 44.12 3.51
2268 2776 3.544244 GCGATTGATTAGCACTCGGTTTC 60.544 47.826 11.72 0.00 46.16 2.78
2281 2810 7.708998 AGCACTCGGTTTCATTTAAAACTTAA 58.291 30.769 0.00 0.00 38.81 1.85
2283 2812 8.263950 GCACTCGGTTTCATTTAAAACTTAAAC 58.736 33.333 0.00 1.44 38.81 2.01
2286 2815 9.177304 CTCGGTTTCATTTAAAACTTAAACTCC 57.823 33.333 13.24 0.00 38.81 3.85
2298 2827 5.327737 ACTTAAACTCCCATTGGTGGTTA 57.672 39.130 1.20 1.02 44.48 2.85
2301 2830 1.755200 ACTCCCATTGGTGGTTAGGT 58.245 50.000 1.20 0.00 44.48 3.08
2310 2839 1.454539 GTGGTTAGGTGTGGCTGGT 59.545 57.895 0.00 0.00 0.00 4.00
2365 2895 8.956426 CAAATTTCCTGAATACTGGCTACTTAA 58.044 33.333 0.00 0.00 35.51 1.85
2369 2899 5.665812 TCCTGAATACTGGCTACTTAATGGT 59.334 40.000 0.00 0.00 35.51 3.55
2372 2902 7.136822 TGAATACTGGCTACTTAATGGTGAT 57.863 36.000 0.00 0.00 0.00 3.06
2380 2910 6.328934 TGGCTACTTAATGGTGATGATTCCTA 59.671 38.462 0.00 0.00 0.00 2.94
2382 2912 7.217200 GCTACTTAATGGTGATGATTCCTACA 58.783 38.462 0.00 0.00 0.00 2.74
2422 2952 7.394816 TCTCCTTGTTAGATTTTGTTCCCTAG 58.605 38.462 0.00 0.00 0.00 3.02
2423 2953 6.481643 TCCTTGTTAGATTTTGTTCCCTAGG 58.518 40.000 0.06 0.06 0.00 3.02
2424 2954 5.125578 CCTTGTTAGATTTTGTTCCCTAGGC 59.874 44.000 2.05 0.00 0.00 3.93
2425 2955 5.249780 TGTTAGATTTTGTTCCCTAGGCA 57.750 39.130 2.05 0.00 0.00 4.75
2434 2965 1.202348 GTTCCCTAGGCATTGTGTTGC 59.798 52.381 2.05 0.00 42.01 4.17
2438 2969 0.523072 CTAGGCATTGTGTTGCGCTT 59.477 50.000 9.73 0.00 43.71 4.68
2444 2975 2.053627 CATTGTGTTGCGCTTTTCTCC 58.946 47.619 9.73 0.00 0.00 3.71
2479 3010 2.498078 TGGCATGAGTGTACCGTATGAA 59.502 45.455 0.00 0.00 0.00 2.57
2490 3021 7.159372 AGTGTACCGTATGAATTTTCTTGACT 58.841 34.615 0.00 0.00 0.00 3.41
2516 3047 8.958119 TTTGATTGTAAAGCGAAGGTCTATAT 57.042 30.769 0.00 0.00 37.06 0.86
2551 3082 5.827666 TGATGAATTAATGCTGCTGACATG 58.172 37.500 0.00 0.00 0.00 3.21
2558 3089 1.375551 TGCTGCTGACATGTGCATAG 58.624 50.000 1.15 0.00 38.59 2.23
2603 3134 5.277857 AGATGTTAGGAACCTTGTATCCG 57.722 43.478 0.00 0.00 40.78 4.18
2606 3137 4.824289 TGTTAGGAACCTTGTATCCGAAC 58.176 43.478 9.85 9.85 45.81 3.95
2619 3150 5.893687 TGTATCCGAACGTATGCTTCTTAA 58.106 37.500 0.00 0.00 0.00 1.85
2624 3155 3.061697 CGAACGTATGCTTCTTAACCACC 59.938 47.826 0.00 0.00 0.00 4.61
2630 3161 3.128852 TGCTTCTTAACCACCGCTTAA 57.871 42.857 0.00 0.00 0.00 1.85
2631 3162 3.478509 TGCTTCTTAACCACCGCTTAAA 58.521 40.909 0.00 0.00 0.00 1.52
2639 3170 1.544246 ACCACCGCTTAAAATTCCTGC 59.456 47.619 0.00 0.00 0.00 4.85
2640 3171 1.135112 CCACCGCTTAAAATTCCTGCC 60.135 52.381 0.00 0.00 0.00 4.85
2678 3209 5.452078 TTAATGCTTTTGACAGGAGTTGG 57.548 39.130 0.00 0.00 0.00 3.77
2693 3224 6.656693 ACAGGAGTTGGATTCTGTGAAATTAG 59.343 38.462 0.00 0.00 38.80 1.73
2696 3227 7.725844 AGGAGTTGGATTCTGTGAAATTAGTTT 59.274 33.333 0.00 0.00 0.00 2.66
2726 3258 4.926238 GCATATCATTCCAGAGTTCTACGG 59.074 45.833 0.00 0.00 0.00 4.02
2747 3279 3.251004 GGATGGTCCTTGAATTGCGTATC 59.749 47.826 0.00 0.00 32.53 2.24
2748 3280 3.342377 TGGTCCTTGAATTGCGTATCA 57.658 42.857 0.00 0.00 0.00 2.15
2759 3291 6.947258 TGAATTGCGTATCAATACTGACATG 58.053 36.000 0.00 0.00 44.23 3.21
2768 3300 7.216881 CGTATCAATACTGACATGCACTTTTTG 59.783 37.037 0.00 0.00 33.30 2.44
2776 3308 6.154203 TGACATGCACTTTTTGTCCAAATA 57.846 33.333 13.39 0.00 39.17 1.40
2779 3311 6.581712 ACATGCACTTTTTGTCCAAATAGTT 58.418 32.000 11.54 0.00 39.43 2.24
2780 3312 6.479660 ACATGCACTTTTTGTCCAAATAGTTG 59.520 34.615 11.54 10.56 39.43 3.16
2871 3407 3.142838 CGCTTTGGGCCTGGATGG 61.143 66.667 4.53 0.00 37.74 3.51
2906 3447 6.198216 CACTGCACTTTACATGTTTTGTTACC 59.802 38.462 2.30 0.00 39.87 2.85
2917 3473 7.703328 ACATGTTTTGTTACCTGTCTTTAGTG 58.297 34.615 0.00 0.00 33.74 2.74
2919 3475 5.648526 TGTTTTGTTACCTGTCTTTAGTGCA 59.351 36.000 0.00 0.00 0.00 4.57
2927 3483 6.992063 ACCTGTCTTTAGTGCATCTATTTG 57.008 37.500 0.00 0.00 0.00 2.32
2935 3491 9.665719 TCTTTAGTGCATCTATTTGTACAATCA 57.334 29.630 9.56 0.00 35.01 2.57
2939 3495 8.565896 AGTGCATCTATTTGTACAATCAAAGA 57.434 30.769 9.56 10.05 40.00 2.52
2940 3496 9.013229 AGTGCATCTATTTGTACAATCAAAGAA 57.987 29.630 9.56 0.00 40.00 2.52
2941 3497 9.065871 GTGCATCTATTTGTACAATCAAAGAAC 57.934 33.333 9.56 7.49 40.00 3.01
2953 3509 6.385033 ACAATCAAAGAACAGAAAGCTATGC 58.615 36.000 0.00 0.00 0.00 3.14
2986 3615 5.411361 TGTTCGAATCATCAACTTACCTTGG 59.589 40.000 0.00 0.00 0.00 3.61
2991 3620 7.279981 TCGAATCATCAACTTACCTTGGTATTG 59.720 37.037 0.00 3.99 0.00 1.90
2999 3630 4.021456 ACTTACCTTGGTATTGCCTTTTGC 60.021 41.667 0.00 0.00 41.77 3.68
3133 3764 4.344237 CCAATGGGAAGGACCTGC 57.656 61.111 0.00 0.00 38.98 4.85
3138 3769 3.217626 CAATGGGAAGGACCTGCTAATC 58.782 50.000 0.00 0.00 38.98 1.75
3166 3799 4.718774 AGGATCTCACAGATTAGCCTTTGA 59.281 41.667 0.00 0.00 34.53 2.69
3173 3806 5.100259 CACAGATTAGCCTTTGATGCTTTG 58.900 41.667 0.00 0.00 40.23 2.77
3188 3821 3.826524 TGCTTTGACTTGTCCCATACAA 58.173 40.909 0.00 0.00 45.90 2.41
3203 3836 6.600822 GTCCCATACAATCCTATCCATTGATG 59.399 42.308 0.00 0.55 35.54 3.07
3216 3849 8.680903 CCTATCCATTGATGATGCCTAATTTAC 58.319 37.037 0.00 0.00 34.25 2.01
3482 4131 7.922699 AGGATTCTATGGTAGTAAAGAAGCT 57.077 36.000 0.00 0.00 35.32 3.74
3611 4260 5.482908 CAGAGTAGCACAATAACAGGAACT 58.517 41.667 0.00 0.00 43.88 3.01
3857 4509 5.279156 GCAAGTCATGGGAGTTTTCAGAATT 60.279 40.000 0.00 0.00 34.43 2.17
3880 4532 4.150980 TGGTCGTAAAATGCAAGTAAGTCG 59.849 41.667 0.00 0.00 0.00 4.18
3882 4534 5.303485 GTCGTAAAATGCAAGTAAGTCGTC 58.697 41.667 0.00 0.00 0.00 4.20
3982 4637 4.846779 TCTGTGTGAAAAGCATTTACCC 57.153 40.909 0.00 0.00 37.28 3.69
3983 4638 3.572255 TCTGTGTGAAAAGCATTTACCCC 59.428 43.478 0.00 0.00 37.28 4.95
3987 4642 4.765339 GTGTGAAAAGCATTTACCCCTAGT 59.235 41.667 0.00 0.00 37.28 2.57
4069 4725 4.568956 AGGTTAAAAATGCTGGCACATTC 58.431 39.130 13.21 4.00 39.32 2.67
4113 4769 3.911260 TGTAACCAGTGTTCCCTTATGGA 59.089 43.478 0.00 0.00 43.18 3.41
4114 4770 7.889263 AGTGTAACCAGTGTTCCCTTATGGAA 61.889 42.308 0.00 0.00 45.29 3.53
4174 4830 5.705441 TGGTTCACGATTCTAGATTTTGCTT 59.295 36.000 0.00 0.00 0.00 3.91
4221 4877 2.220133 TCAACAAAAGCTTCGTCGCTAC 59.780 45.455 0.00 0.00 39.86 3.58
4390 5060 3.810386 GCCCCTTTGTTTAAATTTCGCAA 59.190 39.130 0.00 0.00 0.00 4.85
4415 5085 4.519540 TCAAGATGATGACGTTCTCACA 57.480 40.909 3.45 0.00 0.00 3.58
4573 5243 0.613260 ACTTGCCTACGCCTCATTCA 59.387 50.000 0.00 0.00 0.00 2.57
4815 5487 3.570975 TGGTTGTAGCTCTTTGACTCGTA 59.429 43.478 0.00 0.00 0.00 3.43
4823 5495 2.486982 CTCTTTGACTCGTACGGAAGGA 59.513 50.000 16.52 8.32 0.00 3.36
4860 5532 3.011818 CAGTGAATTGGTGATGCTGCTA 58.988 45.455 0.00 0.00 0.00 3.49
4918 5590 2.102109 TTGTCGGCGGACTAAAGGCA 62.102 55.000 22.99 0.52 43.79 4.75
5087 5760 2.213499 GATACTTCGGTGCTGGGAATG 58.787 52.381 0.00 0.00 0.00 2.67
5276 5953 7.861176 TTTTCAAAAATAATACACTGTCGGC 57.139 32.000 0.00 0.00 0.00 5.54
5277 5954 5.554822 TCAAAAATAATACACTGTCGGCC 57.445 39.130 0.00 0.00 0.00 6.13
5278 5955 4.396790 TCAAAAATAATACACTGTCGGCCC 59.603 41.667 0.00 0.00 0.00 5.80
5279 5956 2.234300 AATAATACACTGTCGGCCCG 57.766 50.000 0.00 0.00 0.00 6.13
5280 5957 0.249741 ATAATACACTGTCGGCCCGC 60.250 55.000 0.00 0.00 0.00 6.13
5281 5958 1.324740 TAATACACTGTCGGCCCGCT 61.325 55.000 0.00 0.00 0.00 5.52
5282 5959 2.852495 AATACACTGTCGGCCCGCTG 62.852 60.000 0.00 0.22 0.00 5.18
5313 5990 3.390521 CCTAGTCGGCCCACAGCA 61.391 66.667 2.46 0.00 46.50 4.41
5314 5991 2.185350 CTAGTCGGCCCACAGCAG 59.815 66.667 2.46 0.00 46.50 4.24
5315 5992 3.376935 CTAGTCGGCCCACAGCAGG 62.377 68.421 2.46 0.00 46.50 4.85
5322 5999 3.136123 CCCACAGCAGGCCGATTG 61.136 66.667 0.00 0.00 0.00 2.67
5323 6000 3.136123 CCACAGCAGGCCGATTGG 61.136 66.667 0.00 0.00 38.77 3.16
5324 6001 2.046023 CACAGCAGGCCGATTGGA 60.046 61.111 1.98 0.00 37.49 3.53
5331 6008 2.990479 GGCCGATTGGACTCCAGT 59.010 61.111 1.98 0.00 41.70 4.00
5332 6009 1.153349 GGCCGATTGGACTCCAGTC 60.153 63.158 10.01 10.01 41.70 3.51
5335 6012 4.522971 GATTGGACTCCAGTCGGC 57.477 61.111 4.91 0.00 45.65 5.54
5336 6013 1.153349 GATTGGACTCCAGTCGGCC 60.153 63.158 4.91 0.00 45.65 6.13
5337 6014 1.613630 ATTGGACTCCAGTCGGCCT 60.614 57.895 0.00 0.00 45.65 5.19
5338 6015 0.325296 ATTGGACTCCAGTCGGCCTA 60.325 55.000 0.00 0.00 45.65 3.93
5339 6016 1.255667 TTGGACTCCAGTCGGCCTAC 61.256 60.000 0.00 0.00 45.65 3.18
5340 6017 1.681327 GGACTCCAGTCGGCCTACA 60.681 63.158 10.45 0.00 45.65 2.74
5341 6018 1.668101 GGACTCCAGTCGGCCTACAG 61.668 65.000 10.45 0.99 45.65 2.74
5342 6019 2.286127 GACTCCAGTCGGCCTACAGC 62.286 65.000 10.45 0.00 36.58 4.40
5343 6020 2.037367 TCCAGTCGGCCTACAGCT 59.963 61.111 10.45 0.00 43.05 4.24
5351 6028 3.775654 GCCTACAGCTGGCCGACT 61.776 66.667 19.93 0.00 44.32 4.18
5352 6029 2.185350 CCTACAGCTGGCCGACTG 59.815 66.667 19.93 20.22 39.86 3.51
5353 6030 2.185350 CTACAGCTGGCCGACTGG 59.815 66.667 24.17 7.92 38.25 4.00
5372 6049 4.704833 CCCTGTCGGCCCACTGTG 62.705 72.222 1.09 0.00 0.00 3.66
5373 6050 4.704833 CCTGTCGGCCCACTGTGG 62.705 72.222 20.01 20.01 37.25 4.17
5382 6059 4.007457 CCACTGTGGGCTGATTGG 57.993 61.111 19.23 0.00 32.67 3.16
5383 6060 1.679977 CCACTGTGGGCTGATTGGG 60.680 63.158 19.23 0.00 32.67 4.12
5384 6061 1.075482 CACTGTGGGCTGATTGGGT 59.925 57.895 0.00 0.00 0.00 4.51
5385 6062 0.962356 CACTGTGGGCTGATTGGGTC 60.962 60.000 0.00 0.00 0.00 4.46
5386 6063 1.379044 CTGTGGGCTGATTGGGTCC 60.379 63.158 0.00 0.00 0.00 4.46
5387 6064 1.852157 TGTGGGCTGATTGGGTCCT 60.852 57.895 0.00 0.00 0.00 3.85
5388 6065 1.379044 GTGGGCTGATTGGGTCCTG 60.379 63.158 0.00 0.00 0.00 3.86
5389 6066 1.852157 TGGGCTGATTGGGTCCTGT 60.852 57.895 0.00 0.00 0.00 4.00
5390 6067 1.077429 GGGCTGATTGGGTCCTGTC 60.077 63.158 0.00 0.00 0.00 3.51
5391 6068 1.450312 GGCTGATTGGGTCCTGTCG 60.450 63.158 0.00 0.00 0.00 4.35
5392 6069 1.450312 GCTGATTGGGTCCTGTCGG 60.450 63.158 0.00 0.00 0.00 4.79
5393 6070 1.450312 CTGATTGGGTCCTGTCGGC 60.450 63.158 0.00 0.00 0.00 5.54
5394 6071 2.124695 GATTGGGTCCTGTCGGCC 60.125 66.667 0.00 0.00 0.00 6.13
5395 6072 3.699134 GATTGGGTCCTGTCGGCCC 62.699 68.421 0.00 0.00 43.19 5.80
5399 6076 4.394712 GGTCCTGTCGGCCCACTG 62.395 72.222 1.09 0.59 0.00 3.66
5400 6077 3.626924 GTCCTGTCGGCCCACTGT 61.627 66.667 1.09 0.00 0.00 3.55
5401 6078 3.625897 TCCTGTCGGCCCACTGTG 61.626 66.667 1.09 0.00 0.00 3.66
5402 6079 4.704833 CCTGTCGGCCCACTGTGG 62.705 72.222 20.01 20.01 37.25 4.17
5411 6088 4.704833 CCACTGTGGGCCGACTGG 62.705 72.222 24.80 18.26 32.67 4.00
5412 6089 3.625897 CACTGTGGGCCGACTGGA 61.626 66.667 24.80 3.18 37.49 3.86
5413 6090 3.314331 ACTGTGGGCCGACTGGAG 61.314 66.667 24.80 14.43 37.49 3.86
5414 6091 4.767255 CTGTGGGCCGACTGGAGC 62.767 72.222 19.42 0.00 37.49 4.70
5416 6093 3.075005 GTGGGCCGACTGGAGCTA 61.075 66.667 11.17 0.00 37.49 3.32
5417 6094 2.284331 TGGGCCGACTGGAGCTAA 60.284 61.111 0.00 0.00 37.49 3.09
5418 6095 1.689233 TGGGCCGACTGGAGCTAAT 60.689 57.895 0.00 0.00 37.49 1.73
5419 6096 1.271840 TGGGCCGACTGGAGCTAATT 61.272 55.000 0.00 0.00 37.49 1.40
5420 6097 0.756903 GGGCCGACTGGAGCTAATTA 59.243 55.000 0.00 0.00 37.49 1.40
5421 6098 1.270358 GGGCCGACTGGAGCTAATTAG 60.270 57.143 8.20 8.20 37.49 1.73
5422 6099 1.503294 GCCGACTGGAGCTAATTAGC 58.497 55.000 26.79 26.79 42.05 3.09
5432 6109 1.221414 GCTAATTAGCTCGCTGTGGG 58.779 55.000 26.79 0.00 45.62 4.61
5433 6110 1.221414 CTAATTAGCTCGCTGTGGGC 58.779 55.000 4.57 4.57 37.64 5.36
5434 6111 0.830648 TAATTAGCTCGCTGTGGGCT 59.169 50.000 20.61 20.61 39.13 5.19
5435 6112 0.830648 AATTAGCTCGCTGTGGGCTA 59.169 50.000 18.33 18.33 39.13 3.93
5436 6113 2.282827 TTAGCTCGCTGTGGGCTAA 58.717 52.632 26.87 26.87 43.41 3.09
5437 6114 0.830648 TTAGCTCGCTGTGGGCTAAT 59.169 50.000 26.87 5.06 41.62 1.73
5438 6115 0.830648 TAGCTCGCTGTGGGCTAATT 59.169 50.000 19.79 0.00 35.91 1.40
5439 6116 0.745845 AGCTCGCTGTGGGCTAATTG 60.746 55.000 15.04 0.00 39.13 2.32
5440 6117 1.026718 GCTCGCTGTGGGCTAATTGT 61.027 55.000 5.68 0.00 39.13 2.71
5441 6118 1.453155 CTCGCTGTGGGCTAATTGTT 58.547 50.000 0.00 0.00 39.13 2.83
5442 6119 1.812571 CTCGCTGTGGGCTAATTGTTT 59.187 47.619 0.00 0.00 39.13 2.83
5443 6120 2.228822 CTCGCTGTGGGCTAATTGTTTT 59.771 45.455 0.00 0.00 39.13 2.43
5444 6121 2.625790 TCGCTGTGGGCTAATTGTTTTT 59.374 40.909 0.00 0.00 39.13 1.94
5445 6122 2.730928 CGCTGTGGGCTAATTGTTTTTG 59.269 45.455 0.00 0.00 39.13 2.44
5446 6123 2.480037 GCTGTGGGCTAATTGTTTTTGC 59.520 45.455 0.00 0.00 38.06 3.68
5447 6124 3.726607 CTGTGGGCTAATTGTTTTTGCA 58.273 40.909 0.00 0.00 0.00 4.08
5448 6125 4.125703 CTGTGGGCTAATTGTTTTTGCAA 58.874 39.130 0.00 0.00 0.00 4.08
5449 6126 4.517285 TGTGGGCTAATTGTTTTTGCAAA 58.483 34.783 8.05 8.05 31.63 3.68
5450 6127 4.943705 TGTGGGCTAATTGTTTTTGCAAAA 59.056 33.333 20.46 20.46 31.63 2.44
5451 6128 5.415701 TGTGGGCTAATTGTTTTTGCAAAAA 59.584 32.000 28.85 28.85 35.67 1.94
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
73 161 1.533625 TGAATGGTTGTAGCACCTGC 58.466 50.000 0.00 0.00 37.75 4.85
96 184 0.390998 TTCGCAGGTCGCATCATTCA 60.391 50.000 0.00 0.00 42.60 2.57
115 203 3.879180 AAAATTGTCGGGGGCGGCT 62.879 57.895 9.56 0.00 0.00 5.52
135 223 0.179094 AGTGTCAAAGACGGTTGCGA 60.179 50.000 0.00 0.00 34.95 5.10
136 224 0.655733 AAGTGTCAAAGACGGTTGCG 59.344 50.000 0.00 0.00 34.95 4.85
168 256 4.277174 TGAATGGTTGTAGCAATTGTCGTT 59.723 37.500 7.40 0.00 0.00 3.85
209 297 3.882102 TCCCCGATTTCCATGAATGAT 57.118 42.857 0.00 0.00 0.00 2.45
212 300 2.687935 CGTTTCCCCGATTTCCATGAAT 59.312 45.455 0.00 0.00 0.00 2.57
217 305 1.240256 CAACGTTTCCCCGATTTCCA 58.760 50.000 0.00 0.00 0.00 3.53
225 313 1.227615 TCGGTCACAACGTTTCCCC 60.228 57.895 0.00 0.00 0.00 4.81
233 321 1.468520 CCCATGAATGTCGGTCACAAC 59.531 52.381 0.00 0.00 38.97 3.32
450 541 4.832266 TCCTTTTCCTTAAATCAGCAAGCA 59.168 37.500 0.00 0.00 0.00 3.91
453 544 7.233348 ACATCTTCCTTTTCCTTAAATCAGCAA 59.767 33.333 0.00 0.00 0.00 3.91
510 601 2.893682 ATTTAGCCGCTCACCTGCCC 62.894 60.000 0.00 0.00 0.00 5.36
511 602 1.440145 GATTTAGCCGCTCACCTGCC 61.440 60.000 0.00 0.00 0.00 4.85
512 603 1.766143 CGATTTAGCCGCTCACCTGC 61.766 60.000 0.00 0.00 0.00 4.85
513 604 2.301505 CGATTTAGCCGCTCACCTG 58.698 57.895 0.00 0.00 0.00 4.00
514 605 4.835927 CGATTTAGCCGCTCACCT 57.164 55.556 0.00 0.00 0.00 4.00
524 615 7.858052 AAAATCTTTTGACTGTGCGATTTAG 57.142 32.000 0.00 0.00 32.60 1.85
536 627 8.015087 TCATCGTGTGATACAAAATCTTTTGAC 58.985 33.333 19.35 9.32 40.76 3.18
538 629 8.726650 TTCATCGTGTGATACAAAATCTTTTG 57.273 30.769 12.61 12.61 43.51 2.44
556 848 1.296715 GGTGGCCTCACTTCATCGT 59.703 57.895 3.32 0.00 43.17 3.73
640 941 6.942005 TCCATGTGACTCTTGTATGACAATTT 59.058 34.615 0.00 0.00 37.48 1.82
707 1008 9.656040 AAATGATAGTCTTTGCAATGCATTTTA 57.344 25.926 9.39 0.00 38.76 1.52
766 1088 2.357952 GCGATTTCTATTGGTTGTCCCC 59.642 50.000 0.00 0.00 0.00 4.81
767 1089 2.357952 GGCGATTTCTATTGGTTGTCCC 59.642 50.000 0.00 0.00 0.00 4.46
793 1115 1.410882 CTGCTAGTCCTACTCTTGGCC 59.589 57.143 0.00 0.00 0.00 5.36
875 1204 1.677052 GTGACTCCACTATCTCGACCC 59.323 57.143 0.00 0.00 40.10 4.46
1695 2053 5.221864 CCCTGTCTACTATCAAATTACCCCC 60.222 48.000 0.00 0.00 0.00 5.40
1709 2067 2.047061 TGTTTCAGCACCCTGTCTACT 58.953 47.619 0.00 0.00 40.09 2.57
1717 2075 3.412386 ACTATTCTGTGTTTCAGCACCC 58.588 45.455 0.00 0.00 43.32 4.61
1767 2261 6.048732 TCTTTTGGAAAAATCCCTAATGCC 57.951 37.500 0.00 0.00 0.00 4.40
1896 2390 6.456501 GTCCTCAAACTAATGTGACACTACT 58.543 40.000 7.20 0.00 0.00 2.57
2068 2562 7.013655 TCTCATAGGGCAGAATGAATTAAAAGC 59.986 37.037 0.00 0.00 39.69 3.51
2106 2600 6.183361 TGGGTTCTTGTCAAGGTAAATGTCTA 60.183 38.462 12.66 0.00 0.00 2.59
2172 2680 8.030106 AGTCTCTGTAGTTGCTATGTAGAAAAC 58.970 37.037 0.00 0.00 0.00 2.43
2181 2689 9.810545 GAAAATTCTAGTCTCTGTAGTTGCTAT 57.189 33.333 0.00 0.00 0.00 2.97
2195 2703 8.762426 ACTGTAACGTTTCAGAAAATTCTAGTC 58.238 33.333 33.09 0.00 35.34 2.59
2199 2707 7.548196 TCACTGTAACGTTTCAGAAAATTCT 57.452 32.000 33.09 12.59 38.25 2.40
2200 2708 8.609478 TTTCACTGTAACGTTTCAGAAAATTC 57.391 30.769 33.09 0.00 35.84 2.17
2212 2720 7.280205 ACTTTTCTGATCTTTTCACTGTAACGT 59.720 33.333 0.00 0.00 0.00 3.99
2214 2722 9.788960 AAACTTTTCTGATCTTTTCACTGTAAC 57.211 29.630 0.00 0.00 0.00 2.50
2217 2725 7.830739 ACAAACTTTTCTGATCTTTTCACTGT 58.169 30.769 0.00 0.00 0.00 3.55
2234 2742 7.273381 GTGCTAATCAATCGCATAACAAACTTT 59.727 33.333 0.00 0.00 35.93 2.66
2256 2764 5.767816 AGTTTTAAATGAAACCGAGTGCT 57.232 34.783 0.00 0.00 39.71 4.40
2262 2770 7.921745 TGGGAGTTTAAGTTTTAAATGAAACCG 59.078 33.333 0.55 0.00 39.71 4.44
2268 2776 8.987890 CACCAATGGGAGTTTAAGTTTTAAATG 58.012 33.333 3.55 0.00 38.05 2.32
2298 2827 0.252974 TACCCATACCAGCCACACCT 60.253 55.000 0.00 0.00 0.00 4.00
2301 2830 1.705745 TGTTTACCCATACCAGCCACA 59.294 47.619 0.00 0.00 0.00 4.17
2310 2839 7.463431 ACTACTTGGTTCAATGTTTACCCATA 58.537 34.615 0.00 0.00 0.00 2.74
2342 2871 7.721399 CCATTAAGTAGCCAGTATTCAGGAAAT 59.279 37.037 0.00 0.00 0.00 2.17
2354 2883 5.471456 GGAATCATCACCATTAAGTAGCCAG 59.529 44.000 0.00 0.00 0.00 4.85
2365 2895 9.479549 AATAAAGTTTGTAGGAATCATCACCAT 57.520 29.630 0.00 0.00 0.00 3.55
2380 2910 8.237811 ACAAGGAGATCACAAATAAAGTTTGT 57.762 30.769 0.00 0.63 42.75 2.83
2422 2952 0.508213 GAAAAGCGCAACACAATGCC 59.492 50.000 11.47 0.00 43.47 4.40
2423 2953 1.453148 GAGAAAAGCGCAACACAATGC 59.547 47.619 11.47 0.00 42.94 3.56
2424 2954 2.053627 GGAGAAAAGCGCAACACAATG 58.946 47.619 11.47 0.00 0.00 2.82
2425 2955 1.956477 AGGAGAAAAGCGCAACACAAT 59.044 42.857 11.47 0.00 0.00 2.71
2444 2975 4.202336 ACTCATGCCACAATATCTCAGGAG 60.202 45.833 0.00 0.00 40.23 3.69
2479 3010 8.755018 CGCTTTACAATCAAAAGTCAAGAAAAT 58.245 29.630 0.00 0.00 36.52 1.82
2490 3021 7.681939 ATAGACCTTCGCTTTACAATCAAAA 57.318 32.000 0.00 0.00 0.00 2.44
2516 3047 6.183360 GCATTAATTCATCATGCAAAAGCCAA 60.183 34.615 0.00 0.00 42.49 4.52
2576 3107 5.763876 ACAAGGTTCCTAACATCTAGCTT 57.236 39.130 0.00 0.00 0.00 3.74
2579 3110 6.264744 TCGGATACAAGGTTCCTAACATCTAG 59.735 42.308 0.00 0.00 0.00 2.43
2603 3134 3.061697 CGGTGGTTAAGAAGCATACGTTC 59.938 47.826 0.00 0.00 41.44 3.95
2606 3137 1.326548 GCGGTGGTTAAGAAGCATACG 59.673 52.381 11.52 11.52 41.44 3.06
2619 3150 1.544246 GCAGGAATTTTAAGCGGTGGT 59.456 47.619 0.00 0.00 0.00 4.16
2624 3155 4.376340 AGAATGGCAGGAATTTTAAGCG 57.624 40.909 0.00 0.00 0.00 4.68
2693 3224 9.807649 ACTCTGGAATGATATGCAAATAAAAAC 57.192 29.630 0.00 0.00 0.00 2.43
2696 3227 9.412460 AGAACTCTGGAATGATATGCAAATAAA 57.588 29.630 0.00 0.00 0.00 1.40
2707 3238 4.039730 CCATCCGTAGAACTCTGGAATGAT 59.960 45.833 0.00 0.00 33.48 2.45
2713 3244 1.409427 GGACCATCCGTAGAACTCTGG 59.591 57.143 0.00 0.00 0.00 3.86
2718 3250 3.604875 TTCAAGGACCATCCGTAGAAC 57.395 47.619 0.00 0.00 42.75 3.01
2726 3258 3.876914 TGATACGCAATTCAAGGACCATC 59.123 43.478 0.00 0.00 0.00 3.51
2747 3279 5.630680 GGACAAAAAGTGCATGTCAGTATTG 59.369 40.000 16.85 14.61 44.05 1.90
2748 3280 5.301551 TGGACAAAAAGTGCATGTCAGTATT 59.698 36.000 16.85 0.00 44.19 1.89
2759 3291 4.808364 TGCAACTATTTGGACAAAAAGTGC 59.192 37.500 1.17 9.49 39.32 4.40
2768 3300 5.181690 TGTGAGTTTGCAACTATTTGGAC 57.818 39.130 0.00 0.00 43.03 4.02
2776 3308 5.126061 AGTTCTGAATTGTGAGTTTGCAACT 59.874 36.000 0.00 0.00 46.38 3.16
2779 3311 6.882610 ATAGTTCTGAATTGTGAGTTTGCA 57.117 33.333 0.00 0.00 0.00 4.08
2780 3312 7.362662 TGAATAGTTCTGAATTGTGAGTTTGC 58.637 34.615 0.00 0.00 0.00 3.68
2825 3359 9.003658 GGTATAAATTCAGATGGACCATAACAG 57.996 37.037 7.05 0.00 0.00 3.16
2826 3360 8.723365 AGGTATAAATTCAGATGGACCATAACA 58.277 33.333 7.05 0.00 0.00 2.41
2827 3361 9.574516 AAGGTATAAATTCAGATGGACCATAAC 57.425 33.333 7.05 0.00 0.00 1.89
2828 3362 9.793259 GAAGGTATAAATTCAGATGGACCATAA 57.207 33.333 7.05 0.00 0.00 1.90
2830 3364 6.936900 CGAAGGTATAAATTCAGATGGACCAT 59.063 38.462 6.71 6.71 0.00 3.55
2833 3367 5.992217 AGCGAAGGTATAAATTCAGATGGAC 59.008 40.000 0.00 0.00 35.08 4.02
2835 3369 6.867662 AAGCGAAGGTATAAATTCAGATGG 57.132 37.500 0.00 0.00 37.06 3.51
2836 3370 7.134815 CCAAAGCGAAGGTATAAATTCAGATG 58.865 38.462 0.00 0.00 37.06 2.90
2871 3407 6.995511 TGTAAAGTGCAGTGATATTAACCC 57.004 37.500 0.00 0.00 0.00 4.11
2900 3441 5.483685 AGATGCACTAAAGACAGGTAACA 57.516 39.130 0.00 0.00 41.41 2.41
2906 3447 8.479313 TGTACAAATAGATGCACTAAAGACAG 57.521 34.615 0.00 0.00 34.56 3.51
2917 3473 9.282247 CTGTTCTTTGATTGTACAAATAGATGC 57.718 33.333 13.23 9.08 38.73 3.91
2927 3483 7.483059 GCATAGCTTTCTGTTCTTTGATTGTAC 59.517 37.037 0.00 0.00 0.00 2.90
2935 3491 4.431661 GCTGCATAGCTTTCTGTTCTTT 57.568 40.909 0.00 0.00 46.57 2.52
2953 3509 8.081208 AGTTGATGATTCGAACAATATAGCTG 57.919 34.615 0.00 0.00 0.00 4.24
2966 3522 7.409697 CAATACCAAGGTAAGTTGATGATTCG 58.590 38.462 2.62 0.00 33.99 3.34
2991 3620 4.576053 AGAAAAATGAAACTGGCAAAAGGC 59.424 37.500 0.00 0.00 43.74 4.35
2999 3630 8.408601 TCTCAAGAGAAAGAAAAATGAAACTGG 58.591 33.333 0.00 0.00 33.91 4.00
3133 3764 6.582677 ATCTGTGAGATCCTTACCGATTAG 57.417 41.667 0.00 0.00 25.75 1.73
3138 3769 4.551388 GCTAATCTGTGAGATCCTTACCG 58.449 47.826 0.00 0.00 32.89 4.02
3188 3821 6.647461 TTAGGCATCATCAATGGATAGGAT 57.353 37.500 0.00 0.00 35.77 3.24
3216 3849 5.675538 TTTTGGAACCAAAATACCTGTTGG 58.324 37.500 22.61 0.91 46.80 3.77
3587 4236 3.861840 TCCTGTTATTGTGCTACTCTGC 58.138 45.455 0.00 0.00 0.00 4.26
3611 4260 6.545666 CACCCATTATAAACTGTCCAGCATAA 59.454 38.462 0.00 0.00 0.00 1.90
3857 4509 4.150980 CGACTTACTTGCATTTTACGACCA 59.849 41.667 0.00 0.00 0.00 4.02
3880 4532 4.908481 AGGATTAGATCTGGGGTTAAGGAC 59.092 45.833 5.18 0.00 0.00 3.85
3882 4534 5.608860 AGAAGGATTAGATCTGGGGTTAAGG 59.391 44.000 5.18 0.00 0.00 2.69
3955 4610 5.779529 AATGCTTTTCACACAGAACATCT 57.220 34.783 0.00 0.00 35.56 2.90
3982 4637 4.895889 TCCAGAGAATATGGTGTGACTAGG 59.104 45.833 0.00 0.00 39.01 3.02
3983 4638 5.010516 CCTCCAGAGAATATGGTGTGACTAG 59.989 48.000 0.00 0.00 39.01 2.57
3987 4642 3.041211 CCCTCCAGAGAATATGGTGTGA 58.959 50.000 0.00 0.00 39.01 3.58
4043 4699 4.217550 TGTGCCAGCATTTTTAACCTAGAC 59.782 41.667 0.00 0.00 0.00 2.59
4113 4769 6.660949 AGCTAGCCTCTACAATTTGTCAATTT 59.339 34.615 12.13 0.00 29.41 1.82
4114 4770 6.094603 CAGCTAGCCTCTACAATTTGTCAATT 59.905 38.462 12.13 0.00 32.36 2.32
4115 4771 5.587844 CAGCTAGCCTCTACAATTTGTCAAT 59.412 40.000 12.13 0.00 0.00 2.57
4116 4772 4.937620 CAGCTAGCCTCTACAATTTGTCAA 59.062 41.667 12.13 0.00 0.00 3.18
4117 4773 4.020218 ACAGCTAGCCTCTACAATTTGTCA 60.020 41.667 12.13 0.00 0.00 3.58
4118 4774 4.331168 CACAGCTAGCCTCTACAATTTGTC 59.669 45.833 12.13 0.00 0.00 3.18
4119 4775 4.020218 TCACAGCTAGCCTCTACAATTTGT 60.020 41.667 12.13 7.30 0.00 2.83
4120 4776 4.507710 TCACAGCTAGCCTCTACAATTTG 58.492 43.478 12.13 1.11 0.00 2.32
4174 4830 7.112122 AGAATGCACCTATAACTGAATTGTGA 58.888 34.615 0.00 0.00 0.00 3.58
4390 5060 5.349817 GTGAGAACGTCATCATCTTGAACAT 59.650 40.000 6.00 0.00 37.56 2.71
4415 5085 2.040012 TGCATGGAAATGCCCAAACATT 59.960 40.909 8.13 0.00 46.43 2.71
4815 5487 3.308188 CCTGTAAATTTCCCTCCTTCCGT 60.308 47.826 0.00 0.00 0.00 4.69
4823 5495 2.378547 TCACTGCCCTGTAAATTTCCCT 59.621 45.455 0.00 0.00 0.00 4.20
4918 5590 6.262273 CCGCTTCTACTCTTCTCTTTCTCTAT 59.738 42.308 0.00 0.00 0.00 1.98
5151 5828 7.243487 TCTATTCTTATTTTCGCACAGCAAAG 58.757 34.615 0.00 0.00 0.00 2.77
5251 5928 7.382759 GGCCGACAGTGTATTATTTTTGAAAAA 59.617 33.333 5.47 5.47 0.00 1.94
5252 5929 6.864165 GGCCGACAGTGTATTATTTTTGAAAA 59.136 34.615 0.00 0.00 0.00 2.29
5253 5930 6.383415 GGCCGACAGTGTATTATTTTTGAAA 58.617 36.000 0.00 0.00 0.00 2.69
5254 5931 5.106078 GGGCCGACAGTGTATTATTTTTGAA 60.106 40.000 0.00 0.00 0.00 2.69
5255 5932 4.396790 GGGCCGACAGTGTATTATTTTTGA 59.603 41.667 0.00 0.00 0.00 2.69
5256 5933 4.668289 GGGCCGACAGTGTATTATTTTTG 58.332 43.478 0.00 0.00 0.00 2.44
5257 5934 3.375922 CGGGCCGACAGTGTATTATTTTT 59.624 43.478 24.41 0.00 0.00 1.94
5258 5935 2.940410 CGGGCCGACAGTGTATTATTTT 59.060 45.455 24.41 0.00 0.00 1.82
5259 5936 2.557317 CGGGCCGACAGTGTATTATTT 58.443 47.619 24.41 0.00 0.00 1.40
5260 5937 1.808891 GCGGGCCGACAGTGTATTATT 60.809 52.381 33.44 0.00 0.00 1.40
5261 5938 0.249741 GCGGGCCGACAGTGTATTAT 60.250 55.000 33.44 0.00 0.00 1.28
5262 5939 1.142314 GCGGGCCGACAGTGTATTA 59.858 57.895 33.44 0.00 0.00 0.98
5263 5940 2.125269 GCGGGCCGACAGTGTATT 60.125 61.111 33.44 0.00 0.00 1.89
5264 5941 3.075005 AGCGGGCCGACAGTGTAT 61.075 61.111 33.44 0.64 0.00 2.29
5265 5942 4.063967 CAGCGGGCCGACAGTGTA 62.064 66.667 33.44 0.00 0.00 2.90
5296 5973 3.376935 CTGCTGTGGGCCGACTAGG 62.377 68.421 19.42 10.07 44.97 3.02
5297 5974 2.185350 CTGCTGTGGGCCGACTAG 59.815 66.667 19.42 14.72 40.92 2.57
5298 5975 3.390521 CCTGCTGTGGGCCGACTA 61.391 66.667 19.42 4.76 40.92 2.59
5305 5982 3.136123 CAATCGGCCTGCTGTGGG 61.136 66.667 0.00 0.00 0.00 4.61
5306 5983 3.136123 CCAATCGGCCTGCTGTGG 61.136 66.667 0.00 0.00 0.00 4.17
5307 5984 2.046023 TCCAATCGGCCTGCTGTG 60.046 61.111 0.00 0.00 0.00 3.66
5308 5985 2.045926 GTCCAATCGGCCTGCTGT 60.046 61.111 0.00 0.00 0.00 4.40
5309 5986 1.817099 GAGTCCAATCGGCCTGCTG 60.817 63.158 0.00 0.00 0.00 4.41
5310 5987 2.586792 GAGTCCAATCGGCCTGCT 59.413 61.111 0.00 0.00 0.00 4.24
5311 5988 2.514824 GGAGTCCAATCGGCCTGC 60.515 66.667 3.60 0.00 0.00 4.85
5312 5989 1.153289 CTGGAGTCCAATCGGCCTG 60.153 63.158 14.17 0.00 30.80 4.85
5313 5990 1.613630 ACTGGAGTCCAATCGGCCT 60.614 57.895 14.17 0.00 30.80 5.19
5314 5991 1.153349 GACTGGAGTCCAATCGGCC 60.153 63.158 14.17 0.00 39.07 6.13
5315 5992 4.522971 GACTGGAGTCCAATCGGC 57.477 61.111 14.17 0.00 39.07 5.54
5318 5995 1.153349 GGCCGACTGGAGTCCAATC 60.153 63.158 14.17 12.36 41.86 2.67
5319 5996 0.325296 TAGGCCGACTGGAGTCCAAT 60.325 55.000 14.17 1.94 41.86 3.16
5320 5997 1.077805 TAGGCCGACTGGAGTCCAA 59.922 57.895 14.17 0.00 41.86 3.53
5321 5998 1.681327 GTAGGCCGACTGGAGTCCA 60.681 63.158 12.40 12.40 41.86 4.02
5322 5999 1.668101 CTGTAGGCCGACTGGAGTCC 61.668 65.000 17.46 0.73 41.86 3.85
5323 6000 1.810532 CTGTAGGCCGACTGGAGTC 59.189 63.158 17.46 0.00 41.47 3.36
5324 6001 2.352032 GCTGTAGGCCGACTGGAGT 61.352 63.158 21.31 0.00 37.49 3.85
5325 6002 2.055042 AGCTGTAGGCCGACTGGAG 61.055 63.158 21.31 10.55 43.05 3.86
5326 6003 2.037367 AGCTGTAGGCCGACTGGA 59.963 61.111 21.31 0.01 43.05 3.86
5327 6004 2.185350 CAGCTGTAGGCCGACTGG 59.815 66.667 21.31 13.30 43.05 4.00
5328 6005 2.185350 CCAGCTGTAGGCCGACTG 59.815 66.667 17.46 17.16 43.05 3.51
5329 6006 3.775654 GCCAGCTGTAGGCCGACT 61.776 66.667 17.46 0.00 46.50 4.18
5335 6012 2.185350 CAGTCGGCCAGCTGTAGG 59.815 66.667 13.81 0.00 0.00 3.18
5336 6013 2.185350 CCAGTCGGCCAGCTGTAG 59.815 66.667 13.81 3.41 0.00 2.74
5355 6032 4.704833 CACAGTGGGCCGACAGGG 62.705 72.222 20.91 9.69 38.20 4.45
5356 6033 4.704833 CCACAGTGGGCCGACAGG 62.705 72.222 20.91 14.33 41.62 4.00
5365 6042 1.679977 CCCAATCAGCCCACAGTGG 60.680 63.158 13.35 13.35 37.25 4.00
5366 6043 0.962356 GACCCAATCAGCCCACAGTG 60.962 60.000 0.00 0.00 0.00 3.66
5367 6044 1.380302 GACCCAATCAGCCCACAGT 59.620 57.895 0.00 0.00 0.00 3.55
5368 6045 1.379044 GGACCCAATCAGCCCACAG 60.379 63.158 0.00 0.00 0.00 3.66
5369 6046 1.852157 AGGACCCAATCAGCCCACA 60.852 57.895 0.00 0.00 0.00 4.17
5370 6047 1.379044 CAGGACCCAATCAGCCCAC 60.379 63.158 0.00 0.00 0.00 4.61
5371 6048 1.852157 ACAGGACCCAATCAGCCCA 60.852 57.895 0.00 0.00 0.00 5.36
5372 6049 1.077429 GACAGGACCCAATCAGCCC 60.077 63.158 0.00 0.00 0.00 5.19
5373 6050 1.450312 CGACAGGACCCAATCAGCC 60.450 63.158 0.00 0.00 0.00 4.85
5374 6051 1.450312 CCGACAGGACCCAATCAGC 60.450 63.158 0.00 0.00 41.02 4.26
5375 6052 1.450312 GCCGACAGGACCCAATCAG 60.450 63.158 0.00 0.00 41.02 2.90
5376 6053 2.668632 GCCGACAGGACCCAATCA 59.331 61.111 0.00 0.00 41.02 2.57
5377 6054 2.124695 GGCCGACAGGACCCAATC 60.125 66.667 0.00 0.00 40.69 2.67
5384 6061 3.625897 CACAGTGGGCCGACAGGA 61.626 66.667 20.91 0.00 41.02 3.86
5385 6062 4.704833 CCACAGTGGGCCGACAGG 62.705 72.222 20.91 14.33 41.62 4.00
5394 6071 4.704833 CCAGTCGGCCCACAGTGG 62.705 72.222 13.35 13.35 37.25 4.00
5395 6072 3.596066 CTCCAGTCGGCCCACAGTG 62.596 68.421 2.46 0.00 0.00 3.66
5396 6073 3.314331 CTCCAGTCGGCCCACAGT 61.314 66.667 2.46 0.00 0.00 3.55
5397 6074 4.767255 GCTCCAGTCGGCCCACAG 62.767 72.222 2.46 0.00 0.00 3.66
5398 6075 3.897681 TAGCTCCAGTCGGCCCACA 62.898 63.158 2.46 0.00 0.00 4.17
5399 6076 1.972660 ATTAGCTCCAGTCGGCCCAC 61.973 60.000 0.00 0.00 0.00 4.61
5400 6077 1.271840 AATTAGCTCCAGTCGGCCCA 61.272 55.000 0.00 0.00 0.00 5.36
5401 6078 0.756903 TAATTAGCTCCAGTCGGCCC 59.243 55.000 0.00 0.00 0.00 5.80
5402 6079 1.874320 GCTAATTAGCTCCAGTCGGCC 60.874 57.143 26.79 0.00 45.62 6.13
5403 6080 1.503294 GCTAATTAGCTCCAGTCGGC 58.497 55.000 26.79 0.52 45.62 5.54
5414 6091 1.221414 GCCCACAGCGAGCTAATTAG 58.779 55.000 8.20 8.20 0.00 1.73
5415 6092 3.379650 GCCCACAGCGAGCTAATTA 57.620 52.632 0.00 0.00 0.00 1.40
5416 6093 4.225497 GCCCACAGCGAGCTAATT 57.775 55.556 0.00 0.00 0.00 1.40
5425 6102 2.480037 GCAAAAACAATTAGCCCACAGC 59.520 45.455 0.00 0.00 44.25 4.40
5426 6103 3.726607 TGCAAAAACAATTAGCCCACAG 58.273 40.909 0.00 0.00 0.00 3.66
5427 6104 3.827008 TGCAAAAACAATTAGCCCACA 57.173 38.095 0.00 0.00 0.00 4.17
5428 6105 5.491635 TTTTGCAAAAACAATTAGCCCAC 57.508 34.783 21.94 0.00 0.00 4.61


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

AutoCloner maintained by Alex Coulton.