Multiple sequence alignment - TraesCS3D01G374600

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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 TraesCS3D01G374600 chr3D 100.000 2936 0 0 1 2936 488058879 488061814 0.000000e+00 5422.0
1 TraesCS3D01G374600 chr3B 93.352 1790 55 32 805 2560 650841251 650843010 0.000000e+00 2588.0
2 TraesCS3D01G374600 chr3B 87.719 513 49 12 303 806 650838537 650839044 1.170000e-163 586.0
3 TraesCS3D01G374600 chr3B 85.632 174 21 3 570 741 68913469 68913640 2.320000e-41 180.0
4 TraesCS3D01G374600 chr3A 91.463 1886 79 43 758 2613 631709712 631711545 0.000000e+00 2516.0
5 TraesCS3D01G374600 chr3A 88.761 694 39 7 1 692 631617352 631618008 0.000000e+00 813.0
6 TraesCS3D01G374600 chr3A 92.308 247 15 1 2645 2891 744763944 744764186 6.020000e-92 348.0
7 TraesCS3D01G374600 chr6A 95.890 292 10 1 2645 2936 449967562 449967273 3.430000e-129 472.0
8 TraesCS3D01G374600 chr2A 95.848 289 12 0 2648 2936 12322221 12322509 4.430000e-128 468.0
9 TraesCS3D01G374600 chr2A 84.158 303 43 3 1422 1723 755990058 755989760 3.700000e-74 289.0
10 TraesCS3D01G374600 chr2A 87.654 162 18 1 580 739 566852092 566852253 1.390000e-43 187.0
11 TraesCS3D01G374600 chr5A 93.080 289 13 2 2648 2936 538339208 538339489 1.630000e-112 416.0
12 TraesCS3D01G374600 chr5A 89.078 293 27 3 2647 2936 698319366 698319656 2.780000e-95 359.0
13 TraesCS3D01G374600 chr5A 86.127 173 20 3 570 739 320214234 320214405 1.800000e-42 183.0
14 TraesCS3D01G374600 chr7D 91.468 293 25 0 2644 2936 577977322 577977614 1.270000e-108 403.0
15 TraesCS3D01G374600 chr7D 84.615 286 34 2 1438 1723 3213239 3212964 2.880000e-70 276.0
16 TraesCS3D01G374600 chr7D 76.152 499 76 33 1446 1930 409492189 409492658 3.810000e-54 222.0
17 TraesCS3D01G374600 chr7A 91.034 290 24 2 2647 2934 670301149 670300860 9.870000e-105 390.0
18 TraesCS3D01G374600 chr7A 76.829 492 73 31 1451 1930 470591720 470592182 3.780000e-59 239.0
19 TraesCS3D01G374600 chr4A 91.065 291 21 2 2646 2936 731592758 731593043 3.550000e-104 388.0
20 TraesCS3D01G374600 chr5B 89.655 290 27 1 2647 2936 656092060 656092346 1.660000e-97 366.0
21 TraesCS3D01G374600 chr5B 83.962 106 14 2 1479 1582 700989586 700989690 6.700000e-17 99.0
22 TraesCS3D01G374600 chr1A 86.275 306 39 3 1419 1723 42522976 42523279 2.180000e-86 329.0
23 TraesCS3D01G374600 chr7B 75.952 499 77 33 1446 1930 424054955 424055424 1.770000e-52 217.0
24 TraesCS3D01G374600 chr7B 94.737 38 2 0 252 289 738635266 738635229 3.160000e-05 60.2
25 TraesCS3D01G374600 chr7B 94.737 38 2 0 252 289 738766169 738766132 3.160000e-05 60.2
26 TraesCS3D01G374600 chr1D 87.195 164 19 1 580 741 103408718 103408881 5.000000e-43 185.0
27 TraesCS3D01G374600 chr2D 86.667 165 19 2 577 739 296364212 296364049 2.320000e-41 180.0
28 TraesCS3D01G374600 chr2D 86.228 167 20 2 576 739 524963634 524963800 8.360000e-41 178.0
29 TraesCS3D01G374600 chr2B 86.667 165 19 2 577 739 366017516 366017679 2.320000e-41 180.0
30 TraesCS3D01G374600 chr4B 87.395 119 14 1 1596 1714 273984531 273984414 5.100000e-28 135.0
31 TraesCS3D01G374600 chr6B 88.060 67 7 1 359 424 320430117 320430051 8.720000e-11 78.7


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 TraesCS3D01G374600 chr3D 488058879 488061814 2935 False 5422 5422 100.0000 1 2936 1 chr3D.!!$F1 2935
1 TraesCS3D01G374600 chr3B 650838537 650843010 4473 False 1587 2588 90.5355 303 2560 2 chr3B.!!$F2 2257
2 TraesCS3D01G374600 chr3A 631709712 631711545 1833 False 2516 2516 91.4630 758 2613 1 chr3A.!!$F2 1855
3 TraesCS3D01G374600 chr3A 631617352 631618008 656 False 813 813 88.7610 1 692 1 chr3A.!!$F1 691

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
944 3173 0.035458 TCCACACACACACACACACA 59.965 50.0 0.0 0.0 0.0 3.72 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2757 5036 0.033504 AGGTGAAGCACTACGTGTGG 59.966 55.0 16.33 2.67 46.27 4.17 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
329 331 9.901172 AAGTATGGGTTAGTATAGTTTTGAAGG 57.099 33.333 0.00 0.00 0.00 3.46
428 431 3.512033 AAGATCTTGACAGGACTACGC 57.488 47.619 7.30 0.00 0.00 4.42
430 433 1.132643 GATCTTGACAGGACTACGCGT 59.867 52.381 19.17 19.17 0.00 6.01
431 434 0.520404 TCTTGACAGGACTACGCGTC 59.480 55.000 18.63 0.00 42.07 5.19
432 435 0.793478 CTTGACAGGACTACGCGTCG 60.793 60.000 18.63 13.46 43.79 5.12
433 436 1.229975 TTGACAGGACTACGCGTCGA 61.230 55.000 18.63 0.00 43.79 4.20
434 437 1.022982 TGACAGGACTACGCGTCGAT 61.023 55.000 18.63 1.12 43.79 3.59
465 470 2.288702 TGTGAATTGGGCAAATGGTTCG 60.289 45.455 0.00 0.00 0.00 3.95
467 472 2.630098 TGAATTGGGCAAATGGTTCGAA 59.370 40.909 0.00 0.00 0.00 3.71
472 477 2.230992 TGGGCAAATGGTTCGAAAGATG 59.769 45.455 0.00 0.00 41.60 2.90
533 538 3.806949 AACCCACTTATTTCTCCTGCA 57.193 42.857 0.00 0.00 0.00 4.41
653 659 5.883661 ACATACGGAGCAAAATGAATGAAG 58.116 37.500 0.00 0.00 0.00 3.02
662 668 4.321745 GCAAAATGAATGAAGCTACACACG 59.678 41.667 0.00 0.00 0.00 4.49
743 751 2.986050 AGAAAGGGAGGGAGTACACAA 58.014 47.619 0.00 0.00 0.00 3.33
744 752 3.532102 AGAAAGGGAGGGAGTACACAAT 58.468 45.455 0.00 0.00 0.00 2.71
929 3158 2.031870 AGTTGCCTCCTTGTTTTCCAC 58.968 47.619 0.00 0.00 0.00 4.02
931 3160 1.398692 TGCCTCCTTGTTTTCCACAC 58.601 50.000 0.00 0.00 33.98 3.82
933 3162 1.067060 GCCTCCTTGTTTTCCACACAC 59.933 52.381 0.00 0.00 33.98 3.82
935 3164 2.099098 CCTCCTTGTTTTCCACACACAC 59.901 50.000 0.00 0.00 33.98 3.82
936 3165 2.752354 CTCCTTGTTTTCCACACACACA 59.248 45.455 0.00 0.00 33.98 3.72
937 3166 2.490115 TCCTTGTTTTCCACACACACAC 59.510 45.455 0.00 0.00 33.98 3.82
938 3167 2.230025 CCTTGTTTTCCACACACACACA 59.770 45.455 0.00 0.00 33.98 3.72
939 3168 2.999507 TGTTTTCCACACACACACAC 57.000 45.000 0.00 0.00 0.00 3.82
940 3169 2.230660 TGTTTTCCACACACACACACA 58.769 42.857 0.00 0.00 0.00 3.72
941 3170 2.030717 TGTTTTCCACACACACACACAC 60.031 45.455 0.00 0.00 0.00 3.82
942 3171 1.897560 TTTCCACACACACACACACA 58.102 45.000 0.00 0.00 0.00 3.72
943 3172 1.160989 TTCCACACACACACACACAC 58.839 50.000 0.00 0.00 0.00 3.82
944 3173 0.035458 TCCACACACACACACACACA 59.965 50.000 0.00 0.00 0.00 3.72
945 3174 0.167908 CCACACACACACACACACAC 59.832 55.000 0.00 0.00 0.00 3.82
946 3175 0.871057 CACACACACACACACACACA 59.129 50.000 0.00 0.00 0.00 3.72
947 3176 0.871722 ACACACACACACACACACAC 59.128 50.000 0.00 0.00 0.00 3.82
948 3177 0.871057 CACACACACACACACACACA 59.129 50.000 0.00 0.00 0.00 3.72
949 3178 0.871722 ACACACACACACACACACAC 59.128 50.000 0.00 0.00 0.00 3.82
1127 3361 3.242220 CCAACAGCAAAAGATCGATCGAG 60.242 47.826 23.84 9.60 0.00 4.04
1168 3402 1.464376 CGGACCCGGAGCATCTGTAT 61.464 60.000 0.73 0.00 40.87 2.29
1169 3403 1.629043 GGACCCGGAGCATCTGTATA 58.371 55.000 0.73 0.00 40.87 1.47
1291 3551 2.746671 CACCTGCTCTGCTGCCAG 60.747 66.667 0.00 0.00 40.54 4.85
1299 3559 2.436292 CTGCTGCCAGTGCTCCTC 60.436 66.667 0.00 0.00 38.71 3.71
1328 3588 3.444805 GCTGCTCCTCTCCGTCGT 61.445 66.667 0.00 0.00 0.00 4.34
1329 3589 2.795297 CTGCTCCTCTCCGTCGTC 59.205 66.667 0.00 0.00 0.00 4.20
1940 4200 3.151022 GCTCCTCGCCTAGCCTGT 61.151 66.667 0.00 0.00 32.40 4.00
1944 4204 2.351244 CCTCGCCTAGCCTGTCACA 61.351 63.158 0.00 0.00 0.00 3.58
1945 4205 1.591703 CTCGCCTAGCCTGTCACAA 59.408 57.895 0.00 0.00 0.00 3.33
1946 4206 0.459237 CTCGCCTAGCCTGTCACAAG 60.459 60.000 0.00 0.00 0.00 3.16
1947 4207 1.185618 TCGCCTAGCCTGTCACAAGT 61.186 55.000 0.00 0.00 0.00 3.16
1948 4208 1.016130 CGCCTAGCCTGTCACAAGTG 61.016 60.000 0.00 0.00 0.00 3.16
1949 4209 0.321671 GCCTAGCCTGTCACAAGTGA 59.678 55.000 0.00 0.00 37.24 3.41
1960 4220 0.179020 CACAAGTGACTCAAGCCCCA 60.179 55.000 0.00 0.00 0.00 4.96
1991 4251 4.317139 CGCCTGAACGTATTCTGTTTATCG 60.317 45.833 0.00 0.00 35.69 2.92
1992 4252 4.565564 GCCTGAACGTATTCTGTTTATCGT 59.434 41.667 0.00 0.00 35.69 3.73
2020 4281 1.003223 CATGTATGGCACGCATCACAG 60.003 52.381 0.00 0.00 0.00 3.66
2137 4406 1.403249 CGTAAACCGGAGTGTACTGGG 60.403 57.143 9.46 0.00 40.34 4.45
2138 4407 0.609662 TAAACCGGAGTGTACTGGGC 59.390 55.000 9.46 0.00 40.34 5.36
2169 4440 6.265577 ACTGTAACTTTGAAAGTGCATGTTC 58.734 36.000 11.83 0.00 41.91 3.18
2245 4516 3.680490 AGACTGAGATGTCGAGACAAGA 58.320 45.455 10.15 0.00 45.41 3.02
2290 4561 3.194116 AGGCCGATCACGTACTTTTCTTA 59.806 43.478 0.00 0.00 37.88 2.10
2309 4580 1.896220 ATTTGACGCCATCCGCATAT 58.104 45.000 0.00 0.00 41.76 1.78
2381 4652 1.567504 CCACTCGTCTTGTTCAACGT 58.432 50.000 0.00 0.00 39.78 3.99
2382 4653 2.544277 CCCACTCGTCTTGTTCAACGTA 60.544 50.000 0.00 0.00 39.78 3.57
2383 4654 2.470257 CCACTCGTCTTGTTCAACGTAC 59.530 50.000 0.00 0.00 39.78 3.67
2384 4655 2.150611 CACTCGTCTTGTTCAACGTACG 59.849 50.000 15.01 15.01 39.78 3.67
2399 4670 0.378257 GTACGATTGCATGGGCTGTG 59.622 55.000 0.00 0.00 41.91 3.66
2401 4672 1.138036 CGATTGCATGGGCTGTGTG 59.862 57.895 0.00 0.00 41.91 3.82
2403 4674 1.879737 GATTGCATGGGCTGTGTGCA 61.880 55.000 0.00 0.00 46.15 4.57
2413 4684 0.886043 GCTGTGTGCAGTGTGGATGA 60.886 55.000 0.00 0.00 44.32 2.92
2414 4685 1.154197 CTGTGTGCAGTGTGGATGAG 58.846 55.000 0.00 0.00 37.92 2.90
2415 4686 0.250424 TGTGTGCAGTGTGGATGAGG 60.250 55.000 0.00 0.00 0.00 3.86
2416 4687 1.302752 TGTGCAGTGTGGATGAGGC 60.303 57.895 0.00 0.00 0.00 4.70
2417 4688 1.302752 GTGCAGTGTGGATGAGGCA 60.303 57.895 0.00 0.00 0.00 4.75
2479 4758 2.057316 CCATCGCATGTTCTCGATCTC 58.943 52.381 3.36 0.00 42.73 2.75
2492 4771 2.124570 ATCTCGGCAATTGCGGCT 60.125 55.556 27.81 14.88 43.26 5.52
2571 4850 1.079336 GCCGGTGAGTAGGGTGTTC 60.079 63.158 1.90 0.00 0.00 3.18
2580 4859 0.037605 GTAGGGTGTTCTGGTGACCG 60.038 60.000 0.00 0.00 0.00 4.79
2581 4860 1.189524 TAGGGTGTTCTGGTGACCGG 61.190 60.000 3.42 3.42 0.00 5.28
2587 4866 2.890766 TTCTGGTGACCGGGCTTCC 61.891 63.158 9.82 12.37 0.00 3.46
2596 4875 2.584608 CGGGCTTCCTGGACGAAT 59.415 61.111 4.10 0.00 0.00 3.34
2597 4876 1.078426 CGGGCTTCCTGGACGAATT 60.078 57.895 4.10 0.00 0.00 2.17
2654 4933 7.229228 CTTTTGGTTTTAGAAAAGGGAAACG 57.771 36.000 0.00 0.00 36.11 3.60
2655 4934 5.918426 TTGGTTTTAGAAAAGGGAAACGT 57.082 34.783 0.00 0.00 33.86 3.99
2656 4935 5.918426 TGGTTTTAGAAAAGGGAAACGTT 57.082 34.783 0.00 0.00 40.85 3.99
2658 4937 6.331845 TGGTTTTAGAAAAGGGAAACGTTTC 58.668 36.000 28.83 28.83 46.89 2.78
2667 4946 2.249692 GAAACGTTTCCCATCGGCA 58.750 52.632 27.01 0.00 0.00 5.69
2668 4947 0.168128 GAAACGTTTCCCATCGGCAG 59.832 55.000 27.01 0.00 0.00 4.85
2669 4948 0.250553 AAACGTTTCCCATCGGCAGA 60.251 50.000 7.96 0.00 0.00 4.26
2670 4949 0.953960 AACGTTTCCCATCGGCAGAC 60.954 55.000 0.00 0.00 0.00 3.51
2671 4950 2.106683 CGTTTCCCATCGGCAGACC 61.107 63.158 0.00 0.00 0.00 3.85
2683 4962 2.815647 CAGACCGGCCGAAGCTTC 60.816 66.667 30.73 16.84 39.73 3.86
2693 4972 4.736896 GAAGCTTCGGCCGGTCGT 62.737 66.667 29.96 8.64 43.01 4.34
2701 4980 4.849329 GGCCGGTCGTGTCGCTAG 62.849 72.222 1.90 0.00 0.00 3.42
2703 4982 3.812019 CCGGTCGTGTCGCTAGCT 61.812 66.667 13.93 0.00 0.00 3.32
2704 4983 2.277373 CGGTCGTGTCGCTAGCTC 60.277 66.667 13.93 6.50 0.00 4.09
2705 4984 2.102553 GGTCGTGTCGCTAGCTCC 59.897 66.667 13.93 3.25 0.00 4.70
2706 4985 2.102553 GTCGTGTCGCTAGCTCCC 59.897 66.667 13.93 0.55 0.00 4.30
2707 4986 3.506096 TCGTGTCGCTAGCTCCCG 61.506 66.667 13.93 9.01 0.00 5.14
2729 5008 4.713946 CGTAGCACACCCACCAAT 57.286 55.556 0.00 0.00 0.00 3.16
2730 5009 3.844911 CGTAGCACACCCACCAATA 57.155 52.632 0.00 0.00 0.00 1.90
2731 5010 1.365699 CGTAGCACACCCACCAATAC 58.634 55.000 0.00 0.00 0.00 1.89
2732 5011 1.746470 GTAGCACACCCACCAATACC 58.254 55.000 0.00 0.00 0.00 2.73
2733 5012 1.003812 GTAGCACACCCACCAATACCA 59.996 52.381 0.00 0.00 0.00 3.25
2734 5013 0.480690 AGCACACCCACCAATACCAA 59.519 50.000 0.00 0.00 0.00 3.67
2735 5014 0.887933 GCACACCCACCAATACCAAG 59.112 55.000 0.00 0.00 0.00 3.61
2736 5015 1.544724 CACACCCACCAATACCAAGG 58.455 55.000 0.00 0.00 0.00 3.61
2737 5016 1.074727 CACACCCACCAATACCAAGGA 59.925 52.381 0.00 0.00 0.00 3.36
2738 5017 1.354368 ACACCCACCAATACCAAGGAG 59.646 52.381 0.00 0.00 0.00 3.69
2739 5018 0.331616 ACCCACCAATACCAAGGAGC 59.668 55.000 0.00 0.00 0.00 4.70
2740 5019 0.395724 CCCACCAATACCAAGGAGCC 60.396 60.000 0.00 0.00 0.00 4.70
2741 5020 0.331278 CCACCAATACCAAGGAGCCA 59.669 55.000 0.00 0.00 0.00 4.75
2742 5021 1.463674 CACCAATACCAAGGAGCCAC 58.536 55.000 0.00 0.00 0.00 5.01
2743 5022 1.072266 ACCAATACCAAGGAGCCACA 58.928 50.000 0.00 0.00 0.00 4.17
2744 5023 1.271926 ACCAATACCAAGGAGCCACAC 60.272 52.381 0.00 0.00 0.00 3.82
2745 5024 1.086696 CAATACCAAGGAGCCACACG 58.913 55.000 0.00 0.00 0.00 4.49
2746 5025 0.690762 AATACCAAGGAGCCACACGT 59.309 50.000 0.00 0.00 0.00 4.49
2747 5026 0.249398 ATACCAAGGAGCCACACGTC 59.751 55.000 0.00 0.00 0.00 4.34
2748 5027 1.823169 TACCAAGGAGCCACACGTCC 61.823 60.000 0.00 0.00 0.00 4.79
2749 5028 2.743718 CAAGGAGCCACACGTCCT 59.256 61.111 0.00 0.00 45.71 3.85
2750 5029 3.563512 AAGGAGCCACACGTCCTT 58.436 55.556 0.00 0.00 46.49 3.36
2751 5030 2.743718 AGGAGCCACACGTCCTTG 59.256 61.111 0.00 0.00 40.54 3.61
2752 5031 3.050275 GGAGCCACACGTCCTTGC 61.050 66.667 0.00 0.00 0.00 4.01
2753 5032 3.414700 GAGCCACACGTCCTTGCG 61.415 66.667 0.00 0.00 37.94 4.85
2754 5033 4.988598 AGCCACACGTCCTTGCGG 62.989 66.667 0.00 0.00 35.98 5.69
2765 5044 4.690719 CTTGCGGGCCCACACGTA 62.691 66.667 24.92 3.82 0.00 3.57
2766 5045 4.690719 TTGCGGGCCCACACGTAG 62.691 66.667 24.92 4.06 0.00 3.51
2782 5061 2.876550 ACGTAGTGCTTCACCTTTTTCC 59.123 45.455 0.00 0.00 42.51 3.13
2783 5062 3.139077 CGTAGTGCTTCACCTTTTTCCT 58.861 45.455 0.00 0.00 34.49 3.36
2784 5063 4.202284 ACGTAGTGCTTCACCTTTTTCCTA 60.202 41.667 0.00 0.00 42.51 2.94
2785 5064 4.935808 CGTAGTGCTTCACCTTTTTCCTAT 59.064 41.667 0.00 0.00 34.49 2.57
2786 5065 5.063564 CGTAGTGCTTCACCTTTTTCCTATC 59.936 44.000 0.00 0.00 34.49 2.08
2787 5066 5.248380 AGTGCTTCACCTTTTTCCTATCT 57.752 39.130 0.00 0.00 34.49 1.98
2788 5067 5.635120 AGTGCTTCACCTTTTTCCTATCTT 58.365 37.500 0.00 0.00 34.49 2.40
2789 5068 5.707764 AGTGCTTCACCTTTTTCCTATCTTC 59.292 40.000 0.00 0.00 34.49 2.87
2790 5069 5.707764 GTGCTTCACCTTTTTCCTATCTTCT 59.292 40.000 0.00 0.00 0.00 2.85
2791 5070 6.207614 GTGCTTCACCTTTTTCCTATCTTCTT 59.792 38.462 0.00 0.00 0.00 2.52
2792 5071 6.431234 TGCTTCACCTTTTTCCTATCTTCTTC 59.569 38.462 0.00 0.00 0.00 2.87
2793 5072 6.657117 GCTTCACCTTTTTCCTATCTTCTTCT 59.343 38.462 0.00 0.00 0.00 2.85
2794 5073 7.175816 GCTTCACCTTTTTCCTATCTTCTTCTT 59.824 37.037 0.00 0.00 0.00 2.52
2795 5074 8.622948 TTCACCTTTTTCCTATCTTCTTCTTC 57.377 34.615 0.00 0.00 0.00 2.87
2796 5075 7.168905 TCACCTTTTTCCTATCTTCTTCTTCC 58.831 38.462 0.00 0.00 0.00 3.46
2797 5076 7.017651 TCACCTTTTTCCTATCTTCTTCTTCCT 59.982 37.037 0.00 0.00 0.00 3.36
2798 5077 7.667635 CACCTTTTTCCTATCTTCTTCTTCCTT 59.332 37.037 0.00 0.00 0.00 3.36
2799 5078 8.228206 ACCTTTTTCCTATCTTCTTCTTCCTTT 58.772 33.333 0.00 0.00 0.00 3.11
2800 5079 8.735315 CCTTTTTCCTATCTTCTTCTTCCTTTC 58.265 37.037 0.00 0.00 0.00 2.62
2801 5080 9.289782 CTTTTTCCTATCTTCTTCTTCCTTTCA 57.710 33.333 0.00 0.00 0.00 2.69
2802 5081 8.854614 TTTTCCTATCTTCTTCTTCCTTTCAG 57.145 34.615 0.00 0.00 0.00 3.02
2803 5082 6.552445 TCCTATCTTCTTCTTCCTTTCAGG 57.448 41.667 0.00 0.00 36.46 3.86
2804 5083 6.264528 TCCTATCTTCTTCTTCCTTTCAGGA 58.735 40.000 0.00 0.00 44.10 3.86
2806 5085 6.821160 CCTATCTTCTTCTTCCTTTCAGGAAC 59.179 42.308 0.77 0.00 46.88 3.62
2807 5086 5.896073 TCTTCTTCTTCCTTTCAGGAACT 57.104 39.130 0.77 0.00 46.88 3.01
2808 5087 5.859495 TCTTCTTCTTCCTTTCAGGAACTC 58.141 41.667 0.77 0.00 46.88 3.01
2809 5088 5.604650 TCTTCTTCTTCCTTTCAGGAACTCT 59.395 40.000 0.77 0.00 46.88 3.24
2810 5089 5.476091 TCTTCTTCCTTTCAGGAACTCTC 57.524 43.478 0.77 0.00 46.88 3.20
2811 5090 5.151454 TCTTCTTCCTTTCAGGAACTCTCT 58.849 41.667 0.77 0.00 46.88 3.10
2812 5091 5.245075 TCTTCTTCCTTTCAGGAACTCTCTC 59.755 44.000 0.77 0.00 46.88 3.20
2813 5092 4.746466 TCTTCCTTTCAGGAACTCTCTCT 58.254 43.478 0.77 0.00 46.88 3.10
2814 5093 4.770010 TCTTCCTTTCAGGAACTCTCTCTC 59.230 45.833 0.77 0.00 46.88 3.20
2815 5094 4.396357 TCCTTTCAGGAACTCTCTCTCT 57.604 45.455 0.00 0.00 42.51 3.10
2816 5095 4.340617 TCCTTTCAGGAACTCTCTCTCTC 58.659 47.826 0.00 0.00 42.51 3.20
2817 5096 4.044065 TCCTTTCAGGAACTCTCTCTCTCT 59.956 45.833 0.00 0.00 42.51 3.10
2818 5097 4.399303 CCTTTCAGGAACTCTCTCTCTCTC 59.601 50.000 0.00 0.00 37.67 3.20
2819 5098 4.927267 TTCAGGAACTCTCTCTCTCTCT 57.073 45.455 0.00 0.00 34.60 3.10
2820 5099 4.487714 TCAGGAACTCTCTCTCTCTCTC 57.512 50.000 0.00 0.00 34.60 3.20
2821 5100 3.199946 TCAGGAACTCTCTCTCTCTCTCC 59.800 52.174 0.00 0.00 34.60 3.71
2822 5101 2.509964 AGGAACTCTCTCTCTCTCTCCC 59.490 54.545 0.00 0.00 0.00 4.30
2823 5102 2.561569 GAACTCTCTCTCTCTCTCCCG 58.438 57.143 0.00 0.00 0.00 5.14
2824 5103 1.874129 ACTCTCTCTCTCTCTCCCGA 58.126 55.000 0.00 0.00 0.00 5.14
2825 5104 2.408565 ACTCTCTCTCTCTCTCCCGAT 58.591 52.381 0.00 0.00 0.00 4.18
2826 5105 2.104792 ACTCTCTCTCTCTCTCCCGATG 59.895 54.545 0.00 0.00 0.00 3.84
2827 5106 1.202758 TCTCTCTCTCTCTCCCGATGC 60.203 57.143 0.00 0.00 0.00 3.91
2828 5107 0.533978 TCTCTCTCTCTCCCGATGCG 60.534 60.000 0.00 0.00 0.00 4.73
2859 5138 4.264638 GCGCTCCTCCTCTCGCTC 62.265 72.222 0.00 0.00 43.70 5.03
2860 5139 3.591835 CGCTCCTCCTCTCGCTCC 61.592 72.222 0.00 0.00 0.00 4.70
2861 5140 3.591835 GCTCCTCCTCTCGCTCCG 61.592 72.222 0.00 0.00 0.00 4.63
2862 5141 2.190843 CTCCTCCTCTCGCTCCGA 59.809 66.667 0.00 0.00 0.00 4.55
2863 5142 1.228124 CTCCTCCTCTCGCTCCGAT 60.228 63.158 0.00 0.00 34.61 4.18
2864 5143 1.514678 CTCCTCCTCTCGCTCCGATG 61.515 65.000 0.00 0.00 34.61 3.84
2865 5144 2.334653 CTCCTCTCGCTCCGATGC 59.665 66.667 0.00 0.00 34.61 3.91
2866 5145 2.124109 TCCTCTCGCTCCGATGCT 60.124 61.111 0.00 0.00 34.61 3.79
2867 5146 2.128853 CTCCTCTCGCTCCGATGCTC 62.129 65.000 0.00 0.00 34.61 4.26
2868 5147 2.051435 CTCTCGCTCCGATGCTCG 60.051 66.667 0.00 0.00 40.07 5.03
2869 5148 2.824489 TCTCGCTCCGATGCTCGT 60.824 61.111 5.15 0.00 38.40 4.18
2870 5149 2.352915 CTCGCTCCGATGCTCGTC 60.353 66.667 5.15 0.00 38.40 4.20
2871 5150 2.824489 TCGCTCCGATGCTCGTCT 60.824 61.111 5.15 0.00 38.40 4.18
2872 5151 2.352915 CGCTCCGATGCTCGTCTC 60.353 66.667 5.15 0.00 38.40 3.36
2873 5152 2.026879 GCTCCGATGCTCGTCTCC 59.973 66.667 5.15 0.00 38.40 3.71
2874 5153 2.775856 GCTCCGATGCTCGTCTCCA 61.776 63.158 5.15 0.00 38.40 3.86
2875 5154 2.037053 CTCCGATGCTCGTCTCCAT 58.963 57.895 5.15 0.00 38.40 3.41
2876 5155 0.387202 CTCCGATGCTCGTCTCCATT 59.613 55.000 5.15 0.00 38.40 3.16
2877 5156 0.103026 TCCGATGCTCGTCTCCATTG 59.897 55.000 5.15 0.00 38.40 2.82
2878 5157 1.493950 CCGATGCTCGTCTCCATTGC 61.494 60.000 5.15 0.00 38.40 3.56
2879 5158 1.493950 CGATGCTCGTCTCCATTGCC 61.494 60.000 0.00 0.00 34.72 4.52
2880 5159 1.493950 GATGCTCGTCTCCATTGCCG 61.494 60.000 0.00 0.00 0.00 5.69
2881 5160 2.892425 GCTCGTCTCCATTGCCGG 60.892 66.667 0.00 0.00 0.00 6.13
2882 5161 2.892640 CTCGTCTCCATTGCCGGA 59.107 61.111 5.05 0.00 0.00 5.14
2883 5162 1.519455 CTCGTCTCCATTGCCGGAC 60.519 63.158 5.05 0.00 0.00 4.79
2884 5163 2.225791 CTCGTCTCCATTGCCGGACA 62.226 60.000 5.05 0.00 0.00 4.02
2885 5164 2.100631 CGTCTCCATTGCCGGACAC 61.101 63.158 5.05 0.00 0.00 3.67
2886 5165 1.296715 GTCTCCATTGCCGGACACT 59.703 57.895 5.05 0.00 0.00 3.55
2887 5166 0.741221 GTCTCCATTGCCGGACACTC 60.741 60.000 5.05 0.00 0.00 3.51
2888 5167 0.904865 TCTCCATTGCCGGACACTCT 60.905 55.000 5.05 0.00 0.00 3.24
2889 5168 0.460987 CTCCATTGCCGGACACTCTC 60.461 60.000 5.05 0.00 0.00 3.20
2890 5169 1.450312 CCATTGCCGGACACTCTCC 60.450 63.158 5.05 0.00 35.33 3.71
2891 5170 1.599047 CATTGCCGGACACTCTCCT 59.401 57.895 5.05 0.00 36.80 3.69
2892 5171 0.460987 CATTGCCGGACACTCTCCTC 60.461 60.000 5.05 0.00 36.80 3.71
2893 5172 0.616111 ATTGCCGGACACTCTCCTCT 60.616 55.000 5.05 0.00 36.80 3.69
2894 5173 1.251527 TTGCCGGACACTCTCCTCTC 61.252 60.000 5.05 0.00 36.80 3.20
2895 5174 2.419739 GCCGGACACTCTCCTCTCC 61.420 68.421 5.05 0.00 36.80 3.71
2896 5175 1.755008 CCGGACACTCTCCTCTCCC 60.755 68.421 0.00 0.00 36.80 4.30
2897 5176 1.304952 CGGACACTCTCCTCTCCCT 59.695 63.158 0.00 0.00 36.80 4.20
2898 5177 0.323908 CGGACACTCTCCTCTCCCTT 60.324 60.000 0.00 0.00 36.80 3.95
2899 5178 1.893210 CGGACACTCTCCTCTCCCTTT 60.893 57.143 0.00 0.00 36.80 3.11
2900 5179 2.261729 GGACACTCTCCTCTCCCTTTT 58.738 52.381 0.00 0.00 35.89 2.27
2901 5180 2.235155 GGACACTCTCCTCTCCCTTTTC 59.765 54.545 0.00 0.00 35.89 2.29
2902 5181 2.235155 GACACTCTCCTCTCCCTTTTCC 59.765 54.545 0.00 0.00 0.00 3.13
2903 5182 1.557371 CACTCTCCTCTCCCTTTTCCC 59.443 57.143 0.00 0.00 0.00 3.97
2904 5183 1.208706 CTCTCCTCTCCCTTTTCCCC 58.791 60.000 0.00 0.00 0.00 4.81
2905 5184 0.496382 TCTCCTCTCCCTTTTCCCCA 59.504 55.000 0.00 0.00 0.00 4.96
2906 5185 1.082879 TCTCCTCTCCCTTTTCCCCAT 59.917 52.381 0.00 0.00 0.00 4.00
2907 5186 1.213926 CTCCTCTCCCTTTTCCCCATG 59.786 57.143 0.00 0.00 0.00 3.66
2908 5187 0.396278 CCTCTCCCTTTTCCCCATGC 60.396 60.000 0.00 0.00 0.00 4.06
2909 5188 0.627986 CTCTCCCTTTTCCCCATGCT 59.372 55.000 0.00 0.00 0.00 3.79
2910 5189 0.625849 TCTCCCTTTTCCCCATGCTC 59.374 55.000 0.00 0.00 0.00 4.26
2911 5190 0.749454 CTCCCTTTTCCCCATGCTCG 60.749 60.000 0.00 0.00 0.00 5.03
2912 5191 2.418083 CCCTTTTCCCCATGCTCGC 61.418 63.158 0.00 0.00 0.00 5.03
2913 5192 2.418083 CCTTTTCCCCATGCTCGCC 61.418 63.158 0.00 0.00 0.00 5.54
2914 5193 2.749839 TTTTCCCCATGCTCGCCG 60.750 61.111 0.00 0.00 0.00 6.46
2930 5209 4.247380 CGCCATGGCCTCCTCCTC 62.247 72.222 30.79 0.24 37.98 3.71
2931 5210 3.883549 GCCATGGCCTCCTCCTCC 61.884 72.222 27.24 0.00 34.56 4.30
2932 5211 2.040043 CCATGGCCTCCTCCTCCT 60.040 66.667 3.32 0.00 0.00 3.69
2933 5212 2.146061 CCATGGCCTCCTCCTCCTC 61.146 68.421 3.32 0.00 0.00 3.71
2934 5213 2.146061 CATGGCCTCCTCCTCCTCC 61.146 68.421 3.32 0.00 0.00 4.30
2935 5214 2.340025 ATGGCCTCCTCCTCCTCCT 61.340 63.158 3.32 0.00 0.00 3.69
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
95 97 8.863049 GCGAACATTTTCTGAATTCATGTTTAT 58.137 29.630 19.93 4.34 31.85 1.40
96 98 7.328249 GGCGAACATTTTCTGAATTCATGTTTA 59.672 33.333 19.93 3.69 31.85 2.01
289 291 9.757227 CTAACCCATACTTCAAAAATTTGTGAA 57.243 29.630 20.18 20.18 39.18 3.18
290 292 8.919145 ACTAACCCATACTTCAAAAATTTGTGA 58.081 29.630 6.98 6.98 39.18 3.58
419 422 2.789092 CGTTTTATCGACGCGTAGTCCT 60.789 50.000 13.97 4.40 46.92 3.85
428 431 3.774282 TCACAAACCGTTTTATCGACG 57.226 42.857 0.00 0.00 40.05 5.12
430 433 5.453648 CCAATTCACAAACCGTTTTATCGA 58.546 37.500 0.00 0.00 0.00 3.59
431 434 4.619336 CCCAATTCACAAACCGTTTTATCG 59.381 41.667 0.00 0.00 0.00 2.92
432 435 4.387559 GCCCAATTCACAAACCGTTTTATC 59.612 41.667 0.00 0.00 0.00 1.75
433 436 4.202264 TGCCCAATTCACAAACCGTTTTAT 60.202 37.500 0.00 0.00 0.00 1.40
434 437 3.132289 TGCCCAATTCACAAACCGTTTTA 59.868 39.130 0.00 0.00 0.00 1.52
511 516 3.826157 TGCAGGAGAAATAAGTGGGTTTG 59.174 43.478 0.00 0.00 0.00 2.93
622 628 8.500753 TCATTTTGCTCCGTATGTAGTTTATT 57.499 30.769 0.00 0.00 0.00 1.40
625 631 6.811253 TTCATTTTGCTCCGTATGTAGTTT 57.189 33.333 0.00 0.00 0.00 2.66
653 659 2.926165 AGACGTACTTTCGTGTGTAGC 58.074 47.619 0.00 0.00 44.21 3.58
713 719 7.525158 ACTCCCTCCCTTTCTAAATAATTCA 57.475 36.000 0.00 0.00 0.00 2.57
728 736 0.462047 CGCATTGTGTACTCCCTCCC 60.462 60.000 0.00 0.00 0.00 4.30
929 3158 0.871057 TGTGTGTGTGTGTGTGTGTG 59.129 50.000 0.00 0.00 0.00 3.82
931 3160 0.871057 TGTGTGTGTGTGTGTGTGTG 59.129 50.000 0.00 0.00 0.00 3.82
933 3162 2.225255 TCTTTGTGTGTGTGTGTGTGTG 59.775 45.455 0.00 0.00 0.00 3.82
935 3164 2.728846 GCTCTTTGTGTGTGTGTGTGTG 60.729 50.000 0.00 0.00 0.00 3.82
936 3165 1.468520 GCTCTTTGTGTGTGTGTGTGT 59.531 47.619 0.00 0.00 0.00 3.72
937 3166 1.739466 AGCTCTTTGTGTGTGTGTGTG 59.261 47.619 0.00 0.00 0.00 3.82
938 3167 1.739466 CAGCTCTTTGTGTGTGTGTGT 59.261 47.619 0.00 0.00 0.00 3.72
939 3168 1.532505 GCAGCTCTTTGTGTGTGTGTG 60.533 52.381 0.00 0.00 0.00 3.82
940 3169 0.734889 GCAGCTCTTTGTGTGTGTGT 59.265 50.000 0.00 0.00 0.00 3.72
941 3170 0.029834 GGCAGCTCTTTGTGTGTGTG 59.970 55.000 0.00 0.00 0.00 3.82
942 3171 0.107017 AGGCAGCTCTTTGTGTGTGT 60.107 50.000 0.00 0.00 0.00 3.72
943 3172 0.590195 GAGGCAGCTCTTTGTGTGTG 59.410 55.000 0.00 0.00 0.00 3.82
944 3173 0.536006 GGAGGCAGCTCTTTGTGTGT 60.536 55.000 0.00 0.00 0.00 3.72
945 3174 0.250640 AGGAGGCAGCTCTTTGTGTG 60.251 55.000 0.00 0.00 0.00 3.82
946 3175 0.036022 GAGGAGGCAGCTCTTTGTGT 59.964 55.000 0.00 0.00 0.00 3.72
947 3176 0.676151 GGAGGAGGCAGCTCTTTGTG 60.676 60.000 0.00 0.00 0.00 3.33
948 3177 1.130054 TGGAGGAGGCAGCTCTTTGT 61.130 55.000 0.00 0.00 0.00 2.83
949 3178 0.037303 TTGGAGGAGGCAGCTCTTTG 59.963 55.000 0.00 0.00 0.00 2.77
1168 3402 6.910191 CCCCCAGATTTGGCATGTATATATA 58.090 40.000 0.00 0.00 43.58 0.86
1169 3403 5.769835 CCCCCAGATTTGGCATGTATATAT 58.230 41.667 0.00 0.00 43.58 0.86
1259 3519 2.700773 GGTGAGGGCGCCATTGTTC 61.701 63.158 30.85 16.85 44.29 3.18
1291 3551 3.791586 GGGCAGGAGGAGGAGCAC 61.792 72.222 0.00 0.00 0.00 4.40
1940 4200 0.108585 GGGGCTTGAGTCACTTGTGA 59.891 55.000 0.00 0.00 0.00 3.58
1944 4204 1.425066 TCAATGGGGCTTGAGTCACTT 59.575 47.619 0.00 0.00 31.65 3.16
1945 4205 1.067295 TCAATGGGGCTTGAGTCACT 58.933 50.000 0.00 0.00 31.65 3.41
1946 4206 2.019984 GATCAATGGGGCTTGAGTCAC 58.980 52.381 0.00 0.00 38.47 3.67
1947 4207 1.064463 GGATCAATGGGGCTTGAGTCA 60.064 52.381 0.00 0.00 38.47 3.41
1948 4208 1.685148 GGATCAATGGGGCTTGAGTC 58.315 55.000 0.00 0.00 38.47 3.36
1949 4209 0.259938 GGGATCAATGGGGCTTGAGT 59.740 55.000 0.00 0.00 38.47 3.41
1950 4210 0.820891 CGGGATCAATGGGGCTTGAG 60.821 60.000 0.00 0.00 38.47 3.02
1951 4211 1.227102 CGGGATCAATGGGGCTTGA 59.773 57.895 0.00 0.00 39.35 3.02
1952 4212 2.492773 GCGGGATCAATGGGGCTTG 61.493 63.158 0.00 0.00 0.00 4.01
1953 4213 2.123726 GCGGGATCAATGGGGCTT 60.124 61.111 0.00 0.00 0.00 4.35
1960 4220 0.828022 TACGTTCAGGCGGGATCAAT 59.172 50.000 0.00 0.00 35.98 2.57
1991 4251 3.683989 CGTGCCATACATGAATCACAAC 58.316 45.455 0.00 0.00 37.49 3.32
1992 4252 2.097304 GCGTGCCATACATGAATCACAA 59.903 45.455 0.00 0.00 37.49 3.33
2020 4281 9.824534 TTATTCGTCTAACGGGAAATTTAAAAC 57.175 29.630 0.00 0.00 42.81 2.43
2106 4367 1.790623 CCGGTTTACGCTCGATAATGG 59.209 52.381 0.00 0.00 42.52 3.16
2137 4406 7.564988 CACTTTCAAAGTTACAGTAGTAGTGC 58.435 38.462 0.00 0.00 40.46 4.40
2138 4407 7.223971 TGCACTTTCAAAGTTACAGTAGTAGTG 59.776 37.037 0.00 3.30 40.46 2.74
2169 4440 3.548587 CTGAACTCAAATTCTGTGTGCG 58.451 45.455 0.00 0.00 30.65 5.34
2206 4477 8.992349 TCTCAGTCTTGGATCCATCTTTTTATA 58.008 33.333 17.06 0.00 0.00 0.98
2309 4580 6.491745 CCTCTCCAAGCAGTAGAGACAATATA 59.508 42.308 0.00 0.00 39.29 0.86
2381 4652 0.035534 ACACAGCCCATGCAATCGTA 60.036 50.000 0.00 0.00 41.13 3.43
2382 4653 1.303561 ACACAGCCCATGCAATCGT 60.304 52.632 0.00 0.00 41.13 3.73
2383 4654 1.138036 CACACAGCCCATGCAATCG 59.862 57.895 0.00 0.00 41.13 3.34
2384 4655 1.153706 GCACACAGCCCATGCAATC 60.154 57.895 0.00 0.00 41.13 2.67
2399 4670 0.890542 TTGCCTCATCCACACTGCAC 60.891 55.000 0.00 0.00 0.00 4.57
2401 4672 1.310933 CCTTGCCTCATCCACACTGC 61.311 60.000 0.00 0.00 0.00 4.40
2403 4674 1.001641 GCCTTGCCTCATCCACACT 60.002 57.895 0.00 0.00 0.00 3.55
2479 4758 2.318578 CATTATTAGCCGCAATTGCCG 58.681 47.619 24.24 18.71 37.91 5.69
2517 4796 3.005539 TGGAGAGCTGCCCCAGTC 61.006 66.667 0.00 0.00 33.43 3.51
2562 4841 1.189524 CCGGTCACCAGAACACCCTA 61.190 60.000 0.00 0.00 0.00 3.53
2571 4850 3.322466 AGGAAGCCCGGTCACCAG 61.322 66.667 0.00 0.00 37.58 4.00
2580 4859 1.545841 AAAATTCGTCCAGGAAGCCC 58.454 50.000 0.00 0.00 0.00 5.19
2617 4896 9.726438 TCTAAAACCAAAAGGTTTGAATTTTGA 57.274 25.926 12.87 13.15 45.13 2.69
2630 4909 6.814644 ACGTTTCCCTTTTCTAAAACCAAAAG 59.185 34.615 0.00 0.00 38.72 2.27
2631 4910 6.699366 ACGTTTCCCTTTTCTAAAACCAAAA 58.301 32.000 0.00 0.00 0.00 2.44
2632 4911 6.283544 ACGTTTCCCTTTTCTAAAACCAAA 57.716 33.333 0.00 0.00 0.00 3.28
2633 4912 5.918426 ACGTTTCCCTTTTCTAAAACCAA 57.082 34.783 0.00 0.00 0.00 3.67
2634 4913 5.918426 AACGTTTCCCTTTTCTAAAACCA 57.082 34.783 0.00 0.00 0.00 3.67
2635 4914 6.817270 GAAACGTTTCCCTTTTCTAAAACC 57.183 37.500 27.01 0.00 0.00 3.27
2649 4928 0.168128 CTGCCGATGGGAAACGTTTC 59.832 55.000 28.83 28.83 36.46 2.78
2650 4929 0.250553 TCTGCCGATGGGAAACGTTT 60.251 50.000 14.57 14.57 34.06 3.60
2651 4930 0.953960 GTCTGCCGATGGGAAACGTT 60.954 55.000 0.00 0.00 34.06 3.99
2652 4931 1.375523 GTCTGCCGATGGGAAACGT 60.376 57.895 0.00 0.00 34.06 3.99
2653 4932 2.106683 GGTCTGCCGATGGGAAACG 61.107 63.158 0.00 0.00 34.06 3.60
2654 4933 3.905249 GGTCTGCCGATGGGAAAC 58.095 61.111 0.00 0.00 34.06 2.78
2666 4945 2.815647 GAAGCTTCGGCCGGTCTG 60.816 66.667 27.83 13.86 43.01 3.51
2667 4946 4.436998 CGAAGCTTCGGCCGGTCT 62.437 66.667 35.58 16.74 46.30 3.85
2676 4955 4.736896 ACGACCGGCCGAAGCTTC 62.737 66.667 30.73 16.84 39.73 3.86
2684 4963 4.849329 CTAGCGACACGACCGGCC 62.849 72.222 0.00 0.00 0.00 6.13
2686 4965 3.736482 GAGCTAGCGACACGACCGG 62.736 68.421 9.55 0.00 0.00 5.28
2687 4966 2.277373 GAGCTAGCGACACGACCG 60.277 66.667 9.55 0.00 0.00 4.79
2688 4967 2.102553 GGAGCTAGCGACACGACC 59.897 66.667 9.55 2.22 0.00 4.79
2689 4968 2.102553 GGGAGCTAGCGACACGAC 59.897 66.667 9.55 0.00 0.00 4.34
2690 4969 3.506096 CGGGAGCTAGCGACACGA 61.506 66.667 26.63 0.00 0.00 4.35
2710 4989 4.673298 TGGTGGGTGTGCTACGCG 62.673 66.667 3.53 3.53 44.60 6.01
2711 4990 0.391927 TATTGGTGGGTGTGCTACGC 60.392 55.000 2.59 2.59 42.21 4.42
2712 4991 1.365699 GTATTGGTGGGTGTGCTACG 58.634 55.000 0.00 0.00 0.00 3.51
2713 4992 1.003812 TGGTATTGGTGGGTGTGCTAC 59.996 52.381 0.00 0.00 0.00 3.58
2714 4993 1.363246 TGGTATTGGTGGGTGTGCTA 58.637 50.000 0.00 0.00 0.00 3.49
2715 4994 0.480690 TTGGTATTGGTGGGTGTGCT 59.519 50.000 0.00 0.00 0.00 4.40
2716 4995 0.887933 CTTGGTATTGGTGGGTGTGC 59.112 55.000 0.00 0.00 0.00 4.57
2717 4996 1.074727 TCCTTGGTATTGGTGGGTGTG 59.925 52.381 0.00 0.00 0.00 3.82
2718 4997 1.354368 CTCCTTGGTATTGGTGGGTGT 59.646 52.381 0.00 0.00 0.00 4.16
2719 4998 1.955208 GCTCCTTGGTATTGGTGGGTG 60.955 57.143 0.00 0.00 0.00 4.61
2720 4999 0.331616 GCTCCTTGGTATTGGTGGGT 59.668 55.000 0.00 0.00 0.00 4.51
2721 5000 0.395724 GGCTCCTTGGTATTGGTGGG 60.396 60.000 0.00 0.00 0.00 4.61
2722 5001 0.331278 TGGCTCCTTGGTATTGGTGG 59.669 55.000 0.00 0.00 0.00 4.61
2723 5002 1.271871 TGTGGCTCCTTGGTATTGGTG 60.272 52.381 0.00 0.00 0.00 4.17
2724 5003 1.072266 TGTGGCTCCTTGGTATTGGT 58.928 50.000 0.00 0.00 0.00 3.67
2725 5004 1.463674 GTGTGGCTCCTTGGTATTGG 58.536 55.000 0.00 0.00 0.00 3.16
2726 5005 1.086696 CGTGTGGCTCCTTGGTATTG 58.913 55.000 0.00 0.00 0.00 1.90
2727 5006 0.690762 ACGTGTGGCTCCTTGGTATT 59.309 50.000 0.00 0.00 0.00 1.89
2728 5007 0.249398 GACGTGTGGCTCCTTGGTAT 59.751 55.000 0.00 0.00 0.00 2.73
2729 5008 1.669440 GACGTGTGGCTCCTTGGTA 59.331 57.895 0.00 0.00 0.00 3.25
2730 5009 2.426023 GACGTGTGGCTCCTTGGT 59.574 61.111 0.00 0.00 0.00 3.67
2731 5010 2.358737 GGACGTGTGGCTCCTTGG 60.359 66.667 0.00 0.00 0.00 3.61
2732 5011 1.071471 AAGGACGTGTGGCTCCTTG 59.929 57.895 4.34 0.00 43.95 3.61
2733 5012 1.071471 CAAGGACGTGTGGCTCCTT 59.929 57.895 0.00 0.00 46.13 3.36
2734 5013 2.743718 CAAGGACGTGTGGCTCCT 59.256 61.111 0.00 0.00 38.67 3.69
2735 5014 3.050275 GCAAGGACGTGTGGCTCC 61.050 66.667 0.00 0.00 0.00 4.70
2736 5015 3.414700 CGCAAGGACGTGTGGCTC 61.415 66.667 0.00 0.00 0.00 4.70
2748 5027 4.690719 TACGTGTGGGCCCGCAAG 62.691 66.667 39.25 39.25 40.67 4.01
2749 5028 4.690719 CTACGTGTGGGCCCGCAA 62.691 66.667 39.02 23.14 38.24 4.85
2753 5032 3.546714 AAGCACTACGTGTGGGCCC 62.547 63.158 17.59 17.59 46.27 5.80
2754 5033 2.032071 AAGCACTACGTGTGGGCC 59.968 61.111 12.86 0.00 46.27 5.80
2755 5034 1.301401 TGAAGCACTACGTGTGGGC 60.301 57.895 16.33 13.17 46.27 5.36
2756 5035 0.949105 GGTGAAGCACTACGTGTGGG 60.949 60.000 16.33 4.61 46.27 4.61
2757 5036 0.033504 AGGTGAAGCACTACGTGTGG 59.966 55.000 16.33 2.67 46.27 4.17
2759 5038 2.614829 AAAGGTGAAGCACTACGTGT 57.385 45.000 0.00 0.00 35.75 4.49
2760 5039 3.303791 GGAAAAAGGTGAAGCACTACGTG 60.304 47.826 0.00 0.00 34.40 4.49
2761 5040 2.876550 GGAAAAAGGTGAAGCACTACGT 59.123 45.455 0.00 0.00 34.40 3.57
2762 5041 3.139077 AGGAAAAAGGTGAAGCACTACG 58.861 45.455 0.00 0.00 34.40 3.51
2763 5042 6.174049 AGATAGGAAAAAGGTGAAGCACTAC 58.826 40.000 0.00 0.00 34.40 2.73
2764 5043 6.374417 AGATAGGAAAAAGGTGAAGCACTA 57.626 37.500 0.00 0.00 34.40 2.74
2765 5044 5.248380 AGATAGGAAAAAGGTGAAGCACT 57.752 39.130 0.00 0.00 34.40 4.40
2766 5045 5.707764 AGAAGATAGGAAAAAGGTGAAGCAC 59.292 40.000 0.00 0.00 0.00 4.40
2767 5046 5.880901 AGAAGATAGGAAAAAGGTGAAGCA 58.119 37.500 0.00 0.00 0.00 3.91
2768 5047 6.657117 AGAAGAAGATAGGAAAAAGGTGAAGC 59.343 38.462 0.00 0.00 0.00 3.86
2769 5048 8.628630 AAGAAGAAGATAGGAAAAAGGTGAAG 57.371 34.615 0.00 0.00 0.00 3.02
2770 5049 7.665974 GGAAGAAGAAGATAGGAAAAAGGTGAA 59.334 37.037 0.00 0.00 0.00 3.18
2771 5050 7.017651 AGGAAGAAGAAGATAGGAAAAAGGTGA 59.982 37.037 0.00 0.00 0.00 4.02
2772 5051 7.171653 AGGAAGAAGAAGATAGGAAAAAGGTG 58.828 38.462 0.00 0.00 0.00 4.00
2773 5052 7.336475 AGGAAGAAGAAGATAGGAAAAAGGT 57.664 36.000 0.00 0.00 0.00 3.50
2774 5053 8.642935 AAAGGAAGAAGAAGATAGGAAAAAGG 57.357 34.615 0.00 0.00 0.00 3.11
2775 5054 9.289782 TGAAAGGAAGAAGAAGATAGGAAAAAG 57.710 33.333 0.00 0.00 0.00 2.27
2776 5055 9.289782 CTGAAAGGAAGAAGAAGATAGGAAAAA 57.710 33.333 0.00 0.00 0.00 1.94
2777 5056 8.854614 CTGAAAGGAAGAAGAAGATAGGAAAA 57.145 34.615 0.00 0.00 0.00 2.29
2796 5075 5.256474 AGAGAGAGAGAGAGTTCCTGAAAG 58.744 45.833 0.00 0.00 0.00 2.62
2797 5076 5.253330 GAGAGAGAGAGAGAGTTCCTGAAA 58.747 45.833 0.00 0.00 0.00 2.69
2798 5077 4.324254 GGAGAGAGAGAGAGAGTTCCTGAA 60.324 50.000 0.00 0.00 0.00 3.02
2799 5078 3.199946 GGAGAGAGAGAGAGAGTTCCTGA 59.800 52.174 0.00 0.00 0.00 3.86
2800 5079 3.545703 GGAGAGAGAGAGAGAGTTCCTG 58.454 54.545 0.00 0.00 0.00 3.86
2801 5080 2.509964 GGGAGAGAGAGAGAGAGTTCCT 59.490 54.545 0.00 0.00 0.00 3.36
2802 5081 2.745152 CGGGAGAGAGAGAGAGAGTTCC 60.745 59.091 0.00 0.00 0.00 3.62
2803 5082 2.169769 TCGGGAGAGAGAGAGAGAGTTC 59.830 54.545 0.00 0.00 0.00 3.01
2804 5083 2.193127 TCGGGAGAGAGAGAGAGAGTT 58.807 52.381 0.00 0.00 0.00 3.01
2805 5084 1.874129 TCGGGAGAGAGAGAGAGAGT 58.126 55.000 0.00 0.00 0.00 3.24
2806 5085 2.771089 CATCGGGAGAGAGAGAGAGAG 58.229 57.143 0.00 0.00 45.48 3.20
2807 5086 1.202758 GCATCGGGAGAGAGAGAGAGA 60.203 57.143 0.00 0.00 45.48 3.10
2808 5087 1.238439 GCATCGGGAGAGAGAGAGAG 58.762 60.000 0.00 0.00 45.48 3.20
2809 5088 0.533978 CGCATCGGGAGAGAGAGAGA 60.534 60.000 0.00 0.00 45.48 3.10
2810 5089 1.514678 CCGCATCGGGAGAGAGAGAG 61.515 65.000 0.00 0.00 44.15 3.20
2811 5090 1.527148 CCGCATCGGGAGAGAGAGA 60.527 63.158 0.00 0.00 44.15 3.10
2812 5091 3.038280 CCGCATCGGGAGAGAGAG 58.962 66.667 0.00 0.00 44.15 3.20
2843 5122 3.591835 GGAGCGAGAGGAGGAGCG 61.592 72.222 0.00 0.00 34.34 5.03
2844 5123 3.591835 CGGAGCGAGAGGAGGAGC 61.592 72.222 0.00 0.00 0.00 4.70
2845 5124 1.228124 ATCGGAGCGAGAGGAGGAG 60.228 63.158 0.00 0.00 39.91 3.69
2846 5125 1.527148 CATCGGAGCGAGAGGAGGA 60.527 63.158 0.00 0.00 39.91 3.71
2847 5126 3.038280 CATCGGAGCGAGAGGAGG 58.962 66.667 0.00 0.00 39.91 4.30
2848 5127 2.128853 GAGCATCGGAGCGAGAGGAG 62.129 65.000 0.00 0.00 39.91 3.69
2849 5128 2.124109 AGCATCGGAGCGAGAGGA 60.124 61.111 0.00 0.00 39.91 3.71
2850 5129 2.334653 GAGCATCGGAGCGAGAGG 59.665 66.667 0.00 0.00 39.91 3.69
2861 5140 1.493950 CGGCAATGGAGACGAGCATC 61.494 60.000 0.00 0.00 0.00 3.91
2862 5141 1.522355 CGGCAATGGAGACGAGCAT 60.522 57.895 0.00 0.00 0.00 3.79
2863 5142 2.125552 CGGCAATGGAGACGAGCA 60.126 61.111 0.00 0.00 0.00 4.26
2864 5143 2.892425 CCGGCAATGGAGACGAGC 60.892 66.667 0.00 0.00 0.00 5.03
2865 5144 1.519455 GTCCGGCAATGGAGACGAG 60.519 63.158 0.00 0.00 39.14 4.18
2866 5145 2.279810 TGTCCGGCAATGGAGACGA 61.280 57.895 0.00 0.00 39.14 4.20
2867 5146 2.100631 GTGTCCGGCAATGGAGACG 61.101 63.158 0.00 0.00 41.74 4.18
2868 5147 3.890674 GTGTCCGGCAATGGAGAC 58.109 61.111 0.00 3.90 43.97 3.36
2869 5148 0.904865 AGAGTGTCCGGCAATGGAGA 60.905 55.000 0.00 0.00 39.14 3.71
2870 5149 0.460987 GAGAGTGTCCGGCAATGGAG 60.461 60.000 0.00 0.00 39.14 3.86
2871 5150 1.596934 GAGAGTGTCCGGCAATGGA 59.403 57.895 0.00 0.00 35.04 3.41
2872 5151 1.450312 GGAGAGTGTCCGGCAATGG 60.450 63.158 0.00 0.00 34.84 3.16
2873 5152 4.208632 GGAGAGTGTCCGGCAATG 57.791 61.111 0.00 0.00 34.84 2.82
2881 5160 2.235155 GGAAAAGGGAGAGGAGAGTGTC 59.765 54.545 0.00 0.00 0.00 3.67
2882 5161 2.261729 GGAAAAGGGAGAGGAGAGTGT 58.738 52.381 0.00 0.00 0.00 3.55
2883 5162 1.557371 GGGAAAAGGGAGAGGAGAGTG 59.443 57.143 0.00 0.00 0.00 3.51
2884 5163 1.556002 GGGGAAAAGGGAGAGGAGAGT 60.556 57.143 0.00 0.00 0.00 3.24
2885 5164 1.208706 GGGGAAAAGGGAGAGGAGAG 58.791 60.000 0.00 0.00 0.00 3.20
2886 5165 0.496382 TGGGGAAAAGGGAGAGGAGA 59.504 55.000 0.00 0.00 0.00 3.71
2887 5166 1.213926 CATGGGGAAAAGGGAGAGGAG 59.786 57.143 0.00 0.00 0.00 3.69
2888 5167 1.298953 CATGGGGAAAAGGGAGAGGA 58.701 55.000 0.00 0.00 0.00 3.71
2889 5168 0.396278 GCATGGGGAAAAGGGAGAGG 60.396 60.000 0.00 0.00 0.00 3.69
2890 5169 0.627986 AGCATGGGGAAAAGGGAGAG 59.372 55.000 0.00 0.00 0.00 3.20
2891 5170 0.625849 GAGCATGGGGAAAAGGGAGA 59.374 55.000 0.00 0.00 0.00 3.71
2892 5171 0.749454 CGAGCATGGGGAAAAGGGAG 60.749 60.000 0.00 0.00 0.00 4.30
2893 5172 1.302949 CGAGCATGGGGAAAAGGGA 59.697 57.895 0.00 0.00 0.00 4.20
2894 5173 2.418083 GCGAGCATGGGGAAAAGGG 61.418 63.158 0.00 0.00 0.00 3.95
2895 5174 2.418083 GGCGAGCATGGGGAAAAGG 61.418 63.158 0.00 0.00 0.00 3.11
2896 5175 2.764314 CGGCGAGCATGGGGAAAAG 61.764 63.158 0.00 0.00 0.00 2.27
2897 5176 2.749839 CGGCGAGCATGGGGAAAA 60.750 61.111 0.00 0.00 0.00 2.29
2913 5192 4.247380 GAGGAGGAGGCCATGGCG 62.247 72.222 29.90 0.00 43.06 5.69
2914 5193 3.883549 GGAGGAGGAGGCCATGGC 61.884 72.222 29.47 29.47 41.06 4.40
2915 5194 2.040043 AGGAGGAGGAGGCCATGG 60.040 66.667 7.63 7.63 0.00 3.66
2916 5195 2.146061 GGAGGAGGAGGAGGCCATG 61.146 68.421 5.01 0.00 0.00 3.66
2917 5196 2.288643 GGAGGAGGAGGAGGCCAT 59.711 66.667 5.01 0.00 0.00 4.40
2918 5197 2.955246 AGGAGGAGGAGGAGGCCA 60.955 66.667 5.01 0.00 0.00 5.36


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

AutoCloner maintained by Alex Coulton.