Multiple sequence alignment - TraesCS5B01G121200

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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 TraesCS5B01G121200 chr5B 100.000 4411 0 0 1 4411 216400067 216395657 0.000000e+00 8146.0
1 TraesCS5B01G121200 chr1B 97.806 1550 24 8 1378 2923 134433211 134434754 0.000000e+00 2665.0
2 TraesCS5B01G121200 chr1B 97.667 1543 31 4 1373 2913 548631749 548630210 0.000000e+00 2645.0
3 TraesCS5B01G121200 chr1B 94.231 52 3 0 3000 3051 663609632 663609683 3.660000e-11 80.5
4 TraesCS5B01G121200 chr6B 96.970 1551 39 5 1377 2925 580482627 580481083 0.000000e+00 2597.0
5 TraesCS5B01G121200 chr6B 95.082 61 1 1 2990 3048 487833356 487833416 1.310000e-15 95.3
6 TraesCS5B01G121200 chr7B 96.714 1552 45 5 1376 2925 84049225 84047678 0.000000e+00 2579.0
7 TraesCS5B01G121200 chr7B 95.616 1551 57 8 1378 2923 64157859 64159403 0.000000e+00 2477.0
8 TraesCS5B01G121200 chr7B 90.698 473 30 9 3629 4100 379416870 379417329 6.270000e-173 617.0
9 TraesCS5B01G121200 chr7B 90.583 223 15 1 4175 4391 379417326 379417548 1.550000e-74 291.0
10 TraesCS5B01G121200 chr5D 95.150 1567 65 10 1372 2932 377412398 377413959 0.000000e+00 2462.0
11 TraesCS5B01G121200 chr5D 92.178 1419 53 14 1 1384 193511921 193510526 0.000000e+00 1953.0
12 TraesCS5B01G121200 chr5D 97.222 576 16 0 3054 3629 193510470 193509895 0.000000e+00 976.0
13 TraesCS5B01G121200 chr5D 88.158 76 9 0 3726 3801 238393606 238393681 1.690000e-14 91.6
14 TraesCS5B01G121200 chrUn 95.023 1527 61 12 1413 2932 112219780 112218262 0.000000e+00 2385.0
15 TraesCS5B01G121200 chrUn 87.013 77 10 0 3629 3705 269320267 269320191 2.190000e-13 87.9
16 TraesCS5B01G121200 chr5A 92.847 1398 55 16 1 1375 248531923 248533298 0.000000e+00 1986.0
17 TraesCS5B01G121200 chr5A 98.787 577 6 1 3054 3629 248533363 248533939 0.000000e+00 1026.0
18 TraesCS5B01G121200 chr5A 96.774 62 1 1 2930 2990 248533296 248533357 7.810000e-18 102.0
19 TraesCS5B01G121200 chr3D 95.356 1012 44 3 1378 2388 24551453 24552462 0.000000e+00 1605.0
20 TraesCS5B01G121200 chr3D 95.671 947 39 2 1378 2323 478359692 478360637 0.000000e+00 1520.0
21 TraesCS5B01G121200 chr3D 94.504 564 20 5 2367 2925 478360639 478361196 0.000000e+00 859.0
22 TraesCS5B01G121200 chr4A 93.930 626 23 7 2312 2926 90414585 90415206 0.000000e+00 931.0
23 TraesCS5B01G121200 chr4A 82.963 135 17 6 3616 3748 655670100 655669970 2.790000e-22 117.0
24 TraesCS5B01G121200 chr2B 89.313 262 20 6 3839 4100 152840417 152840670 5.500000e-84 322.0
25 TraesCS5B01G121200 chr2B 91.480 223 13 1 4175 4391 152840667 152840889 7.170000e-78 302.0
26 TraesCS5B01G121200 chr2B 93.671 158 7 1 3626 3783 152840257 152840411 2.650000e-57 233.0
27 TraesCS5B01G121200 chr2B 87.500 80 10 0 3725 3804 799711404 799711325 4.700000e-15 93.5
28 TraesCS5B01G121200 chr2B 96.154 52 1 1 3003 3054 788199788 788199838 2.830000e-12 84.2
29 TraesCS5B01G121200 chr2B 90.476 63 4 2 3002 3063 772635024 772635085 1.020000e-11 82.4
30 TraesCS5B01G121200 chr2A 82.927 123 18 2 3626 3748 750199856 750199737 1.680000e-19 108.0
31 TraesCS5B01G121200 chr2A 85.542 83 8 4 3719 3800 16635398 16635477 2.830000e-12 84.2
32 TraesCS5B01G121200 chr7D 94.030 67 3 1 3717 3783 182575614 182575549 2.810000e-17 100.0
33 TraesCS5B01G121200 chr7D 80.769 130 20 4 3620 3748 156035743 156035618 3.630000e-16 97.1
34 TraesCS5B01G121200 chr7D 85.526 76 11 0 3726 3801 631182520 631182445 3.660000e-11 80.5
35 TraesCS5B01G121200 chr4B 81.452 124 18 4 3627 3749 672251396 672251515 3.630000e-16 97.1
36 TraesCS5B01G121200 chr7A 84.615 91 14 0 3626 3716 488473416 488473506 1.690000e-14 91.6
37 TraesCS5B01G121200 chr3A 88.571 70 8 0 3635 3704 26192340 26192409 7.860000e-13 86.1
38 TraesCS5B01G121200 chr3A 91.228 57 4 1 3005 3061 32446183 32446128 4.730000e-10 76.8
39 TraesCS5B01G121200 chr2D 96.226 53 1 1 3002 3054 524566871 524566820 7.860000e-13 86.1
40 TraesCS5B01G121200 chr2D 90.164 61 5 1 3719 3779 234348040 234348099 1.320000e-10 78.7
41 TraesCS5B01G121200 chr3B 96.154 52 1 1 3002 3053 132527342 132527292 2.830000e-12 84.2
42 TraesCS5B01G121200 chr3B 94.340 53 2 1 3002 3054 221200907 221200958 3.660000e-11 80.5
43 TraesCS5B01G121200 chr1A 88.406 69 3 3 2986 3050 363454147 363454214 1.320000e-10 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 TraesCS5B01G121200 chr5B 216395657 216400067 4410 True 8146.000000 8146 100.0000 1 4411 1 chr5B.!!$R1 4410
1 TraesCS5B01G121200 chr1B 134433211 134434754 1543 False 2665.000000 2665 97.8060 1378 2923 1 chr1B.!!$F1 1545
2 TraesCS5B01G121200 chr1B 548630210 548631749 1539 True 2645.000000 2645 97.6670 1373 2913 1 chr1B.!!$R1 1540
3 TraesCS5B01G121200 chr6B 580481083 580482627 1544 True 2597.000000 2597 96.9700 1377 2925 1 chr6B.!!$R1 1548
4 TraesCS5B01G121200 chr7B 84047678 84049225 1547 True 2579.000000 2579 96.7140 1376 2925 1 chr7B.!!$R1 1549
5 TraesCS5B01G121200 chr7B 64157859 64159403 1544 False 2477.000000 2477 95.6160 1378 2923 1 chr7B.!!$F1 1545
6 TraesCS5B01G121200 chr7B 379416870 379417548 678 False 454.000000 617 90.6405 3629 4391 2 chr7B.!!$F2 762
7 TraesCS5B01G121200 chr5D 377412398 377413959 1561 False 2462.000000 2462 95.1500 1372 2932 1 chr5D.!!$F2 1560
8 TraesCS5B01G121200 chr5D 193509895 193511921 2026 True 1464.500000 1953 94.7000 1 3629 2 chr5D.!!$R1 3628
9 TraesCS5B01G121200 chrUn 112218262 112219780 1518 True 2385.000000 2385 95.0230 1413 2932 1 chrUn.!!$R1 1519
10 TraesCS5B01G121200 chr5A 248531923 248533939 2016 False 1038.000000 1986 96.1360 1 3629 3 chr5A.!!$F1 3628
11 TraesCS5B01G121200 chr3D 24551453 24552462 1009 False 1605.000000 1605 95.3560 1378 2388 1 chr3D.!!$F1 1010
12 TraesCS5B01G121200 chr3D 478359692 478361196 1504 False 1189.500000 1520 95.0875 1378 2925 2 chr3D.!!$F2 1547
13 TraesCS5B01G121200 chr4A 90414585 90415206 621 False 931.000000 931 93.9300 2312 2926 1 chr4A.!!$F1 614
14 TraesCS5B01G121200 chr2B 152840257 152840889 632 False 285.666667 322 91.4880 3626 4391 3 chr2B.!!$F3 765

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
763 777 0.034283 GTACCTCTCTGGGTCTCGGT 60.034 60.000 0.00 0.0 40.48 4.69 F
1187 1218 0.035439 GGTTGGGGAATTCGAGCTGA 60.035 55.000 0.00 0.0 0.00 4.26 F
1189 1220 0.690192 TTGGGGAATTCGAGCTGACA 59.310 50.000 0.00 0.0 0.00 3.58 F
1506 1546 1.373246 CTTCCGTGCCGTTTCCGTA 60.373 57.895 0.00 0.0 0.00 4.02 F
2563 2617 1.374758 GGCACTCTCACCGGAGTTG 60.375 63.158 9.46 0.0 43.14 3.16 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2066 2110 0.383949 GTCCTCGCTCTAGCCTTCTG 59.616 60.0 0.0 0.0 37.91 3.02 R
2990 3055 0.178970 ACACTACACACGGAGGGAGT 60.179 55.0 0.0 0.0 0.00 3.85 R
2991 3056 0.526662 GACACTACACACGGAGGGAG 59.473 60.0 0.0 0.0 0.00 4.30 R
2993 3058 0.677288 TTGACACTACACACGGAGGG 59.323 55.0 0.0 0.0 0.00 4.30 R
3874 3940 0.035739 GCGTAAGTGGTGAAGGGGAA 59.964 55.0 0.0 0.0 41.68 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
189 190 3.694072 CGAATCCTTTGGAGCACCATTTA 59.306 43.478 2.87 0.00 46.34 1.40
268 269 3.560882 CCATTCAGGTTCTGCTTTCTCCT 60.561 47.826 0.00 0.00 0.00 3.69
301 302 1.475930 GCTGCTCCAGGTTAGGGAATC 60.476 57.143 0.00 0.00 33.11 2.52
344 345 2.945008 CTGTCTGAGCAAAGGAAACACA 59.055 45.455 0.00 0.00 0.00 3.72
369 370 1.744741 GAGAGAAGTGGCAGGCAGC 60.745 63.158 0.00 0.00 44.65 5.25
413 414 3.119388 TCAGGTTACTGCCATACACGTAC 60.119 47.826 0.00 0.00 44.54 3.67
468 469 6.301169 AGGATACCAAGAACTCTGGTAAAG 57.699 41.667 5.85 0.00 40.97 1.85
537 546 6.519382 CATCTACTAGTGGAAGCATGAATCA 58.481 40.000 13.39 0.00 0.00 2.57
592 601 3.116862 ACCTCCAAGAATCGGTAGGGATA 60.117 47.826 0.00 0.00 0.00 2.59
644 653 2.766263 TCGAAGCTCTCTCTCTCTCTCT 59.234 50.000 0.00 0.00 0.00 3.10
645 654 3.126831 CGAAGCTCTCTCTCTCTCTCTC 58.873 54.545 0.00 0.00 0.00 3.20
646 655 3.181471 CGAAGCTCTCTCTCTCTCTCTCT 60.181 52.174 0.00 0.00 0.00 3.10
647 656 4.376146 GAAGCTCTCTCTCTCTCTCTCTC 58.624 52.174 0.00 0.00 0.00 3.20
648 657 3.652055 AGCTCTCTCTCTCTCTCTCTCT 58.348 50.000 0.00 0.00 0.00 3.10
649 658 3.640967 AGCTCTCTCTCTCTCTCTCTCTC 59.359 52.174 0.00 0.00 0.00 3.20
650 659 3.640967 GCTCTCTCTCTCTCTCTCTCTCT 59.359 52.174 0.00 0.00 0.00 3.10
651 660 4.261994 GCTCTCTCTCTCTCTCTCTCTCTC 60.262 54.167 0.00 0.00 0.00 3.20
652 661 5.136068 TCTCTCTCTCTCTCTCTCTCTCT 57.864 47.826 0.00 0.00 0.00 3.10
653 662 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
654 663 5.103728 TCTCTCTCTCTCTCTCTCTCTCTCT 60.104 48.000 0.00 0.00 0.00 3.10
655 664 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
656 665 5.103728 TCTCTCTCTCTCTCTCTCTCTCTCT 60.104 48.000 0.00 0.00 0.00 3.10
743 752 4.221422 GCCTCGCCATCGCCACTA 62.221 66.667 0.00 0.00 35.26 2.74
744 753 2.028190 CCTCGCCATCGCCACTAG 59.972 66.667 0.00 0.00 35.26 2.57
763 777 0.034283 GTACCTCTCTGGGTCTCGGT 60.034 60.000 0.00 0.00 40.48 4.69
891 915 6.578919 GTCGTCTTTCAATTGATTCTTTGACC 59.421 38.462 9.40 0.00 31.87 4.02
892 916 5.565259 CGTCTTTCAATTGATTCTTTGACCG 59.435 40.000 9.40 0.00 31.87 4.79
901 925 4.641396 TGATTCTTTGACCGTGTCTCAAT 58.359 39.130 5.77 0.34 33.15 2.57
902 926 5.063204 TGATTCTTTGACCGTGTCTCAATT 58.937 37.500 5.77 0.00 33.15 2.32
903 927 5.530915 TGATTCTTTGACCGTGTCTCAATTT 59.469 36.000 5.77 0.00 33.15 1.82
904 928 5.828299 TTCTTTGACCGTGTCTCAATTTT 57.172 34.783 5.77 0.00 33.15 1.82
905 929 5.828299 TCTTTGACCGTGTCTCAATTTTT 57.172 34.783 5.77 0.00 33.15 1.94
1124 1155 0.036952 CCTTCTCTTGGCTCTTGCGA 60.037 55.000 0.00 0.00 40.82 5.10
1155 1186 3.830755 AGGGATTCATGCATAATTCTGGC 59.169 43.478 0.00 0.00 0.00 4.85
1186 1217 1.032114 GGGTTGGGGAATTCGAGCTG 61.032 60.000 0.00 0.00 0.00 4.24
1187 1218 0.035439 GGTTGGGGAATTCGAGCTGA 60.035 55.000 0.00 0.00 0.00 4.26
1188 1219 1.087501 GTTGGGGAATTCGAGCTGAC 58.912 55.000 0.00 0.00 0.00 3.51
1189 1220 0.690192 TTGGGGAATTCGAGCTGACA 59.310 50.000 0.00 0.00 0.00 3.58
1221 1253 1.573376 CCTGGTATTGGGATTGGGGAA 59.427 52.381 0.00 0.00 0.00 3.97
1371 1411 3.495331 TGTTGTGGCACTCCATGTTTAT 58.505 40.909 19.83 0.00 45.62 1.40
1506 1546 1.373246 CTTCCGTGCCGTTTCCGTA 60.373 57.895 0.00 0.00 0.00 4.02
1891 1935 2.407616 CTCGATCTACCGCGTGCA 59.592 61.111 4.92 0.00 0.00 4.57
1915 1959 4.400251 GGGATATTGTCGTCGGACCATATA 59.600 45.833 1.91 0.00 39.99 0.86
2298 2342 2.416547 CGTTGTAGTGCTCAATCCTTGG 59.583 50.000 0.00 0.00 0.00 3.61
2342 2386 1.552792 TGGTAGGATGCGTTCATGTCA 59.447 47.619 0.00 0.00 31.96 3.58
2415 2460 4.702081 ACAGACGACGGCGACAGC 62.702 66.667 22.49 3.09 41.64 4.40
2533 2587 2.760385 GAGGCCAGCGGTAGAGGT 60.760 66.667 5.01 0.00 0.00 3.85
2563 2617 1.374758 GGCACTCTCACCGGAGTTG 60.375 63.158 9.46 0.00 43.14 3.16
2564 2618 1.666011 GCACTCTCACCGGAGTTGA 59.334 57.895 9.46 0.00 43.14 3.18
2993 3058 9.717942 AGACAGCATTATCAATATTTCCTACTC 57.282 33.333 0.00 0.00 0.00 2.59
2994 3059 8.854614 ACAGCATTATCAATATTTCCTACTCC 57.145 34.615 0.00 0.00 0.00 3.85
2995 3060 7.885399 ACAGCATTATCAATATTTCCTACTCCC 59.115 37.037 0.00 0.00 0.00 4.30
2996 3061 8.105829 CAGCATTATCAATATTTCCTACTCCCT 58.894 37.037 0.00 0.00 0.00 4.20
2997 3062 8.325046 AGCATTATCAATATTTCCTACTCCCTC 58.675 37.037 0.00 0.00 0.00 4.30
2998 3063 7.554476 GCATTATCAATATTTCCTACTCCCTCC 59.446 40.741 0.00 0.00 0.00 4.30
2999 3064 5.746990 ATCAATATTTCCTACTCCCTCCG 57.253 43.478 0.00 0.00 0.00 4.63
3000 3065 4.553678 TCAATATTTCCTACTCCCTCCGT 58.446 43.478 0.00 0.00 0.00 4.69
3001 3066 4.344102 TCAATATTTCCTACTCCCTCCGTG 59.656 45.833 0.00 0.00 0.00 4.94
3002 3067 2.249309 ATTTCCTACTCCCTCCGTGT 57.751 50.000 0.00 0.00 0.00 4.49
3003 3068 1.263356 TTTCCTACTCCCTCCGTGTG 58.737 55.000 0.00 0.00 0.00 3.82
3004 3069 0.113776 TTCCTACTCCCTCCGTGTGT 59.886 55.000 0.00 0.00 0.00 3.72
3005 3070 0.994247 TCCTACTCCCTCCGTGTGTA 59.006 55.000 0.00 0.00 0.00 2.90
3006 3071 1.064906 TCCTACTCCCTCCGTGTGTAG 60.065 57.143 0.00 0.00 0.00 2.74
3007 3072 1.340795 CCTACTCCCTCCGTGTGTAGT 60.341 57.143 0.00 0.00 31.48 2.73
3008 3073 1.743958 CTACTCCCTCCGTGTGTAGTG 59.256 57.143 0.00 0.00 0.00 2.74
3009 3074 0.178970 ACTCCCTCCGTGTGTAGTGT 60.179 55.000 0.00 0.00 0.00 3.55
3010 3075 0.526662 CTCCCTCCGTGTGTAGTGTC 59.473 60.000 0.00 0.00 0.00 3.67
3011 3076 0.178984 TCCCTCCGTGTGTAGTGTCA 60.179 55.000 0.00 0.00 0.00 3.58
3012 3077 0.677288 CCCTCCGTGTGTAGTGTCAA 59.323 55.000 0.00 0.00 0.00 3.18
3013 3078 1.069513 CCCTCCGTGTGTAGTGTCAAA 59.930 52.381 0.00 0.00 0.00 2.69
3014 3079 2.484065 CCCTCCGTGTGTAGTGTCAAAA 60.484 50.000 0.00 0.00 0.00 2.44
3015 3080 3.199677 CCTCCGTGTGTAGTGTCAAAAA 58.800 45.455 0.00 0.00 0.00 1.94
3037 3102 4.950434 AACGTTTTACATTATGGGACGG 57.050 40.909 0.00 0.00 33.74 4.79
3038 3103 4.205065 ACGTTTTACATTATGGGACGGA 57.795 40.909 13.17 0.00 33.74 4.69
3039 3104 4.186159 ACGTTTTACATTATGGGACGGAG 58.814 43.478 13.17 0.00 33.74 4.63
3040 3105 3.558418 CGTTTTACATTATGGGACGGAGG 59.442 47.826 0.00 0.00 0.00 4.30
3041 3106 3.849563 TTTACATTATGGGACGGAGGG 57.150 47.619 0.00 0.00 0.00 4.30
3042 3107 2.779429 TACATTATGGGACGGAGGGA 57.221 50.000 0.00 0.00 0.00 4.20
3043 3108 1.424638 ACATTATGGGACGGAGGGAG 58.575 55.000 0.00 0.00 0.00 4.30
3044 3109 1.344087 ACATTATGGGACGGAGGGAGT 60.344 52.381 0.00 0.00 0.00 3.85
3045 3110 2.090943 ACATTATGGGACGGAGGGAGTA 60.091 50.000 0.00 0.00 0.00 2.59
3046 3111 3.173965 CATTATGGGACGGAGGGAGTAT 58.826 50.000 0.00 0.00 0.00 2.12
3047 3112 3.339713 TTATGGGACGGAGGGAGTATT 57.660 47.619 0.00 0.00 0.00 1.89
3048 3113 2.191981 ATGGGACGGAGGGAGTATTT 57.808 50.000 0.00 0.00 0.00 1.40
3049 3114 1.961133 TGGGACGGAGGGAGTATTTT 58.039 50.000 0.00 0.00 0.00 1.82
3050 3115 3.119009 TGGGACGGAGGGAGTATTTTA 57.881 47.619 0.00 0.00 0.00 1.52
3051 3116 3.660959 TGGGACGGAGGGAGTATTTTAT 58.339 45.455 0.00 0.00 0.00 1.40
3052 3117 4.818447 TGGGACGGAGGGAGTATTTTATA 58.182 43.478 0.00 0.00 0.00 0.98
3058 3123 8.537858 GGACGGAGGGAGTATTTTATAATATGT 58.462 37.037 0.00 0.00 0.00 2.29
3687 3753 9.681062 TCAAAAGTATAGAAATGGTCCCTTAAG 57.319 33.333 0.00 0.00 0.00 1.85
3715 3781 1.202806 CCAGCAAAACTCAGTCCCTCA 60.203 52.381 0.00 0.00 0.00 3.86
3716 3782 2.553904 CCAGCAAAACTCAGTCCCTCAT 60.554 50.000 0.00 0.00 0.00 2.90
3717 3783 2.746362 CAGCAAAACTCAGTCCCTCATC 59.254 50.000 0.00 0.00 0.00 2.92
3738 3804 6.922957 TCATCAACTATCAAAACCAGCAAAAC 59.077 34.615 0.00 0.00 0.00 2.43
3783 3849 4.159879 CCAGATAAGTTTAGTCCCTCGTGT 59.840 45.833 0.00 0.00 0.00 4.49
3785 3851 2.833631 AAGTTTAGTCCCTCGTGTGG 57.166 50.000 0.00 0.00 0.00 4.17
3800 3866 1.134936 GTGTGGTTGTGGGTGGTTTTC 60.135 52.381 0.00 0.00 0.00 2.29
3852 3918 2.753446 GGAGCAGGGGAAAGCTGC 60.753 66.667 0.00 0.00 42.04 5.25
3878 3944 4.144703 GAGGTCCCTCGCGTTCCC 62.145 72.222 5.77 0.15 33.06 3.97
3881 3947 3.703127 GTCCCTCGCGTTCCCCTT 61.703 66.667 5.77 0.00 0.00 3.95
3883 3949 3.702048 CCCTCGCGTTCCCCTTCA 61.702 66.667 5.77 0.00 0.00 3.02
3884 3950 2.434359 CCTCGCGTTCCCCTTCAC 60.434 66.667 5.77 0.00 0.00 3.18
3885 3951 2.434359 CTCGCGTTCCCCTTCACC 60.434 66.667 5.77 0.00 0.00 4.02
3886 3952 3.234630 CTCGCGTTCCCCTTCACCA 62.235 63.158 5.77 0.00 0.00 4.17
3887 3953 3.047877 CGCGTTCCCCTTCACCAC 61.048 66.667 0.00 0.00 0.00 4.16
3888 3954 2.430367 GCGTTCCCCTTCACCACT 59.570 61.111 0.00 0.00 0.00 4.00
3889 3955 1.228154 GCGTTCCCCTTCACCACTT 60.228 57.895 0.00 0.00 0.00 3.16
3892 3958 1.804601 GTTCCCCTTCACCACTTACG 58.195 55.000 0.00 0.00 0.00 3.18
3897 3963 1.666553 CTTCACCACTTACGCCGCA 60.667 57.895 0.00 0.00 0.00 5.69
3903 3969 1.080772 CACTTACGCCGCAGTCTCA 60.081 57.895 0.00 0.00 0.00 3.27
3976 4042 4.202441 CCATATGCCTGTTAGACTTTGCT 58.798 43.478 0.00 0.00 0.00 3.91
4064 4130 1.307097 GGTCCGCTCGTAGTAGACAT 58.693 55.000 0.00 0.00 0.00 3.06
4071 4137 2.725490 CTCGTAGTAGACATGCTGCAG 58.275 52.381 10.11 10.11 0.00 4.41
4106 4172 3.163594 CACGTATGCAGCAAAGTAAAGC 58.836 45.455 0.00 0.00 0.00 3.51
4107 4173 2.811431 ACGTATGCAGCAAAGTAAAGCA 59.189 40.909 0.00 0.00 39.79 3.91
4108 4174 3.120199 ACGTATGCAGCAAAGTAAAGCAG 60.120 43.478 0.00 0.00 38.75 4.24
4109 4175 3.125146 CGTATGCAGCAAAGTAAAGCAGA 59.875 43.478 0.00 0.00 38.75 4.26
4110 4176 3.565905 ATGCAGCAAAGTAAAGCAGAC 57.434 42.857 0.00 0.00 38.75 3.51
4111 4177 2.575532 TGCAGCAAAGTAAAGCAGACT 58.424 42.857 0.00 0.00 0.00 3.24
4112 4178 2.291465 TGCAGCAAAGTAAAGCAGACTG 59.709 45.455 0.00 0.00 0.00 3.51
4113 4179 2.351157 GCAGCAAAGTAAAGCAGACTGG 60.351 50.000 4.26 0.00 0.00 4.00
4114 4180 2.880890 CAGCAAAGTAAAGCAGACTGGT 59.119 45.455 0.07 0.07 0.00 4.00
4115 4181 3.058639 CAGCAAAGTAAAGCAGACTGGTC 60.059 47.826 7.78 0.00 0.00 4.02
4116 4182 3.142174 GCAAAGTAAAGCAGACTGGTCT 58.858 45.455 7.78 0.00 41.37 3.85
4117 4183 4.040461 AGCAAAGTAAAGCAGACTGGTCTA 59.960 41.667 7.78 0.00 37.98 2.59
4118 4184 4.152580 GCAAAGTAAAGCAGACTGGTCTAC 59.847 45.833 7.78 8.84 37.98 2.59
4119 4185 5.542779 CAAAGTAAAGCAGACTGGTCTACT 58.457 41.667 13.66 13.66 37.98 2.57
4120 4186 6.688578 CAAAGTAAAGCAGACTGGTCTACTA 58.311 40.000 18.47 2.31 37.98 1.82
4121 4187 6.518208 AAGTAAAGCAGACTGGTCTACTAG 57.482 41.667 18.47 0.00 37.98 2.57
4122 4188 4.951094 AGTAAAGCAGACTGGTCTACTAGG 59.049 45.833 17.05 0.00 37.98 3.02
4123 4189 3.741245 AAGCAGACTGGTCTACTAGGA 57.259 47.619 7.78 0.00 37.98 2.94
4124 4190 3.290948 AGCAGACTGGTCTACTAGGAG 57.709 52.381 0.07 0.00 37.98 3.69
4125 4191 2.847449 AGCAGACTGGTCTACTAGGAGA 59.153 50.000 0.00 0.00 37.98 3.71
4126 4192 3.118038 AGCAGACTGGTCTACTAGGAGAG 60.118 52.174 4.39 0.00 37.98 3.20
4127 4193 3.371166 GCAGACTGGTCTACTAGGAGAGT 60.371 52.174 4.39 0.00 42.69 3.24
4128 4194 4.850680 CAGACTGGTCTACTAGGAGAGTT 58.149 47.826 4.39 0.00 39.81 3.01
4129 4195 5.629600 GCAGACTGGTCTACTAGGAGAGTTA 60.630 48.000 4.39 0.00 39.81 2.24
4130 4196 6.053005 CAGACTGGTCTACTAGGAGAGTTAG 58.947 48.000 4.39 6.71 39.81 2.34
4131 4197 4.784177 ACTGGTCTACTAGGAGAGTTAGC 58.216 47.826 4.39 0.00 39.81 3.09
4132 4198 4.475747 ACTGGTCTACTAGGAGAGTTAGCT 59.524 45.833 4.39 0.00 39.81 3.32
4133 4199 5.038651 TGGTCTACTAGGAGAGTTAGCTC 57.961 47.826 4.39 0.00 39.81 4.09
4134 4200 4.473922 TGGTCTACTAGGAGAGTTAGCTCA 59.526 45.833 4.39 0.00 44.00 4.26
4135 4201 4.818005 GGTCTACTAGGAGAGTTAGCTCAC 59.182 50.000 4.39 2.29 44.00 3.51
4136 4202 4.508861 GTCTACTAGGAGAGTTAGCTCACG 59.491 50.000 4.39 0.00 44.00 4.35
4137 4203 3.353370 ACTAGGAGAGTTAGCTCACGT 57.647 47.619 9.43 6.89 44.00 4.49
4138 4204 4.484537 ACTAGGAGAGTTAGCTCACGTA 57.515 45.455 9.43 7.66 44.00 3.57
4139 4205 5.038651 ACTAGGAGAGTTAGCTCACGTAT 57.961 43.478 9.43 0.00 44.00 3.06
4140 4206 4.817464 ACTAGGAGAGTTAGCTCACGTATG 59.183 45.833 9.43 5.79 44.00 2.39
4141 4207 2.359531 AGGAGAGTTAGCTCACGTATGC 59.640 50.000 9.43 4.06 44.00 3.14
4142 4208 2.376956 GAGAGTTAGCTCACGTATGCG 58.623 52.381 9.43 0.19 44.00 4.73
4143 4209 2.014857 AGAGTTAGCTCACGTATGCGA 58.985 47.619 11.07 0.00 44.00 5.10
4144 4210 2.032302 AGAGTTAGCTCACGTATGCGAG 59.968 50.000 11.07 1.32 44.00 5.03
4145 4211 1.743958 AGTTAGCTCACGTATGCGAGT 59.256 47.619 11.07 0.00 42.00 4.18
4146 4212 2.163815 AGTTAGCTCACGTATGCGAGTT 59.836 45.455 11.07 0.00 42.00 3.01
4147 4213 3.376234 AGTTAGCTCACGTATGCGAGTTA 59.624 43.478 11.07 0.00 42.00 2.24
4148 4214 2.933495 AGCTCACGTATGCGAGTTAA 57.067 45.000 11.07 0.00 42.00 2.01
4149 4215 3.438297 AGCTCACGTATGCGAGTTAAT 57.562 42.857 11.07 0.00 42.00 1.40
4150 4216 3.782046 AGCTCACGTATGCGAGTTAATT 58.218 40.909 11.07 0.00 42.00 1.40
4151 4217 3.551890 AGCTCACGTATGCGAGTTAATTG 59.448 43.478 11.07 0.00 42.00 2.32
4152 4218 3.550275 GCTCACGTATGCGAGTTAATTGA 59.450 43.478 11.07 0.00 42.00 2.57
4153 4219 4.209288 GCTCACGTATGCGAGTTAATTGAT 59.791 41.667 11.07 0.00 42.00 2.57
4154 4220 5.610552 GCTCACGTATGCGAGTTAATTGATC 60.611 44.000 11.07 0.00 42.00 2.92
4155 4221 5.588240 TCACGTATGCGAGTTAATTGATCT 58.412 37.500 11.07 0.00 42.00 2.75
4156 4222 6.731164 TCACGTATGCGAGTTAATTGATCTA 58.269 36.000 11.07 0.00 42.00 1.98
4157 4223 6.856426 TCACGTATGCGAGTTAATTGATCTAG 59.144 38.462 11.07 0.00 42.00 2.43
4158 4224 5.629849 ACGTATGCGAGTTAATTGATCTAGC 59.370 40.000 11.07 0.00 42.00 3.42
4159 4225 5.859114 CGTATGCGAGTTAATTGATCTAGCT 59.141 40.000 0.00 0.00 41.33 3.32
4160 4226 6.183359 CGTATGCGAGTTAATTGATCTAGCTG 60.183 42.308 0.00 0.00 41.33 4.24
4161 4227 5.262588 TGCGAGTTAATTGATCTAGCTGA 57.737 39.130 0.00 0.00 32.64 4.26
4162 4228 5.847304 TGCGAGTTAATTGATCTAGCTGAT 58.153 37.500 0.00 0.00 38.27 2.90
4163 4229 6.283694 TGCGAGTTAATTGATCTAGCTGATT 58.716 36.000 0.00 0.00 35.14 2.57
4164 4230 6.201615 TGCGAGTTAATTGATCTAGCTGATTG 59.798 38.462 0.00 0.00 35.14 2.67
4165 4231 6.588552 CGAGTTAATTGATCTAGCTGATTGC 58.411 40.000 0.00 0.00 43.29 3.56
4234 4306 2.402305 CGACCTGATTGATGAGCTAGC 58.598 52.381 6.62 6.62 0.00 3.42
4237 4309 2.502947 ACCTGATTGATGAGCTAGCACA 59.497 45.455 17.37 17.37 0.00 4.57
4268 4340 3.455990 TGCACAACAAAATCACAGCAT 57.544 38.095 0.00 0.00 0.00 3.79
4303 4375 1.022735 CTAGTACACCAGCGACGGAT 58.977 55.000 0.00 0.00 0.00 4.18
4324 4396 0.037326 TTGCTCATCCCACTCGTCAC 60.037 55.000 0.00 0.00 0.00 3.67
4334 4406 4.456253 CTCGTCACGCCGCGTAGT 62.456 66.667 19.71 0.73 38.32 2.73
4387 4459 4.222847 CCCTTCGTCCGGCCTAGC 62.223 72.222 0.00 0.00 0.00 3.42
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
12 13 3.461085 AGATGCTGGGTGATTTGAGGTAT 59.539 43.478 0.00 0.00 0.00 2.73
189 190 1.973515 TGGAGCTTCTGTCTCACATGT 59.026 47.619 0.00 0.00 32.38 3.21
235 236 2.530661 TGAATGGGGGTCGGTGGT 60.531 61.111 0.00 0.00 0.00 4.16
236 237 2.272146 CTGAATGGGGGTCGGTGG 59.728 66.667 0.00 0.00 0.00 4.61
237 238 2.137177 AACCTGAATGGGGGTCGGTG 62.137 60.000 0.00 0.00 41.11 4.94
268 269 1.604604 GAGCAGCTTACAAACCACCA 58.395 50.000 0.00 0.00 0.00 4.17
301 302 6.794369 ACAGTACTGTGTCTATGGAACACATG 60.794 42.308 27.41 7.60 42.26 3.21
319 320 4.141711 TGTTTCCTTTGCTCAGACAGTACT 60.142 41.667 0.00 0.00 0.00 2.73
413 414 7.074502 GCTCATCTAAGTCTGTTTTCTGTTTG 58.925 38.462 0.00 0.00 0.00 2.93
468 469 0.974525 AGCCGTAACTAGGTCCCCAC 60.975 60.000 0.00 0.00 0.00 4.61
537 546 0.520404 CACTTGCTTCATCGCTTGCT 59.480 50.000 0.00 0.00 0.00 3.91
592 601 0.461961 GAGCTTCTGCGGATACCACT 59.538 55.000 0.00 0.00 45.42 4.00
644 653 2.362397 GAGCGAGAGAGAGAGAGAGAGA 59.638 54.545 0.00 0.00 0.00 3.10
645 654 2.363680 AGAGCGAGAGAGAGAGAGAGAG 59.636 54.545 0.00 0.00 0.00 3.20
646 655 2.362397 GAGAGCGAGAGAGAGAGAGAGA 59.638 54.545 0.00 0.00 0.00 3.10
647 656 2.546795 GGAGAGCGAGAGAGAGAGAGAG 60.547 59.091 0.00 0.00 0.00 3.20
648 657 1.412710 GGAGAGCGAGAGAGAGAGAGA 59.587 57.143 0.00 0.00 0.00 3.10
649 658 1.414181 AGGAGAGCGAGAGAGAGAGAG 59.586 57.143 0.00 0.00 0.00 3.20
650 659 1.412710 GAGGAGAGCGAGAGAGAGAGA 59.587 57.143 0.00 0.00 0.00 3.10
651 660 1.414181 AGAGGAGAGCGAGAGAGAGAG 59.586 57.143 0.00 0.00 0.00 3.20
652 661 1.496060 AGAGGAGAGCGAGAGAGAGA 58.504 55.000 0.00 0.00 0.00 3.10
653 662 2.332063 AAGAGGAGAGCGAGAGAGAG 57.668 55.000 0.00 0.00 0.00 3.20
654 663 3.244422 GGATAAGAGGAGAGCGAGAGAGA 60.244 52.174 0.00 0.00 0.00 3.10
655 664 3.074412 GGATAAGAGGAGAGCGAGAGAG 58.926 54.545 0.00 0.00 0.00 3.20
656 665 2.708861 AGGATAAGAGGAGAGCGAGAGA 59.291 50.000 0.00 0.00 0.00 3.10
741 750 2.485835 CCGAGACCCAGAGAGGTACTAG 60.486 59.091 0.00 0.00 41.55 2.57
744 753 0.034283 ACCGAGACCCAGAGAGGTAC 60.034 60.000 0.00 0.00 41.42 3.34
763 777 2.904866 GCTCCGTTGTGTGGCCAA 60.905 61.111 7.24 0.00 0.00 4.52
908 932 6.033341 CGAACCAACAAGTCAAAGAATCAAA 58.967 36.000 0.00 0.00 0.00 2.69
1124 1155 1.138266 GCATGAATCCCTTGCAGCAAT 59.862 47.619 8.67 0.00 43.22 3.56
1206 1238 3.465588 CCTAGGTTTCCCCAATCCCAATA 59.534 47.826 0.00 0.00 34.66 1.90
1221 1253 2.846827 AGCTCCAATGCTTACCTAGGTT 59.153 45.455 22.11 4.29 40.93 3.50
1229 1261 1.289160 AGGTCCAGCTCCAATGCTTA 58.711 50.000 0.00 0.00 41.98 3.09
1334 1374 5.569413 CCACAACAAGACTCAACTAAACAC 58.431 41.667 0.00 0.00 0.00 3.32
1345 1385 0.546122 TGGAGTGCCACAACAAGACT 59.454 50.000 0.00 0.00 39.92 3.24
1506 1546 3.089788 GTCAACCCACTTTGACCGT 57.910 52.632 4.91 0.00 46.60 4.83
1891 1935 1.038280 GGTCCGACGACAATATCCCT 58.962 55.000 0.00 0.00 41.13 4.20
1915 1959 2.663852 CCGTTTGTTCCGGCGACT 60.664 61.111 9.30 0.00 38.85 4.18
2066 2110 0.383949 GTCCTCGCTCTAGCCTTCTG 59.616 60.000 0.00 0.00 37.91 3.02
2298 2342 4.734108 GCCTACTAATTCGACCAGAGACAC 60.734 50.000 0.00 0.00 0.00 3.67
2342 2386 1.043673 ACTCGCCGGGAAGCTCTTAT 61.044 55.000 2.18 0.00 0.00 1.73
2415 2460 1.013005 CAAGCACGCTGGAGAGTGAG 61.013 60.000 13.93 0.34 46.58 3.51
2563 2617 1.711060 CCGACGCCACTCTCTCTCTC 61.711 65.000 0.00 0.00 0.00 3.20
2564 2618 1.747367 CCGACGCCACTCTCTCTCT 60.747 63.158 0.00 0.00 0.00 3.10
2931 2996 2.469826 CTGATACGCAATAAGCACCGA 58.530 47.619 0.00 0.00 46.13 4.69
2932 2997 1.070577 GCTGATACGCAATAAGCACCG 60.071 52.381 3.35 0.00 41.34 4.94
2990 3055 0.178970 ACACTACACACGGAGGGAGT 60.179 55.000 0.00 0.00 0.00 3.85
2991 3056 0.526662 GACACTACACACGGAGGGAG 59.473 60.000 0.00 0.00 0.00 4.30
2993 3058 0.677288 TTGACACTACACACGGAGGG 59.323 55.000 0.00 0.00 0.00 4.30
2994 3059 2.519377 TTTGACACTACACACGGAGG 57.481 50.000 0.00 0.00 0.00 4.30
3013 3078 6.016443 TCCGTCCCATAATGTAAAACGTTTTT 60.016 34.615 29.42 15.16 0.00 1.94
3014 3079 5.472820 TCCGTCCCATAATGTAAAACGTTTT 59.527 36.000 27.65 27.65 0.00 2.43
3015 3080 5.002516 TCCGTCCCATAATGTAAAACGTTT 58.997 37.500 7.96 7.96 0.00 3.60
3016 3081 4.577875 TCCGTCCCATAATGTAAAACGTT 58.422 39.130 0.00 0.00 0.00 3.99
3017 3082 4.186159 CTCCGTCCCATAATGTAAAACGT 58.814 43.478 0.00 0.00 0.00 3.99
3018 3083 3.558418 CCTCCGTCCCATAATGTAAAACG 59.442 47.826 0.00 0.00 0.00 3.60
3019 3084 3.881089 CCCTCCGTCCCATAATGTAAAAC 59.119 47.826 0.00 0.00 0.00 2.43
3020 3085 3.781407 TCCCTCCGTCCCATAATGTAAAA 59.219 43.478 0.00 0.00 0.00 1.52
3021 3086 3.386063 TCCCTCCGTCCCATAATGTAAA 58.614 45.455 0.00 0.00 0.00 2.01
3022 3087 2.969950 CTCCCTCCGTCCCATAATGTAA 59.030 50.000 0.00 0.00 0.00 2.41
3023 3088 2.090943 ACTCCCTCCGTCCCATAATGTA 60.091 50.000 0.00 0.00 0.00 2.29
3024 3089 1.344087 ACTCCCTCCGTCCCATAATGT 60.344 52.381 0.00 0.00 0.00 2.71
3025 3090 1.424638 ACTCCCTCCGTCCCATAATG 58.575 55.000 0.00 0.00 0.00 1.90
3026 3091 3.562108 ATACTCCCTCCGTCCCATAAT 57.438 47.619 0.00 0.00 0.00 1.28
3027 3092 3.339713 AATACTCCCTCCGTCCCATAA 57.660 47.619 0.00 0.00 0.00 1.90
3028 3093 3.339713 AAATACTCCCTCCGTCCCATA 57.660 47.619 0.00 0.00 0.00 2.74
3029 3094 2.191981 AAATACTCCCTCCGTCCCAT 57.808 50.000 0.00 0.00 0.00 4.00
3030 3095 1.961133 AAAATACTCCCTCCGTCCCA 58.039 50.000 0.00 0.00 0.00 4.37
3031 3096 5.813513 TTATAAAATACTCCCTCCGTCCC 57.186 43.478 0.00 0.00 0.00 4.46
3032 3097 8.537858 ACATATTATAAAATACTCCCTCCGTCC 58.462 37.037 0.00 0.00 30.42 4.79
3033 3098 9.939802 AACATATTATAAAATACTCCCTCCGTC 57.060 33.333 0.00 0.00 30.42 4.79
3034 3099 9.720769 CAACATATTATAAAATACTCCCTCCGT 57.279 33.333 0.00 0.00 30.42 4.69
3035 3100 9.162764 CCAACATATTATAAAATACTCCCTCCG 57.837 37.037 0.00 0.00 30.42 4.63
3050 3115 9.316730 GATGCAATCAAAACACCAACATATTAT 57.683 29.630 0.00 0.00 44.70 1.28
3051 3116 8.700722 GATGCAATCAAAACACCAACATATTA 57.299 30.769 0.00 0.00 44.70 0.98
3052 3117 7.599630 GATGCAATCAAAACACCAACATATT 57.400 32.000 0.00 0.00 44.70 1.28
3472 3537 4.873817 TGGAATTTGTGAACTGCAGAATG 58.126 39.130 23.35 0.00 40.87 2.67
3545 3611 2.930826 AACCTCAACCACACGATTCT 57.069 45.000 0.00 0.00 0.00 2.40
3687 3753 4.494484 ACTGAGTTTTGCTGGTTTTGAAC 58.506 39.130 0.00 0.00 0.00 3.18
3715 3781 7.054491 AGTTTTGCTGGTTTTGATAGTTGAT 57.946 32.000 0.00 0.00 0.00 2.57
3716 3782 6.463995 AGTTTTGCTGGTTTTGATAGTTGA 57.536 33.333 0.00 0.00 0.00 3.18
3717 3783 7.920682 ACTAAGTTTTGCTGGTTTTGATAGTTG 59.079 33.333 0.00 0.00 0.00 3.16
3738 3804 6.472887 TGGTTTTGATAGTTGAGGGACTAAG 58.527 40.000 0.00 0.00 41.55 2.18
3783 3849 1.038130 CGGAAAACCACCCACAACCA 61.038 55.000 0.00 0.00 0.00 3.67
3785 3851 1.066752 GCGGAAAACCACCCACAAC 59.933 57.895 0.00 0.00 0.00 3.32
3800 3866 1.622607 TACCACTCCAGGATTGGCGG 61.623 60.000 23.14 6.93 44.63 6.13
3804 3870 6.479972 TTACACTATACCACTCCAGGATTG 57.520 41.667 0.00 0.00 0.00 2.67
3807 3873 6.499350 AGTTTTTACACTATACCACTCCAGGA 59.501 38.462 0.00 0.00 0.00 3.86
3808 3874 6.594159 CAGTTTTTACACTATACCACTCCAGG 59.406 42.308 0.00 0.00 0.00 4.45
3809 3875 7.383687 TCAGTTTTTACACTATACCACTCCAG 58.616 38.462 0.00 0.00 0.00 3.86
3822 3888 2.814336 CCCTGCTCCTCAGTTTTTACAC 59.186 50.000 0.00 0.00 41.25 2.90
3872 3938 1.804601 GTAAGTGGTGAAGGGGAACG 58.195 55.000 0.00 0.00 0.00 3.95
3873 3939 1.804601 CGTAAGTGGTGAAGGGGAAC 58.195 55.000 0.00 0.00 0.00 3.62
3874 3940 0.035739 GCGTAAGTGGTGAAGGGGAA 59.964 55.000 0.00 0.00 41.68 3.97
3875 3941 1.675219 GCGTAAGTGGTGAAGGGGA 59.325 57.895 0.00 0.00 41.68 4.81
3876 3942 1.376812 GGCGTAAGTGGTGAAGGGG 60.377 63.158 0.00 0.00 41.68 4.79
3878 3944 2.388232 GCGGCGTAAGTGGTGAAGG 61.388 63.158 9.37 0.00 41.68 3.46
3880 3946 1.666553 CTGCGGCGTAAGTGGTGAA 60.667 57.895 9.37 0.00 41.68 3.18
3881 3947 2.048597 CTGCGGCGTAAGTGGTGA 60.049 61.111 9.37 0.00 41.68 4.02
3883 3949 2.048503 GACTGCGGCGTAAGTGGT 60.049 61.111 19.51 4.76 41.68 4.16
3884 3950 1.805945 GAGACTGCGGCGTAAGTGG 60.806 63.158 19.51 1.40 41.68 4.00
3885 3951 1.080772 TGAGACTGCGGCGTAAGTG 60.081 57.895 19.51 1.77 41.68 3.16
3886 3952 1.080705 GTGAGACTGCGGCGTAAGT 60.081 57.895 15.55 15.55 41.68 2.24
3887 3953 1.805945 GGTGAGACTGCGGCGTAAG 60.806 63.158 9.37 9.56 43.44 2.34
3888 3954 2.260434 GGTGAGACTGCGGCGTAA 59.740 61.111 9.37 0.00 0.00 3.18
3889 3955 4.111016 CGGTGAGACTGCGGCGTA 62.111 66.667 9.37 1.99 0.00 4.42
3897 3963 3.865929 CTTGTGCGCCGGTGAGACT 62.866 63.158 21.76 0.00 0.00 3.24
3908 3974 1.964290 GCTACTGCTCTGCTTGTGCG 61.964 60.000 0.00 0.00 37.94 5.34
3953 4019 3.947834 GCAAAGTCTAACAGGCATATGGT 59.052 43.478 4.56 0.00 0.00 3.55
4000 4066 2.105128 CTCGGCGTCCATCAGACC 59.895 66.667 6.85 0.00 43.08 3.85
4002 4068 2.121538 CCTCTCGGCGTCCATCAGA 61.122 63.158 6.85 0.00 0.00 3.27
4091 4157 2.291465 CAGTCTGCTTTACTTTGCTGCA 59.709 45.455 0.00 0.00 0.00 4.41
4096 4162 5.847670 GTAGACCAGTCTGCTTTACTTTG 57.152 43.478 10.59 0.00 40.71 2.77
4105 4171 3.211045 CTCTCCTAGTAGACCAGTCTGC 58.789 54.545 10.59 9.11 40.71 4.26
4106 4172 4.497291 ACTCTCCTAGTAGACCAGTCTG 57.503 50.000 10.59 0.00 40.71 3.51
4107 4173 5.397109 GCTAACTCTCCTAGTAGACCAGTCT 60.397 48.000 5.50 5.50 43.40 3.24
4108 4174 4.818005 GCTAACTCTCCTAGTAGACCAGTC 59.182 50.000 0.00 0.00 37.50 3.51
4109 4175 4.475747 AGCTAACTCTCCTAGTAGACCAGT 59.524 45.833 0.00 0.00 37.50 4.00
4110 4176 5.043737 AGCTAACTCTCCTAGTAGACCAG 57.956 47.826 0.00 0.00 37.50 4.00
4111 4177 4.473922 TGAGCTAACTCTCCTAGTAGACCA 59.526 45.833 0.00 0.00 43.85 4.02
4112 4178 4.818005 GTGAGCTAACTCTCCTAGTAGACC 59.182 50.000 0.00 0.00 43.85 3.85
4113 4179 4.508861 CGTGAGCTAACTCTCCTAGTAGAC 59.491 50.000 0.00 0.00 43.85 2.59
4114 4180 4.161942 ACGTGAGCTAACTCTCCTAGTAGA 59.838 45.833 0.00 0.00 43.85 2.59
4115 4181 4.444536 ACGTGAGCTAACTCTCCTAGTAG 58.555 47.826 0.00 0.00 43.85 2.57
4116 4182 4.484537 ACGTGAGCTAACTCTCCTAGTA 57.515 45.455 0.00 0.00 43.85 1.82
4117 4183 3.353370 ACGTGAGCTAACTCTCCTAGT 57.647 47.619 0.00 0.00 43.85 2.57
4118 4184 4.319911 GCATACGTGAGCTAACTCTCCTAG 60.320 50.000 0.00 0.00 43.85 3.02
4119 4185 3.564644 GCATACGTGAGCTAACTCTCCTA 59.435 47.826 0.00 0.00 43.85 2.94
4120 4186 2.359531 GCATACGTGAGCTAACTCTCCT 59.640 50.000 0.00 0.00 43.85 3.69
4121 4187 2.733517 GCATACGTGAGCTAACTCTCC 58.266 52.381 0.00 0.00 43.85 3.71
4122 4188 2.031807 TCGCATACGTGAGCTAACTCTC 59.968 50.000 0.00 0.00 40.03 3.20
4123 4189 2.014857 TCGCATACGTGAGCTAACTCT 58.985 47.619 0.00 0.00 40.03 3.24
4124 4190 2.376956 CTCGCATACGTGAGCTAACTC 58.623 52.381 0.00 0.00 42.54 3.01
4125 4191 2.476873 CTCGCATACGTGAGCTAACT 57.523 50.000 0.00 0.00 42.54 2.24
4132 4198 5.588240 AGATCAATTAACTCGCATACGTGA 58.412 37.500 0.00 0.00 41.18 4.35
4133 4199 5.890110 AGATCAATTAACTCGCATACGTG 57.110 39.130 0.00 0.00 41.18 4.49
4134 4200 5.629849 GCTAGATCAATTAACTCGCATACGT 59.370 40.000 0.00 0.00 41.18 3.57
4135 4201 5.859114 AGCTAGATCAATTAACTCGCATACG 59.141 40.000 0.00 0.00 42.01 3.06
4136 4202 6.863645 TCAGCTAGATCAATTAACTCGCATAC 59.136 38.462 0.00 0.00 0.00 2.39
4137 4203 6.981722 TCAGCTAGATCAATTAACTCGCATA 58.018 36.000 0.00 0.00 0.00 3.14
4138 4204 5.847304 TCAGCTAGATCAATTAACTCGCAT 58.153 37.500 0.00 0.00 0.00 4.73
4139 4205 5.262588 TCAGCTAGATCAATTAACTCGCA 57.737 39.130 0.00 0.00 0.00 5.10
4140 4206 6.588552 CAATCAGCTAGATCAATTAACTCGC 58.411 40.000 0.00 0.00 35.39 5.03
4141 4207 6.588552 GCAATCAGCTAGATCAATTAACTCG 58.411 40.000 0.00 0.00 41.15 4.18
4157 4223 3.521796 GGCCCCGAAGCAATCAGC 61.522 66.667 0.00 0.00 46.19 4.26
4158 4224 1.250154 TTTGGCCCCGAAGCAATCAG 61.250 55.000 0.00 0.00 0.00 2.90
4159 4225 1.228706 TTTGGCCCCGAAGCAATCA 60.229 52.632 0.00 0.00 0.00 2.57
4160 4226 1.215382 GTTTGGCCCCGAAGCAATC 59.785 57.895 0.00 0.00 0.00 2.67
4161 4227 2.635443 CGTTTGGCCCCGAAGCAAT 61.635 57.895 0.00 0.00 0.00 3.56
4162 4228 3.291383 CGTTTGGCCCCGAAGCAA 61.291 61.111 0.00 0.00 0.00 3.91
4165 4231 4.038080 GTGCGTTTGGCCCCGAAG 62.038 66.667 0.00 0.00 42.61 3.79
4234 4306 0.890542 TGTGCAAAGCTAGCCCTGTG 60.891 55.000 12.13 5.65 0.00 3.66
4237 4309 0.178992 TGTTGTGCAAAGCTAGCCCT 60.179 50.000 12.13 0.00 0.00 5.19
4249 4321 3.382855 TCATGCTGTGATTTTGTTGTGC 58.617 40.909 0.00 0.00 0.00 4.57
4268 4340 7.395206 TGGTGTACTAGCTAATGTAGTTCTTCA 59.605 37.037 0.00 0.00 32.81 3.02
4303 4375 2.107366 TGACGAGTGGGATGAGCAATA 58.893 47.619 0.00 0.00 0.00 1.90
4324 4396 1.132199 CAGTAACTGACTACGCGGCG 61.132 60.000 22.36 22.36 35.64 6.46
4334 4406 0.243907 GACGGCAGCTCAGTAACTGA 59.756 55.000 0.00 0.00 38.25 3.41
4371 4443 4.222847 GGCTAGGCCGGACGAAGG 62.223 72.222 5.05 0.00 39.62 3.46


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

AutoCloner maintained by Alex Coulton.