Multiple sequence alignment - TraesCS2A01G307000

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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 TraesCS2A01G307000 chr2A 100.000 3203 0 0 1 3203 527899259 527902461 0.000000e+00 5915.0
1 TraesCS2A01G307000 chr2A 80.829 193 34 3 3012 3203 532431550 532431360 7.160000e-32 148.0
2 TraesCS2A01G307000 chr2B 93.903 1837 60 16 949 2756 462883024 462884837 0.000000e+00 2724.0
3 TraesCS2A01G307000 chr2B 87.991 891 42 31 91 941 462882116 462882981 0.000000e+00 992.0
4 TraesCS2A01G307000 chr2B 80.731 301 49 7 2905 3203 462884835 462885128 3.210000e-55 226.0
5 TraesCS2A01G307000 chr2D 92.246 1741 90 19 949 2677 391260727 391262434 0.000000e+00 2425.0
6 TraesCS2A01G307000 chr2D 90.693 1010 35 22 1 978 391259728 391260710 0.000000e+00 1290.0
7 TraesCS2A01G307000 chr3D 80.303 264 47 4 2943 3202 488121197 488120935 9.070000e-46 195.0
8 TraesCS2A01G307000 chr4A 79.253 241 45 4 2961 3197 544168866 544169105 2.560000e-36 163.0
9 TraesCS2A01G307000 chr4A 80.189 212 40 1 2993 3202 737050485 737050696 1.190000e-34 158.0
10 TraesCS2A01G307000 chr5B 80.597 201 37 1 3005 3203 166322441 166322241 1.540000e-33 154.0
11 TraesCS2A01G307000 chr5B 94.792 96 2 3 2515 2609 450665270 450665363 2.570000e-31 147.0
12 TraesCS2A01G307000 chr1A 77.606 259 48 8 2950 3203 100041485 100041232 7.160000e-32 148.0
13 TraesCS2A01G307000 chr1A 94.737 95 3 2 2523 2616 531051446 531051539 2.570000e-31 147.0
14 TraesCS2A01G307000 chr1A 76.829 246 52 5 2960 3203 248619899 248619657 2.000000e-27 134.0
15 TraesCS2A01G307000 chr7A 93.939 99 2 4 2506 2604 227030899 227030993 2.570000e-31 147.0
16 TraesCS2A01G307000 chr1D 96.591 88 2 1 2523 2609 432400396 432400483 9.260000e-31 145.0
17 TraesCS2A01G307000 chr1B 96.552 87 3 0 2523 2609 583974455 583974541 9.260000e-31 145.0
18 TraesCS2A01G307000 chr6A 95.556 90 2 2 2520 2609 441496775 441496862 3.330000e-30 143.0
19 TraesCS2A01G307000 chr6A 85.714 77 8 1 2159 2235 484068031 484068104 9.530000e-11 78.7
20 TraesCS2A01G307000 chr3B 92.079 101 6 2 2523 2621 723266471 723266371 1.200000e-29 141.0
21 TraesCS2A01G307000 chr3A 78.017 232 43 8 2975 3203 732916022 732915796 4.310000e-29 139.0


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 TraesCS2A01G307000 chr2A 527899259 527902461 3202 False 5915.0 5915 100.000000 1 3203 1 chr2A.!!$F1 3202
1 TraesCS2A01G307000 chr2B 462882116 462885128 3012 False 1314.0 2724 87.541667 91 3203 3 chr2B.!!$F1 3112
2 TraesCS2A01G307000 chr2D 391259728 391262434 2706 False 1857.5 2425 91.469500 1 2677 2 chr2D.!!$F1 2676

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
469 489 0.040499 ACACACCTCCTCCTCTCTCC 59.96 60.0 0.0 0.0 0.0 3.71 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2416 2521 0.458025 CTCCTACGTCGCAGTTTCCC 60.458 60.0 0.0 0.0 0.0 3.97 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
21 22 2.092646 AGTCCACAGTTGGCAAACAGTA 60.093 45.455 6.76 0.00 43.56 2.74
22 23 2.032924 GTCCACAGTTGGCAAACAGTAC 59.967 50.000 6.76 0.00 43.56 2.73
23 24 1.336755 CCACAGTTGGCAAACAGTACC 59.663 52.381 6.76 0.00 38.88 3.34
217 229 7.014230 GCAGAACAGGCCTATTAATCCATTTTA 59.986 37.037 3.98 0.00 0.00 1.52
237 254 1.848652 AAAATGCTGCAGCCTCTCAT 58.151 45.000 34.64 18.88 41.18 2.90
238 255 1.390565 AAATGCTGCAGCCTCTCATC 58.609 50.000 34.64 6.50 41.18 2.92
240 257 0.107081 ATGCTGCAGCCTCTCATCTC 59.893 55.000 34.64 4.94 41.18 2.75
241 258 1.262640 TGCTGCAGCCTCTCATCTCA 61.263 55.000 34.64 10.20 41.18 3.27
242 259 0.107800 GCTGCAGCCTCTCATCTCAA 60.108 55.000 28.76 0.00 34.31 3.02
243 260 1.942677 CTGCAGCCTCTCATCTCAAG 58.057 55.000 0.00 0.00 0.00 3.02
244 261 1.207570 CTGCAGCCTCTCATCTCAAGT 59.792 52.381 0.00 0.00 0.00 3.16
245 262 1.627329 TGCAGCCTCTCATCTCAAGTT 59.373 47.619 0.00 0.00 0.00 2.66
246 263 2.008329 GCAGCCTCTCATCTCAAGTTG 58.992 52.381 0.00 0.00 0.00 3.16
247 264 2.354503 GCAGCCTCTCATCTCAAGTTGA 60.355 50.000 5.25 5.25 0.00 3.18
248 265 3.523547 CAGCCTCTCATCTCAAGTTGAG 58.476 50.000 24.37 24.37 45.59 3.02
249 266 2.500910 AGCCTCTCATCTCAAGTTGAGG 59.499 50.000 28.33 15.94 44.39 3.86
250 267 2.235898 GCCTCTCATCTCAAGTTGAGGT 59.764 50.000 28.33 21.61 44.39 3.85
251 268 3.307339 GCCTCTCATCTCAAGTTGAGGTT 60.307 47.826 28.33 15.99 44.39 3.50
252 269 4.252073 CCTCTCATCTCAAGTTGAGGTTG 58.748 47.826 28.33 24.37 44.39 3.77
253 270 4.252073 CTCTCATCTCAAGTTGAGGTTGG 58.748 47.826 28.33 17.61 44.39 3.77
254 271 2.746362 CTCATCTCAAGTTGAGGTTGGC 59.254 50.000 28.33 0.00 44.39 4.52
255 272 1.815003 CATCTCAAGTTGAGGTTGGCC 59.185 52.381 28.33 0.00 44.39 5.36
256 273 0.250295 TCTCAAGTTGAGGTTGGCCG 60.250 55.000 28.33 5.69 44.39 6.13
257 274 0.535102 CTCAAGTTGAGGTTGGCCGT 60.535 55.000 22.95 0.00 40.71 5.68
258 275 0.106918 TCAAGTTGAGGTTGGCCGTT 60.107 50.000 0.08 0.00 40.50 4.44
276 293 0.749818 TTCCGTTCCAAGCTGCACAA 60.750 50.000 1.02 0.00 0.00 3.33
469 489 0.040499 ACACACCTCCTCCTCTCTCC 59.960 60.000 0.00 0.00 0.00 3.71
470 490 0.686112 CACACCTCCTCCTCTCTCCC 60.686 65.000 0.00 0.00 0.00 4.30
471 491 0.853586 ACACCTCCTCCTCTCTCCCT 60.854 60.000 0.00 0.00 0.00 4.20
472 492 0.106217 CACCTCCTCCTCTCTCCCTC 60.106 65.000 0.00 0.00 0.00 4.30
476 496 0.622154 TCCTCCTCTCTCCCTCGTCT 60.622 60.000 0.00 0.00 0.00 4.18
496 516 2.520741 CTCGCTCCTCCTCTCCCC 60.521 72.222 0.00 0.00 0.00 4.81
497 517 3.024356 TCGCTCCTCCTCTCCCCT 61.024 66.667 0.00 0.00 0.00 4.79
505 525 0.478507 CTCCTCTCCCCTCTCTCTCC 59.521 65.000 0.00 0.00 0.00 3.71
506 526 0.047176 TCCTCTCCCCTCTCTCTCCT 59.953 60.000 0.00 0.00 0.00 3.69
509 529 0.253868 TCTCCCCTCTCTCTCCTCCA 60.254 60.000 0.00 0.00 0.00 3.86
510 530 0.633921 CTCCCCTCTCTCTCCTCCAA 59.366 60.000 0.00 0.00 0.00 3.53
511 531 0.633921 TCCCCTCTCTCTCCTCCAAG 59.366 60.000 0.00 0.00 0.00 3.61
515 535 2.378038 CCTCTCTCTCCTCCAAGACAG 58.622 57.143 0.00 0.00 0.00 3.51
516 536 2.378038 CTCTCTCTCCTCCAAGACAGG 58.622 57.143 0.00 0.00 0.00 4.00
707 743 1.136611 GTTTCGTCTGCTGCTGTTACG 60.137 52.381 12.40 12.40 34.99 3.18
738 774 3.117776 CCATGGATTCTTGATGGGAGTGA 60.118 47.826 5.56 0.00 34.14 3.41
759 801 2.046507 GGGAGTGAGTGCCAGCAG 60.047 66.667 0.00 0.00 36.40 4.24
762 804 3.541950 GAGTGAGTGCCAGCAGCCA 62.542 63.158 0.00 0.00 42.71 4.75
763 805 3.054503 GTGAGTGCCAGCAGCCAG 61.055 66.667 0.00 0.00 42.71 4.85
764 806 3.563224 TGAGTGCCAGCAGCCAGT 61.563 61.111 0.00 0.00 42.71 4.00
765 807 2.282040 GAGTGCCAGCAGCCAGTT 60.282 61.111 0.00 0.00 42.71 3.16
770 821 1.273327 GTGCCAGCAGCCAGTTAAAAT 59.727 47.619 0.00 0.00 42.71 1.82
774 825 2.099756 CCAGCAGCCAGTTAAAATAGCC 59.900 50.000 0.00 0.00 0.00 3.93
859 910 0.449388 CCGGAGCTGCAGATTTGTTC 59.551 55.000 20.43 0.00 0.00 3.18
866 917 1.741706 CTGCAGATTTGTTCGCCATCT 59.258 47.619 8.42 0.00 0.00 2.90
881 933 3.664107 GCCATCTTTTTGGGGTTTTCTC 58.336 45.455 0.00 0.00 37.24 2.87
902 954 5.655090 TCTCGATGAGTTCTTGGTTGGTATA 59.345 40.000 0.00 0.00 0.00 1.47
943 995 2.481952 CTCTTTTTCCTGCTTGGACGAG 59.518 50.000 0.00 0.97 46.14 4.18
951 1050 0.830648 TGCTTGGACGAGGGATTAGG 59.169 55.000 0.00 0.00 0.00 2.69
1092 1195 2.202440 CAGACGTACGACCGCCAG 60.202 66.667 24.41 0.00 0.00 4.85
1176 1279 4.367023 GGCGACACCACCGTGCTA 62.367 66.667 0.00 0.00 44.40 3.49
1405 1508 2.853542 TGCAGCTGGGGTTCCTGA 60.854 61.111 17.12 0.00 34.32 3.86
1413 1516 2.656069 GGGGTTCCTGAGCGTGCTA 61.656 63.158 0.00 0.00 0.00 3.49
1563 1666 3.072915 TCAACATGCTCAAGAAGGAGGAA 59.927 43.478 0.00 0.00 38.78 3.36
1564 1667 3.064900 ACATGCTCAAGAAGGAGGAAC 57.935 47.619 0.00 0.00 38.78 3.62
1880 1983 4.347453 GTCGTGGTGGGCGTACGT 62.347 66.667 17.90 0.00 38.80 3.57
2215 2318 0.683973 CAGGTGAACCAGAGCTGAGT 59.316 55.000 1.62 0.00 40.66 3.41
2216 2319 1.895798 CAGGTGAACCAGAGCTGAGTA 59.104 52.381 1.62 0.00 40.66 2.59
2217 2320 1.896465 AGGTGAACCAGAGCTGAGTAC 59.104 52.381 1.62 0.00 38.89 2.73
2218 2321 1.896465 GGTGAACCAGAGCTGAGTACT 59.104 52.381 0.00 0.00 35.64 2.73
2341 2446 2.813754 TGTAGTGGCAATTCTGTGAAGC 59.186 45.455 0.00 0.00 0.00 3.86
2343 2448 2.590821 AGTGGCAATTCTGTGAAGCTT 58.409 42.857 0.00 0.00 0.00 3.74
2346 2451 2.957680 TGGCAATTCTGTGAAGCTTCAA 59.042 40.909 29.99 15.58 39.21 2.69
2362 2467 3.424170 GCTTCAAGCGTCAATTGAGAGAC 60.424 47.826 8.80 0.00 37.91 3.36
2416 2521 4.481930 TGATTCCAACTGTTTTGCTACG 57.518 40.909 0.00 0.00 0.00 3.51
2428 2535 0.947180 TTGCTACGGGAAACTGCGAC 60.947 55.000 0.00 0.00 41.93 5.19
2520 2632 8.344831 TCTGGAATTACAAATTATGAAGCATCG 58.655 33.333 0.00 0.00 0.00 3.84
2600 2712 1.153647 CCACGCTCACCGCATTCTA 60.154 57.895 0.00 0.00 41.76 2.10
2609 2732 4.795278 GCTCACCGCATTCTATTCTTTTTG 59.205 41.667 0.00 0.00 38.92 2.44
2649 2772 8.442605 TTTCGAAATCGTTCAATATTGTTTCC 57.557 30.769 14.97 1.75 40.80 3.13
2682 2805 4.022935 TGTTGATTTCTGAGCTGCGAAAAT 60.023 37.500 10.12 5.20 33.37 1.82
2688 2811 4.566545 TCTGAGCTGCGAAAATGAAAAA 57.433 36.364 0.00 0.00 0.00 1.94
2690 2813 3.380142 TGAGCTGCGAAAATGAAAAACC 58.620 40.909 0.00 0.00 0.00 3.27
2692 2815 3.791245 AGCTGCGAAAATGAAAAACCAA 58.209 36.364 0.00 0.00 0.00 3.67
2693 2816 3.803778 AGCTGCGAAAATGAAAAACCAAG 59.196 39.130 0.00 0.00 0.00 3.61
2694 2817 3.604543 GCTGCGAAAATGAAAAACCAAGC 60.605 43.478 0.00 0.00 0.00 4.01
2695 2818 3.525537 TGCGAAAATGAAAAACCAAGCA 58.474 36.364 0.00 0.00 0.00 3.91
2696 2819 3.308323 TGCGAAAATGAAAAACCAAGCAC 59.692 39.130 0.00 0.00 0.00 4.40
2697 2820 3.308323 GCGAAAATGAAAAACCAAGCACA 59.692 39.130 0.00 0.00 0.00 4.57
2698 2821 4.201763 GCGAAAATGAAAAACCAAGCACAA 60.202 37.500 0.00 0.00 0.00 3.33
2699 2822 5.672321 GCGAAAATGAAAAACCAAGCACAAA 60.672 36.000 0.00 0.00 0.00 2.83
2757 2897 9.386010 TGAGCTACAAACTAAAGTTTTAACTCA 57.614 29.630 15.99 15.99 45.07 3.41
2804 2944 3.694043 TGGAACAAAGTCATCATCCGA 57.306 42.857 0.00 0.00 31.92 4.55
2805 2945 4.220693 TGGAACAAAGTCATCATCCGAT 57.779 40.909 0.00 0.00 31.92 4.18
2806 2946 4.588899 TGGAACAAAGTCATCATCCGATT 58.411 39.130 0.00 0.00 31.92 3.34
2807 2947 4.635765 TGGAACAAAGTCATCATCCGATTC 59.364 41.667 0.00 0.00 31.92 2.52
2808 2948 4.035675 GGAACAAAGTCATCATCCGATTCC 59.964 45.833 0.00 0.00 0.00 3.01
2809 2949 3.198068 ACAAAGTCATCATCCGATTCCG 58.802 45.455 0.00 0.00 0.00 4.30
2810 2950 3.118775 ACAAAGTCATCATCCGATTCCGA 60.119 43.478 0.00 0.00 38.22 4.55
2811 2951 3.377346 AAGTCATCATCCGATTCCGAG 57.623 47.619 0.00 0.00 38.22 4.63
2812 2952 2.587522 AGTCATCATCCGATTCCGAGA 58.412 47.619 0.00 0.00 38.22 4.04
2813 2953 2.556189 AGTCATCATCCGATTCCGAGAG 59.444 50.000 0.00 0.00 38.22 3.20
2829 2969 3.490078 CCGAGAGGCAGAACTACATTCTC 60.490 52.174 0.00 0.00 44.93 2.87
2830 2970 3.701241 GAGAGGCAGAACTACATTCTCG 58.299 50.000 0.00 0.00 44.99 4.04
2831 2971 3.093057 AGAGGCAGAACTACATTCTCGT 58.907 45.455 0.00 0.00 44.99 4.18
2832 2972 3.119316 AGAGGCAGAACTACATTCTCGTG 60.119 47.826 0.00 0.00 44.99 4.35
2833 2973 1.661112 GGCAGAACTACATTCTCGTGC 59.339 52.381 0.00 0.00 44.99 5.34
2834 2974 2.337583 GCAGAACTACATTCTCGTGCA 58.662 47.619 0.00 0.00 44.99 4.57
2835 2975 2.092838 GCAGAACTACATTCTCGTGCAC 59.907 50.000 6.82 6.82 44.99 4.57
2836 2976 3.317150 CAGAACTACATTCTCGTGCACA 58.683 45.455 18.64 3.15 44.99 4.57
2837 2977 3.740832 CAGAACTACATTCTCGTGCACAA 59.259 43.478 18.64 3.87 44.99 3.33
2838 2978 4.211164 CAGAACTACATTCTCGTGCACAAA 59.789 41.667 18.64 8.19 44.99 2.83
2839 2979 4.211374 AGAACTACATTCTCGTGCACAAAC 59.789 41.667 18.64 0.00 44.99 2.93
2840 2980 3.462982 ACTACATTCTCGTGCACAAACA 58.537 40.909 18.64 0.00 0.00 2.83
2841 2981 4.065088 ACTACATTCTCGTGCACAAACAT 58.935 39.130 18.64 0.00 0.00 2.71
2842 2982 3.272439 ACATTCTCGTGCACAAACATG 57.728 42.857 18.64 14.81 0.00 3.21
2843 2983 1.980844 CATTCTCGTGCACAAACATGC 59.019 47.619 18.64 0.00 46.32 4.06
2844 2984 1.308047 TTCTCGTGCACAAACATGCT 58.692 45.000 18.64 0.00 46.28 3.79
2845 2985 2.162319 TCTCGTGCACAAACATGCTA 57.838 45.000 18.64 0.00 46.28 3.49
2846 2986 1.798223 TCTCGTGCACAAACATGCTAC 59.202 47.619 18.64 0.00 46.28 3.58
2847 2987 1.800586 CTCGTGCACAAACATGCTACT 59.199 47.619 18.64 0.00 46.28 2.57
2848 2988 2.217750 TCGTGCACAAACATGCTACTT 58.782 42.857 18.64 0.00 46.28 2.24
2849 2989 2.223144 TCGTGCACAAACATGCTACTTC 59.777 45.455 18.64 0.00 46.28 3.01
2850 2990 2.574322 GTGCACAAACATGCTACTTCG 58.426 47.619 13.17 0.00 46.28 3.79
2851 2991 2.223144 GTGCACAAACATGCTACTTCGA 59.777 45.455 13.17 0.00 46.28 3.71
2852 2992 2.480037 TGCACAAACATGCTACTTCGAG 59.520 45.455 0.00 0.00 46.28 4.04
2853 2993 2.736721 GCACAAACATGCTACTTCGAGA 59.263 45.455 0.00 0.00 42.62 4.04
2854 2994 3.186409 GCACAAACATGCTACTTCGAGAA 59.814 43.478 0.00 0.00 42.62 2.87
2855 2995 4.667668 GCACAAACATGCTACTTCGAGAAG 60.668 45.833 10.97 10.97 42.62 2.85
2856 2996 3.997021 ACAAACATGCTACTTCGAGAAGG 59.003 43.478 16.16 1.98 42.53 3.46
2857 2997 4.245660 CAAACATGCTACTTCGAGAAGGA 58.754 43.478 16.16 7.63 42.53 3.36
2858 2998 4.744795 AACATGCTACTTCGAGAAGGAT 57.255 40.909 16.16 0.26 42.53 3.24
2859 2999 5.854010 AACATGCTACTTCGAGAAGGATA 57.146 39.130 16.16 1.97 42.53 2.59
2860 3000 5.854010 ACATGCTACTTCGAGAAGGATAA 57.146 39.130 16.16 0.87 42.53 1.75
2861 3001 6.412362 ACATGCTACTTCGAGAAGGATAAT 57.588 37.500 16.16 3.02 42.53 1.28
2862 3002 6.451393 ACATGCTACTTCGAGAAGGATAATC 58.549 40.000 16.16 0.37 42.53 1.75
2863 3003 6.040955 ACATGCTACTTCGAGAAGGATAATCA 59.959 38.462 16.16 5.26 42.53 2.57
2864 3004 5.833082 TGCTACTTCGAGAAGGATAATCAC 58.167 41.667 16.16 0.00 42.53 3.06
2865 3005 5.594725 TGCTACTTCGAGAAGGATAATCACT 59.405 40.000 16.16 0.00 42.53 3.41
2866 3006 6.771267 TGCTACTTCGAGAAGGATAATCACTA 59.229 38.462 16.16 0.00 42.53 2.74
2867 3007 7.448777 TGCTACTTCGAGAAGGATAATCACTAT 59.551 37.037 16.16 0.00 42.53 2.12
2868 3008 8.301002 GCTACTTCGAGAAGGATAATCACTATT 58.699 37.037 16.16 0.00 42.53 1.73
2886 3026 8.087982 TCACTATTTATCCAAATCGAAGATGC 57.912 34.615 0.00 0.00 45.12 3.91
2887 3027 7.714813 TCACTATTTATCCAAATCGAAGATGCA 59.285 33.333 0.00 0.00 45.12 3.96
2888 3028 7.800380 CACTATTTATCCAAATCGAAGATGCAC 59.200 37.037 0.00 0.00 45.12 4.57
2889 3029 6.698008 ATTTATCCAAATCGAAGATGCACA 57.302 33.333 0.00 0.00 45.12 4.57
2890 3030 5.484173 TTATCCAAATCGAAGATGCACAC 57.516 39.130 0.00 0.00 45.12 3.82
2891 3031 2.777094 TCCAAATCGAAGATGCACACA 58.223 42.857 0.00 0.00 45.12 3.72
2892 3032 3.145286 TCCAAATCGAAGATGCACACAA 58.855 40.909 0.00 0.00 45.12 3.33
2893 3033 3.189080 TCCAAATCGAAGATGCACACAAG 59.811 43.478 0.00 0.00 45.12 3.16
2894 3034 2.907910 AATCGAAGATGCACACAAGC 57.092 45.000 0.00 0.00 45.12 4.01
2901 3041 2.101965 TGCACACAAGCACGCAAC 59.898 55.556 0.00 0.00 40.11 4.17
2902 3042 3.018428 GCACACAAGCACGCAACG 61.018 61.111 0.00 0.00 0.00 4.10
2903 3043 3.018428 CACACAAGCACGCAACGC 61.018 61.111 0.00 0.00 0.00 4.84
2904 3044 3.504273 ACACAAGCACGCAACGCA 61.504 55.556 0.00 0.00 0.00 5.24
2905 3045 3.018428 CACAAGCACGCAACGCAC 61.018 61.111 0.00 0.00 0.00 5.34
2906 3046 3.202001 ACAAGCACGCAACGCACT 61.202 55.556 0.00 0.00 0.00 4.40
2907 3047 2.425773 CAAGCACGCAACGCACTC 60.426 61.111 0.00 0.00 0.00 3.51
2939 3079 5.404968 GCCATTTCAGAATCTAGACTCATCG 59.595 44.000 3.70 0.00 0.00 3.84
2941 3081 5.582689 TTTCAGAATCTAGACTCATCGCA 57.417 39.130 3.70 0.00 0.00 5.10
2945 3085 5.126222 TCAGAATCTAGACTCATCGCAAACT 59.874 40.000 3.70 0.00 0.00 2.66
2948 3088 6.975772 AGAATCTAGACTCATCGCAAACTAAC 59.024 38.462 3.70 0.00 0.00 2.34
2955 3095 3.259064 TCATCGCAAACTAACCTGTAGC 58.741 45.455 0.00 0.00 0.00 3.58
2958 3098 1.128692 CGCAAACTAACCTGTAGCTGC 59.871 52.381 0.00 0.00 0.00 5.25
2970 3111 1.928046 TAGCTGCATGGTTGGGGGA 60.928 57.895 1.02 0.00 0.00 4.81
2974 3115 0.178981 CTGCATGGTTGGGGGATAGG 60.179 60.000 0.00 0.00 0.00 2.57
2982 3123 2.699281 GGTTGGGGGATAGGTGGTATCT 60.699 54.545 0.00 0.00 38.14 1.98
2984 3125 1.870327 TGGGGGATAGGTGGTATCTCA 59.130 52.381 0.00 0.00 40.14 3.27
2986 3127 2.907042 GGGGGATAGGTGGTATCTCAAG 59.093 54.545 0.00 0.00 40.14 3.02
2989 3130 2.972713 GGATAGGTGGTATCTCAAGCCA 59.027 50.000 0.00 0.00 38.14 4.75
2990 3131 3.584848 GGATAGGTGGTATCTCAAGCCAT 59.415 47.826 0.00 0.00 38.14 4.40
2991 3132 4.323104 GGATAGGTGGTATCTCAAGCCATC 60.323 50.000 0.00 0.00 38.14 3.51
2992 3133 2.481441 AGGTGGTATCTCAAGCCATCA 58.519 47.619 0.00 0.00 35.93 3.07
2993 3134 2.437281 AGGTGGTATCTCAAGCCATCAG 59.563 50.000 0.00 0.00 35.93 2.90
2994 3135 2.486191 GGTGGTATCTCAAGCCATCAGG 60.486 54.545 0.00 0.00 33.78 3.86
3008 3150 1.815003 CATCAGGGTTCAAGTTCTGGC 59.185 52.381 0.00 0.00 0.00 4.85
3012 3154 1.172812 GGGTTCAAGTTCTGGCGCTT 61.173 55.000 7.64 0.00 0.00 4.68
3014 3156 0.663153 GTTCAAGTTCTGGCGCTTGT 59.337 50.000 7.64 0.00 41.83 3.16
3021 3163 5.064707 TCAAGTTCTGGCGCTTGTATTATTC 59.935 40.000 7.64 0.00 41.83 1.75
3062 3204 0.858583 CGACAATGTGCGTTCAGTGA 59.141 50.000 13.97 0.00 36.97 3.41
3066 3208 2.224042 ACAATGTGCGTTCAGTGAGAGA 60.224 45.455 13.97 0.00 36.97 3.10
3070 3212 2.297315 TGTGCGTTCAGTGAGAGAAGAT 59.703 45.455 0.00 0.00 0.00 2.40
3076 3218 4.321601 CGTTCAGTGAGAGAAGATGTTCCT 60.322 45.833 0.00 0.00 32.48 3.36
3082 3224 3.191581 TGAGAGAAGATGTTCCTGTCGAC 59.808 47.826 9.11 9.11 32.48 4.20
3098 3240 1.443872 GACTACGAGGCGTGTGTGG 60.444 63.158 2.33 0.00 41.39 4.17
3110 3252 1.735018 CGTGTGTGGTGACTTTGTCAA 59.265 47.619 1.73 0.00 44.49 3.18
3113 3255 2.948979 TGTGTGGTGACTTTGTCAATCC 59.051 45.455 1.73 1.76 44.49 3.01
3114 3256 3.214328 GTGTGGTGACTTTGTCAATCCT 58.786 45.455 1.73 0.00 44.49 3.24
3120 3262 5.939883 TGGTGACTTTGTCAATCCTAAGATG 59.060 40.000 1.73 0.00 44.49 2.90
3126 3268 8.388484 ACTTTGTCAATCCTAAGATGATATGC 57.612 34.615 0.00 0.00 31.29 3.14
3130 3272 4.532126 TCAATCCTAAGATGATATGCCGGT 59.468 41.667 1.90 0.00 31.29 5.28
3136 3278 3.845781 AGATGATATGCCGGTTCAGTT 57.154 42.857 1.90 0.00 0.00 3.16
3138 3280 4.526970 AGATGATATGCCGGTTCAGTTTT 58.473 39.130 1.90 0.00 0.00 2.43
3141 3283 4.075682 TGATATGCCGGTTCAGTTTTTCA 58.924 39.130 1.90 0.00 0.00 2.69
3144 3286 1.946768 TGCCGGTTCAGTTTTTCAGAG 59.053 47.619 1.90 0.00 0.00 3.35
3150 3292 3.003793 GGTTCAGTTTTTCAGAGGTGCTC 59.996 47.826 0.00 0.00 0.00 4.26
3151 3293 2.483876 TCAGTTTTTCAGAGGTGCTCG 58.516 47.619 0.00 0.00 35.36 5.03
3154 3296 3.807622 CAGTTTTTCAGAGGTGCTCGTAA 59.192 43.478 0.00 0.00 35.36 3.18
3155 3297 4.272504 CAGTTTTTCAGAGGTGCTCGTAAA 59.727 41.667 0.00 0.00 35.36 2.01
3166 3308 1.822990 TGCTCGTAAAGGTAGGGTCTG 59.177 52.381 0.00 0.00 0.00 3.51
3167 3309 1.471153 GCTCGTAAAGGTAGGGTCTGC 60.471 57.143 0.00 0.00 0.00 4.26
3168 3310 0.813184 TCGTAAAGGTAGGGTCTGCG 59.187 55.000 0.00 0.00 0.00 5.18
3169 3311 0.529378 CGTAAAGGTAGGGTCTGCGT 59.471 55.000 0.00 0.00 0.00 5.24
3170 3312 1.734707 CGTAAAGGTAGGGTCTGCGTG 60.735 57.143 0.00 0.00 0.00 5.34
3171 3313 1.274447 GTAAAGGTAGGGTCTGCGTGT 59.726 52.381 0.00 0.00 0.00 4.49
3172 3314 0.034896 AAAGGTAGGGTCTGCGTGTG 59.965 55.000 0.00 0.00 0.00 3.82
3173 3315 1.119574 AAGGTAGGGTCTGCGTGTGT 61.120 55.000 0.00 0.00 0.00 3.72
3174 3316 1.374252 GGTAGGGTCTGCGTGTGTG 60.374 63.158 0.00 0.00 0.00 3.82
3178 3320 1.522806 GGGTCTGCGTGTGTGTTCA 60.523 57.895 0.00 0.00 0.00 3.18
3181 3323 2.139917 GGTCTGCGTGTGTGTTCATAA 58.860 47.619 0.00 0.00 0.00 1.90
3194 3336 6.818142 TGTGTGTTCATAAGGATGAGTGTATG 59.182 38.462 0.00 0.00 43.03 2.39
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
21 22 3.211045 GTCTACATTTGTGTGGTGTGGT 58.789 45.455 0.00 0.00 0.00 4.16
22 23 3.210227 TGTCTACATTTGTGTGGTGTGG 58.790 45.455 0.00 0.00 0.00 4.17
23 24 3.876914 ACTGTCTACATTTGTGTGGTGTG 59.123 43.478 0.00 0.00 0.00 3.82
217 229 1.624336 TGAGAGGCTGCAGCATTTTT 58.376 45.000 37.63 21.40 44.36 1.94
238 255 0.535102 ACGGCCAACCTCAACTTGAG 60.535 55.000 11.37 11.37 43.91 3.02
240 257 0.310854 GAACGGCCAACCTCAACTTG 59.689 55.000 2.24 0.00 0.00 3.16
241 258 0.822121 GGAACGGCCAACCTCAACTT 60.822 55.000 2.24 0.00 36.34 2.66
242 259 1.228154 GGAACGGCCAACCTCAACT 60.228 57.895 2.24 0.00 36.34 3.16
243 260 3.351450 GGAACGGCCAACCTCAAC 58.649 61.111 2.24 0.00 36.34 3.18
256 273 1.282875 GTGCAGCTTGGAACGGAAC 59.717 57.895 0.00 0.00 0.00 3.62
257 274 0.749818 TTGTGCAGCTTGGAACGGAA 60.750 50.000 0.00 0.00 0.00 4.30
258 275 0.537143 ATTGTGCAGCTTGGAACGGA 60.537 50.000 0.00 0.00 0.00 4.69
276 293 2.124151 GGACTGGCCGGAATGCAT 60.124 61.111 21.41 0.00 0.00 3.96
469 489 1.720694 GAGGAGCGAGGAAGACGAGG 61.721 65.000 0.00 0.00 0.00 4.63
470 490 1.720694 GGAGGAGCGAGGAAGACGAG 61.721 65.000 0.00 0.00 0.00 4.18
471 491 1.749638 GGAGGAGCGAGGAAGACGA 60.750 63.158 0.00 0.00 0.00 4.20
472 492 1.720694 GAGGAGGAGCGAGGAAGACG 61.721 65.000 0.00 0.00 0.00 4.18
476 496 1.076632 GGAGAGGAGGAGCGAGGAA 60.077 63.158 0.00 0.00 0.00 3.36
496 516 2.378038 CCTGTCTTGGAGGAGAGAGAG 58.622 57.143 1.12 0.00 38.87 3.20
497 517 1.618345 GCCTGTCTTGGAGGAGAGAGA 60.618 57.143 1.12 0.00 38.87 3.10
505 525 1.204467 GTCTCTCTGCCTGTCTTGGAG 59.796 57.143 0.00 0.00 0.00 3.86
506 526 1.261480 GTCTCTCTGCCTGTCTTGGA 58.739 55.000 0.00 0.00 0.00 3.53
509 529 1.892474 GTCTGTCTCTCTGCCTGTCTT 59.108 52.381 0.00 0.00 0.00 3.01
510 530 1.202989 TGTCTGTCTCTCTGCCTGTCT 60.203 52.381 0.00 0.00 0.00 3.41
511 531 1.202114 CTGTCTGTCTCTCTGCCTGTC 59.798 57.143 0.00 0.00 0.00 3.51
515 535 1.745087 CTCTCTGTCTGTCTCTCTGCC 59.255 57.143 0.00 0.00 0.00 4.85
516 536 2.679837 CTCTCTCTGTCTGTCTCTCTGC 59.320 54.545 0.00 0.00 0.00 4.26
707 743 3.876914 TCAAGAATCCATGGCGATGTAAC 59.123 43.478 6.96 0.00 0.00 2.50
738 774 1.681666 CTGGCACTCACTCCCATGT 59.318 57.895 0.00 0.00 0.00 3.21
755 797 3.372440 AGGCTATTTTAACTGGCTGCT 57.628 42.857 0.00 0.00 34.03 4.24
756 798 3.696548 AGAAGGCTATTTTAACTGGCTGC 59.303 43.478 0.00 0.00 35.50 5.25
759 801 4.459337 ACACAGAAGGCTATTTTAACTGGC 59.541 41.667 0.00 0.00 0.00 4.85
762 804 5.705905 GGTCACACAGAAGGCTATTTTAACT 59.294 40.000 0.00 0.00 0.00 2.24
763 805 5.390567 CGGTCACACAGAAGGCTATTTTAAC 60.391 44.000 0.00 0.00 0.00 2.01
764 806 4.693566 CGGTCACACAGAAGGCTATTTTAA 59.306 41.667 0.00 0.00 0.00 1.52
765 807 4.250464 CGGTCACACAGAAGGCTATTTTA 58.750 43.478 0.00 0.00 0.00 1.52
770 821 1.292223 GCGGTCACACAGAAGGCTA 59.708 57.895 0.00 0.00 0.00 3.93
774 825 0.798776 GGAATGCGGTCACACAGAAG 59.201 55.000 0.00 0.00 0.00 2.85
859 910 2.037121 AGAAAACCCCAAAAAGATGGCG 59.963 45.455 0.00 0.00 39.26 5.69
866 917 4.211920 ACTCATCGAGAAAACCCCAAAAA 58.788 39.130 0.00 0.00 33.32 1.94
881 933 6.036083 CACTTATACCAACCAAGAACTCATCG 59.964 42.308 0.00 0.00 0.00 3.84
902 954 4.137543 GAGAATCACAAACCACTCCACTT 58.862 43.478 0.00 0.00 33.17 3.16
943 995 5.952347 ACAAGAAATGGAAGAACCTAATCCC 59.048 40.000 0.00 0.00 39.86 3.85
1089 1192 3.190849 CACCGCTCGATGCACTGG 61.191 66.667 0.00 3.64 43.06 4.00
1413 1516 3.303135 TGGAAGACGAGCGGCAGT 61.303 61.111 1.45 1.08 0.00 4.40
1563 1666 3.222354 GACGAAGGACGCCAGGTGT 62.222 63.158 4.94 4.94 46.94 4.16
1564 1667 2.432628 GACGAAGGACGCCAGGTG 60.433 66.667 0.00 0.00 46.94 4.00
2242 2345 8.764524 AACTTACAGCTTACAAGAACATCTAG 57.235 34.615 5.87 0.00 0.00 2.43
2341 2446 3.993081 AGTCTCTCAATTGACGCTTGAAG 59.007 43.478 3.38 0.00 38.16 3.02
2343 2448 3.667497 AGTCTCTCAATTGACGCTTGA 57.333 42.857 3.38 0.00 38.16 3.02
2346 2451 5.934625 ACAATTTAGTCTCTCAATTGACGCT 59.065 36.000 17.52 3.18 37.29 5.07
2362 2467 5.505654 GCCACAATACATCCGGACAATTTAG 60.506 44.000 6.12 0.00 0.00 1.85
2416 2521 0.458025 CTCCTACGTCGCAGTTTCCC 60.458 60.000 0.00 0.00 0.00 3.97
2428 2535 2.936498 CCAGGTTAATGCAACTCCTACG 59.064 50.000 0.00 0.00 37.30 3.51
2495 2607 8.131100 ACGATGCTTCATAATTTGTAATTCCAG 58.869 33.333 0.08 0.00 0.00 3.86
2496 2608 7.995289 ACGATGCTTCATAATTTGTAATTCCA 58.005 30.769 0.08 0.00 0.00 3.53
2498 2610 9.107367 GCTACGATGCTTCATAATTTGTAATTC 57.893 33.333 0.08 0.00 0.00 2.17
2501 2613 6.292649 CCGCTACGATGCTTCATAATTTGTAA 60.293 38.462 0.08 0.00 0.00 2.41
2508 2620 1.270094 CCCCGCTACGATGCTTCATAA 60.270 52.381 0.08 0.00 0.00 1.90
2511 2623 1.399744 ATCCCCGCTACGATGCTTCA 61.400 55.000 0.08 0.00 0.00 3.02
2512 2624 0.601558 TATCCCCGCTACGATGCTTC 59.398 55.000 0.00 0.00 0.00 3.86
2519 2631 1.173444 ACTGAGCTATCCCCGCTACG 61.173 60.000 0.00 0.00 37.96 3.51
2520 2632 1.041437 AACTGAGCTATCCCCGCTAC 58.959 55.000 0.00 0.00 37.96 3.58
2620 2743 8.310677 ACAATATTGAACGATTTCGAAATTCG 57.689 30.769 23.49 25.34 43.02 3.34
2623 2746 9.072294 GGAAACAATATTGAACGATTTCGAAAT 57.928 29.630 22.93 22.93 43.02 2.17
2624 2747 8.076781 TGGAAACAATATTGAACGATTTCGAAA 58.923 29.630 22.16 13.91 39.41 3.46
2625 2748 7.585867 TGGAAACAATATTGAACGATTTCGAA 58.414 30.769 22.16 9.49 39.41 3.71
2634 2757 8.437742 CAGCAAAATCTGGAAACAATATTGAAC 58.562 33.333 22.16 11.49 42.06 3.18
2649 2772 5.345202 GCTCAGAAATCAACAGCAAAATCTG 59.655 40.000 0.00 0.00 39.86 2.90
2682 2805 6.402222 AGTACATTTTGTGCTTGGTTTTTCA 58.598 32.000 0.00 0.00 40.41 2.69
2688 2811 6.476378 AGATAGAGTACATTTTGTGCTTGGT 58.524 36.000 0.00 0.00 43.31 3.67
2690 2813 6.037610 GGGAGATAGAGTACATTTTGTGCTTG 59.962 42.308 0.00 0.00 43.31 4.01
2692 2815 5.675538 GGGAGATAGAGTACATTTTGTGCT 58.324 41.667 0.00 0.00 45.91 4.40
2693 2816 4.508124 CGGGAGATAGAGTACATTTTGTGC 59.492 45.833 0.00 0.00 32.95 4.57
2694 2817 5.902681 TCGGGAGATAGAGTACATTTTGTG 58.097 41.667 0.00 0.00 0.00 3.33
2695 2818 5.657302 ACTCGGGAGATAGAGTACATTTTGT 59.343 40.000 2.08 0.00 44.93 2.83
2696 2819 6.150396 ACTCGGGAGATAGAGTACATTTTG 57.850 41.667 2.08 0.00 44.93 2.44
2697 2820 6.793505 AACTCGGGAGATAGAGTACATTTT 57.206 37.500 2.08 0.00 45.91 1.82
2698 2821 6.793505 AAACTCGGGAGATAGAGTACATTT 57.206 37.500 2.08 0.00 45.91 2.32
2699 2822 6.793505 AAAACTCGGGAGATAGAGTACATT 57.206 37.500 2.08 0.00 45.91 2.71
2777 2917 8.620416 CGGATGATGACTTTGTTCCAATATAAA 58.380 33.333 0.00 0.00 0.00 1.40
2778 2918 7.990314 TCGGATGATGACTTTGTTCCAATATAA 59.010 33.333 0.00 0.00 0.00 0.98
2779 2919 7.505258 TCGGATGATGACTTTGTTCCAATATA 58.495 34.615 0.00 0.00 0.00 0.86
2780 2920 6.356556 TCGGATGATGACTTTGTTCCAATAT 58.643 36.000 0.00 0.00 0.00 1.28
2781 2921 5.739959 TCGGATGATGACTTTGTTCCAATA 58.260 37.500 0.00 0.00 0.00 1.90
2782 2922 4.588899 TCGGATGATGACTTTGTTCCAAT 58.411 39.130 0.00 0.00 0.00 3.16
2783 2923 4.014569 TCGGATGATGACTTTGTTCCAA 57.985 40.909 0.00 0.00 0.00 3.53
2784 2924 3.694043 TCGGATGATGACTTTGTTCCA 57.306 42.857 0.00 0.00 0.00 3.53
2785 2925 4.035675 GGAATCGGATGATGACTTTGTTCC 59.964 45.833 0.00 0.00 34.24 3.62
2786 2926 4.260375 CGGAATCGGATGATGACTTTGTTC 60.260 45.833 0.00 0.00 34.24 3.18
2787 2927 3.623060 CGGAATCGGATGATGACTTTGTT 59.377 43.478 0.00 0.00 34.24 2.83
2788 2928 3.118775 TCGGAATCGGATGATGACTTTGT 60.119 43.478 0.00 0.00 34.24 2.83
2789 2929 3.457234 TCGGAATCGGATGATGACTTTG 58.543 45.455 0.00 0.00 34.24 2.77
2790 2930 3.384789 TCTCGGAATCGGATGATGACTTT 59.615 43.478 0.00 0.00 34.24 2.66
2791 2931 2.959030 TCTCGGAATCGGATGATGACTT 59.041 45.455 0.00 0.00 34.24 3.01
2792 2932 2.556189 CTCTCGGAATCGGATGATGACT 59.444 50.000 0.00 0.00 34.24 3.41
2793 2933 2.352225 CCTCTCGGAATCGGATGATGAC 60.352 54.545 0.00 0.00 34.24 3.06
2794 2934 1.889170 CCTCTCGGAATCGGATGATGA 59.111 52.381 0.00 0.00 34.24 2.92
2795 2935 1.671261 GCCTCTCGGAATCGGATGATG 60.671 57.143 0.00 0.00 34.24 3.07
2796 2936 0.605589 GCCTCTCGGAATCGGATGAT 59.394 55.000 0.00 0.00 36.95 2.45
2797 2937 0.755327 TGCCTCTCGGAATCGGATGA 60.755 55.000 0.00 0.00 36.95 2.92
2798 2938 0.319383 CTGCCTCTCGGAATCGGATG 60.319 60.000 0.00 0.00 36.95 3.51
2799 2939 0.468214 TCTGCCTCTCGGAATCGGAT 60.468 55.000 0.00 0.00 36.95 4.18
2800 2940 0.683179 TTCTGCCTCTCGGAATCGGA 60.683 55.000 0.00 0.00 35.24 4.55
2801 2941 0.528684 GTTCTGCCTCTCGGAATCGG 60.529 60.000 0.00 0.00 41.72 4.18
2802 2942 0.457851 AGTTCTGCCTCTCGGAATCG 59.542 55.000 0.00 0.00 41.72 3.34
2803 2943 2.427453 TGTAGTTCTGCCTCTCGGAATC 59.573 50.000 0.00 0.00 41.72 2.52
2804 2944 2.457598 TGTAGTTCTGCCTCTCGGAAT 58.542 47.619 0.00 0.00 41.72 3.01
2805 2945 1.919240 TGTAGTTCTGCCTCTCGGAA 58.081 50.000 0.00 0.00 37.72 4.30
2806 2946 2.145397 ATGTAGTTCTGCCTCTCGGA 57.855 50.000 0.00 0.00 0.00 4.55
2807 2947 2.428890 AGAATGTAGTTCTGCCTCTCGG 59.571 50.000 0.00 0.00 45.38 4.63
2808 2948 3.791973 AGAATGTAGTTCTGCCTCTCG 57.208 47.619 0.00 0.00 45.38 4.04
2817 2957 4.025229 TGTTTGTGCACGAGAATGTAGTTC 60.025 41.667 13.13 0.00 37.08 3.01
2818 2958 3.874543 TGTTTGTGCACGAGAATGTAGTT 59.125 39.130 13.13 0.00 0.00 2.24
2819 2959 3.462982 TGTTTGTGCACGAGAATGTAGT 58.537 40.909 13.13 0.00 0.00 2.73
2820 2960 4.397382 CATGTTTGTGCACGAGAATGTAG 58.603 43.478 13.13 0.00 0.00 2.74
2821 2961 3.364864 GCATGTTTGTGCACGAGAATGTA 60.365 43.478 22.47 2.26 44.43 2.29
2822 2962 2.605338 GCATGTTTGTGCACGAGAATGT 60.605 45.455 22.47 7.08 44.43 2.71
2823 2963 1.980844 GCATGTTTGTGCACGAGAATG 59.019 47.619 19.59 19.59 44.43 2.67
2824 2964 2.336554 GCATGTTTGTGCACGAGAAT 57.663 45.000 13.13 5.10 44.43 2.40
2825 2965 3.843632 GCATGTTTGTGCACGAGAA 57.156 47.368 13.13 4.16 44.43 2.87
2830 2970 8.931501 CTTCTCGAAGTAGCATGTTTGTGCAC 62.932 46.154 10.75 10.75 39.24 4.57
2831 2971 7.032646 CTTCTCGAAGTAGCATGTTTGTGCA 62.033 44.000 1.47 0.00 39.24 4.57
2832 2972 2.736721 TCTCGAAGTAGCATGTTTGTGC 59.263 45.455 0.00 0.00 45.38 4.57
2833 2973 4.143030 CCTTCTCGAAGTAGCATGTTTGTG 60.143 45.833 5.99 0.00 36.72 3.33
2834 2974 3.997021 CCTTCTCGAAGTAGCATGTTTGT 59.003 43.478 5.99 0.00 36.72 2.83
2835 2975 4.245660 TCCTTCTCGAAGTAGCATGTTTG 58.754 43.478 5.99 0.00 36.72 2.93
2836 2976 4.537135 TCCTTCTCGAAGTAGCATGTTT 57.463 40.909 5.99 0.00 36.72 2.83
2837 2977 4.744795 ATCCTTCTCGAAGTAGCATGTT 57.255 40.909 5.99 0.00 36.72 2.71
2838 2978 5.854010 TTATCCTTCTCGAAGTAGCATGT 57.146 39.130 5.99 0.00 36.72 3.21
2839 2979 6.364706 GTGATTATCCTTCTCGAAGTAGCATG 59.635 42.308 5.99 0.00 36.72 4.06
2840 2980 6.266558 AGTGATTATCCTTCTCGAAGTAGCAT 59.733 38.462 5.99 0.00 36.72 3.79
2841 2981 5.594725 AGTGATTATCCTTCTCGAAGTAGCA 59.405 40.000 5.99 0.00 36.72 3.49
2842 2982 6.079424 AGTGATTATCCTTCTCGAAGTAGC 57.921 41.667 5.99 0.00 36.72 3.58
2860 3000 8.725148 GCATCTTCGATTTGGATAAATAGTGAT 58.275 33.333 0.00 0.00 36.66 3.06
2861 3001 7.714813 TGCATCTTCGATTTGGATAAATAGTGA 59.285 33.333 0.00 0.00 36.66 3.41
2862 3002 7.800380 GTGCATCTTCGATTTGGATAAATAGTG 59.200 37.037 0.00 0.00 36.66 2.74
2863 3003 7.498900 TGTGCATCTTCGATTTGGATAAATAGT 59.501 33.333 0.00 0.00 36.66 2.12
2864 3004 7.800380 GTGTGCATCTTCGATTTGGATAAATAG 59.200 37.037 0.00 0.00 36.66 1.73
2865 3005 7.281999 TGTGTGCATCTTCGATTTGGATAAATA 59.718 33.333 0.00 0.00 36.66 1.40
2866 3006 6.095300 TGTGTGCATCTTCGATTTGGATAAAT 59.905 34.615 0.00 0.00 39.16 1.40
2867 3007 5.414144 TGTGTGCATCTTCGATTTGGATAAA 59.586 36.000 0.00 0.00 0.00 1.40
2868 3008 4.940654 TGTGTGCATCTTCGATTTGGATAA 59.059 37.500 0.00 0.00 0.00 1.75
2869 3009 4.512484 TGTGTGCATCTTCGATTTGGATA 58.488 39.130 0.00 0.00 0.00 2.59
2870 3010 3.346315 TGTGTGCATCTTCGATTTGGAT 58.654 40.909 0.00 0.00 0.00 3.41
2871 3011 2.777094 TGTGTGCATCTTCGATTTGGA 58.223 42.857 0.00 0.00 0.00 3.53
2872 3012 3.495193 CTTGTGTGCATCTTCGATTTGG 58.505 45.455 0.00 0.00 0.00 3.28
2873 3013 2.912967 GCTTGTGTGCATCTTCGATTTG 59.087 45.455 0.00 0.00 0.00 2.32
2874 3014 2.553602 TGCTTGTGTGCATCTTCGATTT 59.446 40.909 0.00 0.00 38.12 2.17
2875 3015 2.095567 GTGCTTGTGTGCATCTTCGATT 60.096 45.455 0.00 0.00 45.23 3.34
2876 3016 1.466167 GTGCTTGTGTGCATCTTCGAT 59.534 47.619 0.00 0.00 45.23 3.59
2877 3017 0.867746 GTGCTTGTGTGCATCTTCGA 59.132 50.000 0.00 0.00 45.23 3.71
2878 3018 0.451628 CGTGCTTGTGTGCATCTTCG 60.452 55.000 0.00 0.00 45.23 3.79
2879 3019 0.727122 GCGTGCTTGTGTGCATCTTC 60.727 55.000 0.00 0.00 45.23 2.87
2880 3020 1.283793 GCGTGCTTGTGTGCATCTT 59.716 52.632 0.00 0.00 45.23 2.40
2881 3021 1.446516 TTGCGTGCTTGTGTGCATCT 61.447 50.000 0.00 0.00 45.23 2.90
2882 3022 1.008652 TTGCGTGCTTGTGTGCATC 60.009 52.632 0.00 0.00 45.23 3.91
2883 3023 1.299316 GTTGCGTGCTTGTGTGCAT 60.299 52.632 0.00 0.00 45.23 3.96
2884 3024 2.101965 GTTGCGTGCTTGTGTGCA 59.898 55.556 0.00 0.00 41.05 4.57
2885 3025 3.018428 CGTTGCGTGCTTGTGTGC 61.018 61.111 0.00 0.00 0.00 4.57
2886 3026 3.018428 GCGTTGCGTGCTTGTGTG 61.018 61.111 0.00 0.00 0.00 3.82
2887 3027 3.504273 TGCGTTGCGTGCTTGTGT 61.504 55.556 0.00 0.00 0.00 3.72
2888 3028 3.018428 GTGCGTTGCGTGCTTGTG 61.018 61.111 0.00 0.00 0.00 3.33
2889 3029 3.168237 GAGTGCGTTGCGTGCTTGT 62.168 57.895 0.00 0.00 0.00 3.16
2890 3030 2.425773 GAGTGCGTTGCGTGCTTG 60.426 61.111 0.00 0.00 0.00 4.01
2891 3031 2.894879 TGAGTGCGTTGCGTGCTT 60.895 55.556 0.00 0.00 0.00 3.91
2892 3032 3.640000 GTGAGTGCGTTGCGTGCT 61.640 61.111 0.00 0.00 0.00 4.40
2893 3033 3.935872 TGTGAGTGCGTTGCGTGC 61.936 61.111 0.00 0.00 0.00 5.34
2894 3034 2.053116 GTGTGAGTGCGTTGCGTG 60.053 61.111 0.00 0.00 0.00 5.34
2895 3035 3.269347 GGTGTGAGTGCGTTGCGT 61.269 61.111 0.00 0.00 0.00 5.24
2896 3036 4.012895 GGGTGTGAGTGCGTTGCG 62.013 66.667 0.00 0.00 0.00 4.85
2897 3037 3.660111 GGGGTGTGAGTGCGTTGC 61.660 66.667 0.00 0.00 0.00 4.17
2898 3038 3.345808 CGGGGTGTGAGTGCGTTG 61.346 66.667 0.00 0.00 0.00 4.10
2902 3042 4.722700 ATGGCGGGGTGTGAGTGC 62.723 66.667 0.00 0.00 0.00 4.40
2903 3043 1.586154 GAAATGGCGGGGTGTGAGTG 61.586 60.000 0.00 0.00 0.00 3.51
2904 3044 1.303317 GAAATGGCGGGGTGTGAGT 60.303 57.895 0.00 0.00 0.00 3.41
2905 3045 1.303236 TGAAATGGCGGGGTGTGAG 60.303 57.895 0.00 0.00 0.00 3.51
2906 3046 1.303236 CTGAAATGGCGGGGTGTGA 60.303 57.895 0.00 0.00 0.00 3.58
2907 3047 0.893270 TTCTGAAATGGCGGGGTGTG 60.893 55.000 0.00 0.00 0.00 3.82
2939 3079 2.151202 TGCAGCTACAGGTTAGTTTGC 58.849 47.619 0.00 0.00 0.00 3.68
2941 3081 3.244911 ACCATGCAGCTACAGGTTAGTTT 60.245 43.478 0.00 0.00 0.00 2.66
2945 3085 2.617788 CCAACCATGCAGCTACAGGTTA 60.618 50.000 15.97 0.00 40.39 2.85
2948 3088 1.033746 CCCAACCATGCAGCTACAGG 61.034 60.000 0.00 0.00 0.00 4.00
2955 3095 0.178981 CCTATCCCCCAACCATGCAG 60.179 60.000 0.00 0.00 0.00 4.41
2958 3098 0.185901 CCACCTATCCCCCAACCATG 59.814 60.000 0.00 0.00 0.00 3.66
2970 3111 4.234550 TGATGGCTTGAGATACCACCTAT 58.765 43.478 0.00 0.00 35.99 2.57
2974 3115 2.486191 CCCTGATGGCTTGAGATACCAC 60.486 54.545 0.00 0.00 35.99 4.16
2982 3123 1.425066 ACTTGAACCCTGATGGCTTGA 59.575 47.619 0.00 0.00 37.83 3.02
2984 3125 2.108952 AGAACTTGAACCCTGATGGCTT 59.891 45.455 0.00 0.00 37.83 4.35
2986 3127 1.815003 CAGAACTTGAACCCTGATGGC 59.185 52.381 0.00 0.00 37.83 4.40
2989 3130 1.611673 CGCCAGAACTTGAACCCTGAT 60.612 52.381 0.00 0.00 0.00 2.90
2990 3131 0.250295 CGCCAGAACTTGAACCCTGA 60.250 55.000 0.00 0.00 0.00 3.86
2991 3132 1.856265 GCGCCAGAACTTGAACCCTG 61.856 60.000 0.00 0.00 0.00 4.45
2992 3133 1.600916 GCGCCAGAACTTGAACCCT 60.601 57.895 0.00 0.00 0.00 4.34
2993 3134 1.172812 AAGCGCCAGAACTTGAACCC 61.173 55.000 2.29 0.00 0.00 4.11
2994 3135 0.040067 CAAGCGCCAGAACTTGAACC 60.040 55.000 2.29 0.00 44.89 3.62
2996 3137 2.248280 TACAAGCGCCAGAACTTGAA 57.752 45.000 2.29 0.00 44.89 2.69
3036 3178 1.160989 ACGCACATTGTCGGCAATTA 58.839 45.000 13.64 0.00 42.91 1.40
3037 3179 0.313672 AACGCACATTGTCGGCAATT 59.686 45.000 13.64 1.99 42.91 2.32
3041 3183 1.154413 CTGAACGCACATTGTCGGC 60.154 57.895 11.45 2.29 0.00 5.54
3042 3184 0.110688 CACTGAACGCACATTGTCGG 60.111 55.000 11.45 0.00 0.00 4.79
3050 3192 2.423926 TCTTCTCTCACTGAACGCAC 57.576 50.000 0.00 0.00 0.00 5.34
3062 3204 3.426615 AGTCGACAGGAACATCTTCTCT 58.573 45.455 19.50 0.00 0.00 3.10
3066 3208 3.079578 TCGTAGTCGACAGGAACATCTT 58.920 45.455 19.50 0.00 41.35 2.40
3070 3212 1.162698 CCTCGTAGTCGACAGGAACA 58.837 55.000 19.50 0.00 41.35 3.18
3076 3218 1.962822 ACACGCCTCGTAGTCGACA 60.963 57.895 19.50 0.48 41.35 4.35
3082 3224 1.733041 CACCACACACGCCTCGTAG 60.733 63.158 0.00 0.00 38.32 3.51
3091 3233 3.243068 GGATTGACAAAGTCACCACACAC 60.243 47.826 0.00 0.00 42.60 3.82
3093 3235 3.214328 AGGATTGACAAAGTCACCACAC 58.786 45.455 0.00 0.00 42.60 3.82
3098 3240 7.856145 ATCATCTTAGGATTGACAAAGTCAC 57.144 36.000 0.00 0.00 42.60 3.67
3110 3252 4.532126 TGAACCGGCATATCATCTTAGGAT 59.468 41.667 0.00 0.00 0.00 3.24
3113 3255 4.887748 ACTGAACCGGCATATCATCTTAG 58.112 43.478 0.00 0.00 0.00 2.18
3114 3256 4.955811 ACTGAACCGGCATATCATCTTA 57.044 40.909 0.00 0.00 0.00 2.10
3120 3262 4.394920 TCTGAAAAACTGAACCGGCATATC 59.605 41.667 0.00 0.00 0.00 1.63
3126 3268 2.290641 CACCTCTGAAAAACTGAACCGG 59.709 50.000 0.00 0.00 0.00 5.28
3130 3272 2.872245 CGAGCACCTCTGAAAAACTGAA 59.128 45.455 0.00 0.00 0.00 3.02
3136 3278 3.181458 ACCTTTACGAGCACCTCTGAAAA 60.181 43.478 0.00 0.00 0.00 2.29
3138 3280 1.968493 ACCTTTACGAGCACCTCTGAA 59.032 47.619 0.00 0.00 0.00 3.02
3141 3283 2.100989 CCTACCTTTACGAGCACCTCT 58.899 52.381 0.00 0.00 0.00 3.69
3144 3286 0.900421 ACCCTACCTTTACGAGCACC 59.100 55.000 0.00 0.00 0.00 5.01
3150 3292 0.529378 ACGCAGACCCTACCTTTACG 59.471 55.000 0.00 0.00 0.00 3.18
3151 3293 1.274447 ACACGCAGACCCTACCTTTAC 59.726 52.381 0.00 0.00 0.00 2.01
3154 3296 1.119574 ACACACGCAGACCCTACCTT 61.120 55.000 0.00 0.00 0.00 3.50
3155 3297 1.533273 ACACACGCAGACCCTACCT 60.533 57.895 0.00 0.00 0.00 3.08
3166 3308 3.000041 TCATCCTTATGAACACACACGC 59.000 45.455 0.00 0.00 39.20 5.34
3167 3309 4.091945 CACTCATCCTTATGAACACACACG 59.908 45.833 0.00 0.00 41.57 4.49
3168 3310 4.997395 ACACTCATCCTTATGAACACACAC 59.003 41.667 0.00 0.00 41.57 3.82
3169 3311 5.227569 ACACTCATCCTTATGAACACACA 57.772 39.130 0.00 0.00 41.57 3.72
3170 3312 6.238211 GCATACACTCATCCTTATGAACACAC 60.238 42.308 0.00 0.00 41.57 3.82
3171 3313 5.817296 GCATACACTCATCCTTATGAACACA 59.183 40.000 0.00 0.00 41.57 3.72
3172 3314 5.050769 CGCATACACTCATCCTTATGAACAC 60.051 44.000 0.00 0.00 41.57 3.32
3173 3315 5.049828 CGCATACACTCATCCTTATGAACA 58.950 41.667 0.00 0.00 41.57 3.18
3174 3316 4.084328 GCGCATACACTCATCCTTATGAAC 60.084 45.833 0.30 0.00 41.57 3.18
3178 3320 2.035961 ACGCGCATACACTCATCCTTAT 59.964 45.455 5.73 0.00 0.00 1.73
3181 3323 1.029681 TACGCGCATACACTCATCCT 58.970 50.000 5.73 0.00 0.00 3.24


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

AutoCloner maintained by Alex Coulton.