Multiple sequence alignment - TraesCS3B01G023600

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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 TraesCS3B01G023600 chr3B 100.000 3668 0 0 1 3668 10171833 10175500 0.000000e+00 6774.0
1 TraesCS3B01G023600 chr3D 94.463 1806 67 11 858 2639 7970654 7972450 0.000000e+00 2750.0
2 TraesCS3B01G023600 chr3D 89.899 495 45 3 3175 3666 7973091 7973583 1.860000e-177 632.0
3 TraesCS3B01G023600 chr3D 89.228 492 18 5 1 457 7969608 7970099 1.900000e-162 582.0
4 TraesCS3B01G023600 chr3D 92.987 385 9 8 498 866 7970089 7970471 2.490000e-151 545.0
5 TraesCS3B01G023600 chr3D 98.340 241 4 0 2636 2876 7972665 7972905 1.220000e-114 424.0
6 TraesCS3B01G023600 chr3D 92.920 113 2 1 2903 3015 7972998 7973104 3.790000e-35 159.0
7 TraesCS3B01G023600 chr3A 95.023 1286 44 7 566 1849 12554928 12553661 0.000000e+00 2002.0
8 TraesCS3B01G023600 chr3A 87.027 370 25 3 1 347 12562745 12562376 2.650000e-106 396.0
9 TraesCS3B01G023600 chr3A 91.480 223 15 1 2658 2876 12553363 12553141 1.660000e-78 303.0
10 TraesCS3B01G023600 chr3A 92.373 118 8 1 3215 3331 12552923 12552806 2.270000e-37 167.0
11 TraesCS3B01G023600 chr3A 93.805 113 1 2 2903 3015 12553039 12552933 8.150000e-37 165.0
12 TraesCS3B01G023600 chr3A 82.166 157 4 4 419 575 12555542 12555410 2.990000e-21 113.0
13 TraesCS3B01G023600 chr3A 98.000 50 1 0 2590 2639 12553664 12553615 1.810000e-13 87.9
14 TraesCS3B01G023600 chr5D 79.610 461 76 11 1040 1497 41026667 41027112 7.650000e-82 315.0
15 TraesCS3B01G023600 chr5D 91.866 209 17 0 1 209 490006476 490006684 3.580000e-75 292.0
16 TraesCS3B01G023600 chr5D 90.698 86 5 1 426 508 529359542 529359457 1.080000e-20 111.0
17 TraesCS3B01G023600 chr5B 83.742 326 53 0 1040 1365 35174349 35174674 3.560000e-80 309.0
18 TraesCS3B01G023600 chr5B 91.866 209 17 0 1 209 604143767 604143975 3.580000e-75 292.0
19 TraesCS3B01G023600 chr5B 90.361 83 5 2 426 505 668200832 668200750 5.010000e-19 106.0
20 TraesCS3B01G023600 chr7D 78.308 461 88 6 1040 1500 622271372 622271820 1.670000e-73 287.0
21 TraesCS3B01G023600 chr5A 91.388 209 18 0 1 209 611632518 611632726 1.670000e-73 287.0
22 TraesCS3B01G023600 chr5A 91.765 85 4 3 426 507 657497363 657497279 8.320000e-22 115.0
23 TraesCS3B01G023600 chr2B 77.419 465 90 11 1039 1501 797059834 797059383 2.810000e-66 263.0
24 TraesCS3B01G023600 chr2B 77.440 461 88 10 1043 1501 794621565 794622011 1.010000e-65 261.0
25 TraesCS3B01G023600 chr2B 86.598 194 24 2 17 209 356316414 356316222 2.870000e-51 213.0
26 TraesCS3B01G023600 chr2A 88.144 194 21 2 17 209 372737073 372737265 2.850000e-56 230.0
27 TraesCS3B01G023600 chr2D 87.629 194 22 2 17 209 298942445 298942637 1.330000e-54 224.0


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 TraesCS3B01G023600 chr3B 10171833 10175500 3667 False 6774.000000 6774 100.000000 1 3668 1 chr3B.!!$F1 3667
1 TraesCS3B01G023600 chr3D 7969608 7973583 3975 False 848.666667 2750 92.972833 1 3666 6 chr3D.!!$F1 3665
2 TraesCS3B01G023600 chr3A 12552806 12555542 2736 True 472.983333 2002 92.141167 419 3331 6 chr3A.!!$R2 2912

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
486 522 0.103208 GGAGTACATGGAGAGCGTGG 59.897 60.0 0.00 0.0 0.00 4.94 F
799 1327 0.253347 AGGAGAGGGAAATGGCCTGA 60.253 55.0 3.32 0.0 0.00 3.86 F
1771 2503 0.107312 GATGCAGCTGTCCCTGATGT 60.107 55.0 16.64 0.0 34.77 3.06 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1705 2437 0.106868 TCCCGGAGATACGAAGCAGA 60.107 55.0 0.73 0.0 35.47 4.26 R
2343 3075 0.107654 GGATGTAGTCCACCACCAGC 60.108 60.0 0.00 0.0 46.96 4.85 R
3083 4140 0.039165 GTTACAAGCCAGCCAGCAAC 60.039 55.0 0.00 0.0 34.23 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
23 24 1.446272 GGAGCGACTTGAGGTTCCG 60.446 63.158 0.00 0.00 0.00 4.30
102 103 1.518572 CGGCGCGAAGATGGTAACT 60.519 57.895 12.10 0.00 37.61 2.24
143 144 4.105727 CAGCGTCTGGATCAGCAG 57.894 61.111 0.00 0.00 0.00 4.24
144 145 1.217511 CAGCGTCTGGATCAGCAGT 59.782 57.895 0.00 0.00 0.00 4.40
208 209 4.394712 GCGCCACCAGCACCTAGT 62.395 66.667 0.00 0.00 44.04 2.57
209 210 2.125512 CGCCACCAGCACCTAGTC 60.126 66.667 0.00 0.00 44.04 2.59
210 211 2.269241 GCCACCAGCACCTAGTCC 59.731 66.667 0.00 0.00 42.97 3.85
211 212 2.592993 GCCACCAGCACCTAGTCCA 61.593 63.158 0.00 0.00 42.97 4.02
325 349 1.746220 CAGGAGTAGGACGAACAGGAG 59.254 57.143 0.00 0.00 0.00 3.69
332 356 3.240134 GACGAACAGGAGCAGGGCA 62.240 63.158 0.00 0.00 0.00 5.36
478 514 0.252330 TTCCACCCGGAGTACATGGA 60.252 55.000 0.73 3.06 44.10 3.41
479 515 0.686441 TCCACCCGGAGTACATGGAG 60.686 60.000 0.73 0.00 35.91 3.86
480 516 0.686441 CCACCCGGAGTACATGGAGA 60.686 60.000 0.73 0.00 31.69 3.71
481 517 0.747255 CACCCGGAGTACATGGAGAG 59.253 60.000 0.73 0.00 0.00 3.20
482 518 1.043673 ACCCGGAGTACATGGAGAGC 61.044 60.000 0.73 0.00 0.00 4.09
483 519 1.360551 CCGGAGTACATGGAGAGCG 59.639 63.158 0.00 0.00 0.00 5.03
484 520 1.384989 CCGGAGTACATGGAGAGCGT 61.385 60.000 0.00 0.00 0.00 5.07
485 521 0.248661 CGGAGTACATGGAGAGCGTG 60.249 60.000 0.00 0.00 0.00 5.34
486 522 0.103208 GGAGTACATGGAGAGCGTGG 59.897 60.000 0.00 0.00 0.00 4.94
487 523 0.528684 GAGTACATGGAGAGCGTGGC 60.529 60.000 0.00 0.00 0.00 5.01
488 524 1.521681 GTACATGGAGAGCGTGGCC 60.522 63.158 0.00 0.00 0.00 5.36
489 525 3.076258 TACATGGAGAGCGTGGCCG 62.076 63.158 0.00 0.00 37.07 6.13
528 564 2.187946 CAGGAGGCATGGTCGTCC 59.812 66.667 0.00 0.00 40.36 4.79
585 1113 0.522076 CGGCGTTGTCTACCTCGTAC 60.522 60.000 0.00 0.00 0.00 3.67
799 1327 0.253347 AGGAGAGGGAAATGGCCTGA 60.253 55.000 3.32 0.00 0.00 3.86
1107 1839 2.187685 CAGGTGGCGCTGCTCATA 59.812 61.111 7.64 0.00 0.00 2.15
1374 2106 4.996434 GTGCAGGTGACAGCCGCT 62.996 66.667 13.59 0.00 43.15 5.52
1377 2109 4.320456 CAGGTGACAGCCGCTGGT 62.320 66.667 24.03 9.97 35.51 4.00
1402 2134 3.350833 GTCCTCTTCTACACCTCCGTTA 58.649 50.000 0.00 0.00 0.00 3.18
1558 2290 1.062525 GCTTTACAGCATTCGGCCG 59.937 57.895 22.12 22.12 46.49 6.13
1564 2296 2.813908 AGCATTCGGCCGTCGTTC 60.814 61.111 27.15 11.75 46.50 3.95
1565 2297 4.204891 GCATTCGGCCGTCGTTCG 62.205 66.667 27.15 10.03 40.32 3.95
1586 2318 2.880890 GCTCACACAACAATCTGGAAGT 59.119 45.455 0.00 0.00 33.76 3.01
1596 2328 8.783093 CACAACAATCTGGAAGTCATACTAAAA 58.217 33.333 0.00 0.00 33.76 1.52
1688 2420 5.209318 ATCAAGGGGCTGATCAACGAAGT 62.209 47.826 0.00 0.00 34.16 3.01
1771 2503 0.107312 GATGCAGCTGTCCCTGATGT 60.107 55.000 16.64 0.00 34.77 3.06
1842 2574 1.662608 CATCCGTATGCTCTCGCCT 59.337 57.895 0.00 0.00 34.43 5.52
1844 2576 1.109920 ATCCGTATGCTCTCGCCTGT 61.110 55.000 0.00 0.00 34.43 4.00
1889 2621 2.016318 GTTCCATCGCCATCAACATCA 58.984 47.619 0.00 0.00 0.00 3.07
1895 2627 1.134848 TCGCCATCAACATCATCGTCA 60.135 47.619 0.00 0.00 0.00 4.35
1896 2628 1.004610 CGCCATCAACATCATCGTCAC 60.005 52.381 0.00 0.00 0.00 3.67
1897 2629 1.331756 GCCATCAACATCATCGTCACC 59.668 52.381 0.00 0.00 0.00 4.02
1898 2630 2.631267 CCATCAACATCATCGTCACCA 58.369 47.619 0.00 0.00 0.00 4.17
1899 2631 3.009026 CCATCAACATCATCGTCACCAA 58.991 45.455 0.00 0.00 0.00 3.67
1900 2632 3.181507 CCATCAACATCATCGTCACCAAC 60.182 47.826 0.00 0.00 0.00 3.77
1942 2674 0.904649 TGTCACCTATGTCCTGCTGG 59.095 55.000 2.58 2.58 0.00 4.85
1956 2688 1.074951 GCTGGTAGGTGCCCTTGTT 59.925 57.895 0.00 0.00 34.61 2.83
1981 2713 1.593209 GTGGTGTCGGCGTTGAGAA 60.593 57.895 6.85 0.00 0.00 2.87
2046 2778 1.591863 GCATTACTCCCTCCGCGAC 60.592 63.158 8.23 0.00 0.00 5.19
2072 2804 2.175621 GTTACATACCCGGCGGCAC 61.176 63.158 23.20 3.78 0.00 5.01
2073 2805 3.388703 TTACATACCCGGCGGCACC 62.389 63.158 23.20 0.00 0.00 5.01
2090 2822 4.377370 CACAACATGGTGGCTCGA 57.623 55.556 16.70 0.00 35.13 4.04
2265 2997 1.382692 GCAAGAGAAGCAGGATGGCC 61.383 60.000 0.00 0.00 35.86 5.36
2270 3002 1.407979 GAGAAGCAGGATGGCCAATTG 59.592 52.381 10.96 9.99 35.86 2.32
2332 3064 3.866582 CCATCCCTGTCTCGCCCC 61.867 72.222 0.00 0.00 0.00 5.80
2359 3091 1.192146 GGAGCTGGTGGTGGACTACA 61.192 60.000 0.00 0.00 0.00 2.74
2393 3125 2.682155 GGTGACCTCAGGCTCTTTAG 57.318 55.000 0.00 0.00 0.00 1.85
2554 3286 2.349755 TGATGAGCAGCAGCAGCA 59.650 55.556 12.92 1.11 45.49 4.41
2555 3287 1.745489 TGATGAGCAGCAGCAGCAG 60.745 57.895 12.92 0.00 45.49 4.24
2824 3801 2.963782 AGTGGAGTACTTCAAACGAGGT 59.036 45.455 5.12 0.00 35.67 3.85
2842 3823 4.473199 GAGGTAAATTCCGTTGAAACAGC 58.527 43.478 0.00 0.00 33.32 4.40
2894 3901 3.879892 GGACAGCAGTTCTTTATCCCATC 59.120 47.826 0.00 0.00 0.00 3.51
2913 3970 5.448654 CCATCTTCCATTAACAGGGATGAA 58.551 41.667 12.64 0.00 39.77 2.57
2981 4038 7.661536 TTGGTTACTCAGAATGCTCTAGTAT 57.338 36.000 0.00 0.00 34.76 2.12
2982 4039 8.762481 TTGGTTACTCAGAATGCTCTAGTATA 57.238 34.615 0.00 0.00 34.76 1.47
2983 4040 8.167605 TGGTTACTCAGAATGCTCTAGTATAC 57.832 38.462 0.00 0.00 34.76 1.47
2984 4041 7.041303 TGGTTACTCAGAATGCTCTAGTATACG 60.041 40.741 0.00 0.00 34.76 3.06
2985 4042 7.172875 GGTTACTCAGAATGCTCTAGTATACGA 59.827 40.741 0.00 0.00 34.76 3.43
2986 4043 6.795098 ACTCAGAATGCTCTAGTATACGAG 57.205 41.667 6.66 6.66 34.76 4.18
3014 4071 7.977789 TTTATATGCATGTGTGTCGGAATAT 57.022 32.000 10.16 0.00 0.00 1.28
3015 4072 7.977789 TTATATGCATGTGTGTCGGAATATT 57.022 32.000 10.16 0.00 0.00 1.28
3016 4073 6.882610 ATATGCATGTGTGTCGGAATATTT 57.117 33.333 10.16 0.00 0.00 1.40
3017 4074 4.614555 TGCATGTGTGTCGGAATATTTC 57.385 40.909 0.00 0.00 0.00 2.17
3018 4075 3.063316 TGCATGTGTGTCGGAATATTTCG 59.937 43.478 10.03 10.03 0.00 3.46
3019 4076 3.308595 GCATGTGTGTCGGAATATTTCGA 59.691 43.478 14.94 14.94 0.00 3.71
3029 4086 6.403333 TCGGAATATTTCGACTTGAGTTTG 57.597 37.500 14.94 0.00 0.00 2.93
3030 4087 5.929992 TCGGAATATTTCGACTTGAGTTTGT 59.070 36.000 14.94 0.00 0.00 2.83
3031 4088 6.015504 CGGAATATTTCGACTTGAGTTTGTG 58.984 40.000 10.83 0.00 0.00 3.33
3032 4089 5.795441 GGAATATTTCGACTTGAGTTTGTGC 59.205 40.000 0.00 0.00 0.00 4.57
3033 4090 5.940192 ATATTTCGACTTGAGTTTGTGCA 57.060 34.783 0.00 0.00 0.00 4.57
3034 4091 3.673746 TTTCGACTTGAGTTTGTGCAG 57.326 42.857 0.00 0.00 0.00 4.41
3035 4092 1.581934 TCGACTTGAGTTTGTGCAGG 58.418 50.000 0.00 0.00 0.00 4.85
3036 4093 0.588252 CGACTTGAGTTTGTGCAGGG 59.412 55.000 0.00 0.00 0.00 4.45
3037 4094 1.810031 CGACTTGAGTTTGTGCAGGGA 60.810 52.381 0.00 0.00 0.00 4.20
3038 4095 1.876156 GACTTGAGTTTGTGCAGGGAG 59.124 52.381 0.00 0.00 0.00 4.30
3039 4096 1.490490 ACTTGAGTTTGTGCAGGGAGA 59.510 47.619 0.00 0.00 0.00 3.71
3040 4097 2.149578 CTTGAGTTTGTGCAGGGAGAG 58.850 52.381 0.00 0.00 0.00 3.20
3041 4098 0.397941 TGAGTTTGTGCAGGGAGAGG 59.602 55.000 0.00 0.00 0.00 3.69
3042 4099 0.687354 GAGTTTGTGCAGGGAGAGGA 59.313 55.000 0.00 0.00 0.00 3.71
3043 4100 1.280421 GAGTTTGTGCAGGGAGAGGAT 59.720 52.381 0.00 0.00 0.00 3.24
3044 4101 2.501723 GAGTTTGTGCAGGGAGAGGATA 59.498 50.000 0.00 0.00 0.00 2.59
3045 4102 2.503356 AGTTTGTGCAGGGAGAGGATAG 59.497 50.000 0.00 0.00 0.00 2.08
3046 4103 2.237392 GTTTGTGCAGGGAGAGGATAGT 59.763 50.000 0.00 0.00 0.00 2.12
3047 4104 1.781786 TGTGCAGGGAGAGGATAGTC 58.218 55.000 0.00 0.00 0.00 2.59
3048 4105 0.671251 GTGCAGGGAGAGGATAGTCG 59.329 60.000 0.00 0.00 0.00 4.18
3049 4106 1.109920 TGCAGGGAGAGGATAGTCGC 61.110 60.000 0.00 0.00 0.00 5.19
3050 4107 0.825840 GCAGGGAGAGGATAGTCGCT 60.826 60.000 0.00 0.00 36.47 4.93
3051 4108 0.958091 CAGGGAGAGGATAGTCGCTG 59.042 60.000 2.50 2.50 44.36 5.18
3052 4109 0.553819 AGGGAGAGGATAGTCGCTGT 59.446 55.000 0.00 0.00 34.86 4.40
3053 4110 1.063567 AGGGAGAGGATAGTCGCTGTT 60.064 52.381 0.00 0.00 34.86 3.16
3054 4111 1.067821 GGGAGAGGATAGTCGCTGTTG 59.932 57.143 0.00 0.00 0.00 3.33
3055 4112 1.067821 GGAGAGGATAGTCGCTGTTGG 59.932 57.143 0.00 0.00 0.00 3.77
3056 4113 0.461961 AGAGGATAGTCGCTGTTGGC 59.538 55.000 0.00 0.00 37.64 4.52
3065 4122 2.266055 GCTGTTGGCGGCTAGACT 59.734 61.111 11.43 0.00 43.44 3.24
3066 4123 1.376037 GCTGTTGGCGGCTAGACTT 60.376 57.895 11.43 0.00 43.44 3.01
3067 4124 0.955919 GCTGTTGGCGGCTAGACTTT 60.956 55.000 11.43 0.00 43.44 2.66
3068 4125 1.079503 CTGTTGGCGGCTAGACTTTC 58.920 55.000 11.43 0.00 0.00 2.62
3069 4126 0.685097 TGTTGGCGGCTAGACTTTCT 59.315 50.000 11.43 0.00 0.00 2.52
3070 4127 1.071699 TGTTGGCGGCTAGACTTTCTT 59.928 47.619 11.43 0.00 0.00 2.52
3071 4128 1.732809 GTTGGCGGCTAGACTTTCTTC 59.267 52.381 11.43 0.00 0.00 2.87
3072 4129 1.267121 TGGCGGCTAGACTTTCTTCT 58.733 50.000 11.43 0.00 0.00 2.85
3073 4130 2.453521 TGGCGGCTAGACTTTCTTCTA 58.546 47.619 11.43 0.00 0.00 2.10
3074 4131 2.427453 TGGCGGCTAGACTTTCTTCTAG 59.573 50.000 11.43 3.24 45.58 2.43
3075 4132 2.688958 GGCGGCTAGACTTTCTTCTAGA 59.311 50.000 10.68 0.00 45.64 2.43
3076 4133 3.319689 GGCGGCTAGACTTTCTTCTAGAT 59.680 47.826 10.68 0.00 45.64 1.98
3077 4134 4.519730 GGCGGCTAGACTTTCTTCTAGATA 59.480 45.833 10.68 0.00 45.64 1.98
3078 4135 5.184287 GGCGGCTAGACTTTCTTCTAGATAT 59.816 44.000 10.68 0.00 45.64 1.63
3079 4136 6.090129 GCGGCTAGACTTTCTTCTAGATATG 58.910 44.000 10.68 0.00 45.64 1.78
3080 4137 6.294286 GCGGCTAGACTTTCTTCTAGATATGT 60.294 42.308 10.68 0.00 45.64 2.29
3081 4138 7.653647 CGGCTAGACTTTCTTCTAGATATGTT 58.346 38.462 10.68 0.00 45.64 2.71
3082 4139 7.593273 CGGCTAGACTTTCTTCTAGATATGTTG 59.407 40.741 10.68 0.00 45.64 3.33
3083 4140 7.870445 GGCTAGACTTTCTTCTAGATATGTTGG 59.130 40.741 10.68 0.00 45.64 3.77
3084 4141 8.417884 GCTAGACTTTCTTCTAGATATGTTGGT 58.582 37.037 10.68 0.00 45.64 3.67
3087 4144 7.550906 AGACTTTCTTCTAGATATGTTGGTTGC 59.449 37.037 0.00 0.00 0.00 4.17
3088 4145 7.398024 ACTTTCTTCTAGATATGTTGGTTGCT 58.602 34.615 0.00 0.00 0.00 3.91
3089 4146 7.335422 ACTTTCTTCTAGATATGTTGGTTGCTG 59.665 37.037 0.00 0.00 0.00 4.41
3090 4147 5.674525 TCTTCTAGATATGTTGGTTGCTGG 58.325 41.667 0.00 0.00 0.00 4.85
3091 4148 3.808728 TCTAGATATGTTGGTTGCTGGC 58.191 45.455 0.00 0.00 0.00 4.85
3092 4149 2.814805 AGATATGTTGGTTGCTGGCT 57.185 45.000 0.00 0.00 0.00 4.75
3093 4150 2.372264 AGATATGTTGGTTGCTGGCTG 58.628 47.619 0.00 0.00 0.00 4.85
3094 4151 1.406539 GATATGTTGGTTGCTGGCTGG 59.593 52.381 0.00 0.00 0.00 4.85
3095 4152 1.250154 TATGTTGGTTGCTGGCTGGC 61.250 55.000 0.00 0.00 0.00 4.85
3096 4153 2.914097 GTTGGTTGCTGGCTGGCT 60.914 61.111 2.00 0.00 0.00 4.75
3097 4154 2.123338 TTGGTTGCTGGCTGGCTT 60.123 55.556 2.00 0.00 0.00 4.35
3098 4155 2.500714 TTGGTTGCTGGCTGGCTTG 61.501 57.895 2.00 0.00 0.00 4.01
3099 4156 2.914097 GGTTGCTGGCTGGCTTGT 60.914 61.111 2.00 0.00 0.00 3.16
3100 4157 1.603455 GGTTGCTGGCTGGCTTGTA 60.603 57.895 2.00 0.00 0.00 2.41
3101 4158 1.178534 GGTTGCTGGCTGGCTTGTAA 61.179 55.000 2.00 0.00 0.00 2.41
3102 4159 0.039165 GTTGCTGGCTGGCTTGTAAC 60.039 55.000 2.00 7.71 0.00 2.50
3103 4160 0.467106 TTGCTGGCTGGCTTGTAACA 60.467 50.000 2.00 0.00 0.00 2.41
3104 4161 0.890542 TGCTGGCTGGCTTGTAACAG 60.891 55.000 2.00 0.00 37.76 3.16
3105 4162 0.606401 GCTGGCTGGCTTGTAACAGA 60.606 55.000 2.00 0.00 36.86 3.41
3106 4163 1.160137 CTGGCTGGCTTGTAACAGAC 58.840 55.000 2.00 0.00 43.12 3.51
3107 4164 0.764890 TGGCTGGCTTGTAACAGACT 59.235 50.000 2.00 0.00 43.23 3.24
3108 4165 1.270839 TGGCTGGCTTGTAACAGACTC 60.271 52.381 2.00 0.00 43.23 3.36
3109 4166 1.071605 GCTGGCTTGTAACAGACTCG 58.928 55.000 0.00 0.00 36.86 4.18
3110 4167 1.605712 GCTGGCTTGTAACAGACTCGT 60.606 52.381 0.00 0.00 36.86 4.18
3111 4168 2.352421 GCTGGCTTGTAACAGACTCGTA 60.352 50.000 0.00 0.00 36.86 3.43
3112 4169 3.502920 CTGGCTTGTAACAGACTCGTAG 58.497 50.000 0.00 0.00 36.86 3.51
3113 4170 2.260481 GGCTTGTAACAGACTCGTAGC 58.740 52.381 0.00 0.00 0.00 3.58
3114 4171 2.094649 GGCTTGTAACAGACTCGTAGCT 60.095 50.000 0.00 0.00 0.00 3.32
3115 4172 3.172824 GCTTGTAACAGACTCGTAGCTC 58.827 50.000 0.00 0.00 0.00 4.09
3116 4173 3.119779 GCTTGTAACAGACTCGTAGCTCT 60.120 47.826 0.00 0.00 0.00 4.09
3117 4174 4.407818 CTTGTAACAGACTCGTAGCTCTG 58.592 47.826 0.00 0.00 39.95 3.35
3118 4175 3.671716 TGTAACAGACTCGTAGCTCTGA 58.328 45.455 5.49 0.00 37.85 3.27
3119 4176 4.070009 TGTAACAGACTCGTAGCTCTGAA 58.930 43.478 5.49 0.00 37.85 3.02
3120 4177 3.562567 AACAGACTCGTAGCTCTGAAC 57.437 47.619 5.49 0.00 37.85 3.18
3121 4178 1.813786 ACAGACTCGTAGCTCTGAACC 59.186 52.381 5.49 0.00 37.85 3.62
3122 4179 2.088423 CAGACTCGTAGCTCTGAACCT 58.912 52.381 0.00 0.00 36.75 3.50
3123 4180 2.490115 CAGACTCGTAGCTCTGAACCTT 59.510 50.000 0.00 0.00 36.75 3.50
3124 4181 3.057174 CAGACTCGTAGCTCTGAACCTTT 60.057 47.826 0.00 0.00 36.75 3.11
3125 4182 3.057174 AGACTCGTAGCTCTGAACCTTTG 60.057 47.826 0.00 0.00 0.00 2.77
3126 4183 2.028930 ACTCGTAGCTCTGAACCTTTGG 60.029 50.000 0.00 0.00 0.00 3.28
3127 4184 1.079503 CGTAGCTCTGAACCTTTGGC 58.920 55.000 0.00 0.00 0.00 4.52
3128 4185 1.338200 CGTAGCTCTGAACCTTTGGCT 60.338 52.381 0.00 0.00 0.00 4.75
3129 4186 2.784347 GTAGCTCTGAACCTTTGGCTT 58.216 47.619 0.00 0.00 0.00 4.35
3130 4187 1.613836 AGCTCTGAACCTTTGGCTTG 58.386 50.000 0.00 0.00 0.00 4.01
3131 4188 0.600057 GCTCTGAACCTTTGGCTTGG 59.400 55.000 0.00 0.00 0.00 3.61
3132 4189 1.986882 CTCTGAACCTTTGGCTTGGT 58.013 50.000 0.00 0.00 38.35 3.67
3134 4191 2.695147 CTCTGAACCTTTGGCTTGGTTT 59.305 45.455 9.83 0.00 45.48 3.27
3135 4192 2.693074 TCTGAACCTTTGGCTTGGTTTC 59.307 45.455 9.83 5.61 45.48 2.78
3136 4193 2.695147 CTGAACCTTTGGCTTGGTTTCT 59.305 45.455 9.83 0.00 45.48 2.52
3137 4194 2.430332 TGAACCTTTGGCTTGGTTTCTG 59.570 45.455 9.83 0.00 45.48 3.02
3138 4195 2.159179 ACCTTTGGCTTGGTTTCTGT 57.841 45.000 0.00 0.00 31.62 3.41
3139 4196 3.306472 ACCTTTGGCTTGGTTTCTGTA 57.694 42.857 0.00 0.00 31.62 2.74
3140 4197 3.637769 ACCTTTGGCTTGGTTTCTGTAA 58.362 40.909 0.00 0.00 31.62 2.41
3141 4198 4.223144 ACCTTTGGCTTGGTTTCTGTAAT 58.777 39.130 0.00 0.00 31.62 1.89
3142 4199 4.039124 ACCTTTGGCTTGGTTTCTGTAATG 59.961 41.667 0.00 0.00 31.62 1.90
3143 4200 3.658757 TTGGCTTGGTTTCTGTAATGC 57.341 42.857 0.00 0.00 0.00 3.56
3144 4201 2.591923 TGGCTTGGTTTCTGTAATGCA 58.408 42.857 0.00 0.00 0.00 3.96
3145 4202 2.961741 TGGCTTGGTTTCTGTAATGCAA 59.038 40.909 0.00 0.00 0.00 4.08
3146 4203 3.386078 TGGCTTGGTTTCTGTAATGCAAA 59.614 39.130 0.00 0.00 0.00 3.68
3147 4204 4.040217 TGGCTTGGTTTCTGTAATGCAAAT 59.960 37.500 0.00 0.00 0.00 2.32
3148 4205 4.627035 GGCTTGGTTTCTGTAATGCAAATC 59.373 41.667 0.00 0.00 0.00 2.17
3149 4206 5.229423 GCTTGGTTTCTGTAATGCAAATCA 58.771 37.500 0.00 0.00 0.00 2.57
3150 4207 5.346822 GCTTGGTTTCTGTAATGCAAATCAG 59.653 40.000 0.00 0.00 0.00 2.90
3151 4208 6.647334 TTGGTTTCTGTAATGCAAATCAGA 57.353 33.333 11.99 11.99 35.54 3.27
3152 4209 6.258230 TGGTTTCTGTAATGCAAATCAGAG 57.742 37.500 14.40 0.00 38.03 3.35
3153 4210 5.183713 TGGTTTCTGTAATGCAAATCAGAGG 59.816 40.000 14.40 0.00 38.03 3.69
3154 4211 5.393461 GGTTTCTGTAATGCAAATCAGAGGG 60.393 44.000 14.40 0.00 38.03 4.30
3155 4212 3.889815 TCTGTAATGCAAATCAGAGGGG 58.110 45.455 11.99 0.00 33.77 4.79
3156 4213 3.523157 TCTGTAATGCAAATCAGAGGGGA 59.477 43.478 11.99 0.00 33.77 4.81
3157 4214 4.018506 TCTGTAATGCAAATCAGAGGGGAA 60.019 41.667 11.99 0.00 33.77 3.97
3158 4215 4.671831 TGTAATGCAAATCAGAGGGGAAA 58.328 39.130 0.00 0.00 0.00 3.13
3159 4216 4.462483 TGTAATGCAAATCAGAGGGGAAAC 59.538 41.667 0.00 0.00 0.00 2.78
3226 4283 4.392138 GGATTTTCTCTACCACTGTTTCCG 59.608 45.833 0.00 0.00 0.00 4.30
3258 4315 3.871006 GACGCCATCACTGATGAATACAA 59.129 43.478 19.04 0.00 42.09 2.41
3263 4320 6.365839 GCCATCACTGATGAATACAATTACG 58.634 40.000 19.04 0.89 42.09 3.18
3277 4334 1.439353 ATTACGAAGCGGGCATGCAG 61.439 55.000 21.36 13.96 37.31 4.41
3315 4373 3.317993 GGAAAGCGGGCATACATTTACAT 59.682 43.478 0.00 0.00 0.00 2.29
3404 4462 9.725019 ATTTCCATTCTAAAACCTTTTTCCATC 57.275 29.630 0.00 0.00 0.00 3.51
3432 4490 7.687941 AGATCATTTTTGAGTCCGTAAACAT 57.312 32.000 0.00 0.00 0.00 2.71
3433 4491 8.110860 AGATCATTTTTGAGTCCGTAAACATT 57.889 30.769 0.00 0.00 0.00 2.71
3564 4623 9.300681 ACTCAGGAATAATTTCAAATTCACTGA 57.699 29.630 0.00 8.19 37.23 3.41
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
3 4 0.390472 GGAACCTCAAGTCGCTCCAG 60.390 60.000 0.00 0.00 0.00 3.86
99 100 1.597027 CGTCGGGAGGCACAAAGTT 60.597 57.895 0.00 0.00 0.00 2.66
143 144 1.376553 GAGCTGGTGGAGAAGGCAC 60.377 63.158 0.00 0.00 0.00 5.01
144 145 2.596851 GGAGCTGGTGGAGAAGGCA 61.597 63.158 0.00 0.00 0.00 4.75
175 176 3.117171 GCTGCTGGACTCGCACTG 61.117 66.667 0.00 0.00 33.19 3.66
205 206 3.402681 GGGGCAGCTGCTGGACTA 61.403 66.667 35.82 0.00 41.70 2.59
572 1100 1.077501 CGGGGGTACGAGGTAGACA 60.078 63.158 0.00 0.00 35.47 3.41
733 1261 1.782752 CCATTATGTCCCTGACCCCAT 59.217 52.381 0.00 0.00 0.00 4.00
799 1327 7.950124 TGACATTTTCCCCTCTTTCTTATTTCT 59.050 33.333 0.00 0.00 0.00 2.52
873 1593 7.446931 TGCAATCTAGGTTTGACACTTAATTCA 59.553 33.333 9.64 0.00 0.00 2.57
1368 2100 2.995574 AGGACGTAACCAGCGGCT 60.996 61.111 0.00 0.00 37.54 5.52
1374 2106 2.821969 GGTGTAGAAGAGGACGTAACCA 59.178 50.000 0.00 0.00 0.00 3.67
1377 2109 3.350833 GGAGGTGTAGAAGAGGACGTAA 58.649 50.000 0.00 0.00 0.00 3.18
1402 2134 1.515954 CCGACTGGCTACCAACGAT 59.484 57.895 12.31 0.00 36.21 3.73
1558 2290 0.648441 TTGTTGTGTGAGCGAACGAC 59.352 50.000 0.00 0.00 0.00 4.34
1564 2296 1.511850 TCCAGATTGTTGTGTGAGCG 58.488 50.000 0.00 0.00 0.00 5.03
1565 2297 2.880890 ACTTCCAGATTGTTGTGTGAGC 59.119 45.455 0.00 0.00 0.00 4.26
1571 2303 8.918202 TTTTAGTATGACTTCCAGATTGTTGT 57.082 30.769 0.00 0.00 0.00 3.32
1688 2420 2.035961 GCAGAAGCATGTCCGTATCCTA 59.964 50.000 0.00 0.00 41.58 2.94
1704 2436 0.744874 CCCGGAGATACGAAGCAGAA 59.255 55.000 0.73 0.00 35.47 3.02
1705 2437 0.106868 TCCCGGAGATACGAAGCAGA 60.107 55.000 0.73 0.00 35.47 4.26
1706 2438 0.312416 CTCCCGGAGATACGAAGCAG 59.688 60.000 9.01 0.00 35.47 4.24
1707 2439 1.107538 CCTCCCGGAGATACGAAGCA 61.108 60.000 16.69 0.00 35.47 3.91
1771 2503 2.483877 CCTTGGTGTACAGTACGTCGTA 59.516 50.000 0.00 0.00 0.00 3.43
1848 2580 3.692406 AGGAAGGCGACGGTGGTC 61.692 66.667 0.00 0.00 39.89 4.02
1889 2621 2.672874 CGATGTTGATGTTGGTGACGAT 59.327 45.455 0.00 0.00 0.00 3.73
1895 2627 2.569853 TCTACCCGATGTTGATGTTGGT 59.430 45.455 0.00 0.00 0.00 3.67
1896 2628 3.260475 TCTACCCGATGTTGATGTTGG 57.740 47.619 0.00 0.00 0.00 3.77
1897 2629 4.801147 CATCTACCCGATGTTGATGTTG 57.199 45.455 15.74 0.51 45.98 3.33
1956 2688 3.311110 GCCGACACCACCTCCAGA 61.311 66.667 0.00 0.00 0.00 3.86
1981 2713 1.555075 TGCCCAACTCGAGAATAAGCT 59.445 47.619 21.68 0.00 0.00 3.74
2046 2778 1.003851 CGGGTATGTAACGCAAGGTG 58.996 55.000 0.00 0.00 40.99 4.00
2053 2785 2.963320 GCCGCCGGGTATGTAACG 60.963 66.667 4.77 0.00 34.97 3.18
2056 2788 3.852307 GGTGCCGCCGGGTATGTA 61.852 66.667 4.77 0.00 34.97 2.29
2073 2805 1.300971 CCTCGAGCCACCATGTTGTG 61.301 60.000 6.99 0.00 35.98 3.33
2074 2806 1.003355 CCTCGAGCCACCATGTTGT 60.003 57.895 6.99 0.00 0.00 3.32
2089 2821 4.175337 TACCCATGCTGCGGCCTC 62.175 66.667 16.57 0.00 37.74 4.70
2090 2822 4.489771 GTACCCATGCTGCGGCCT 62.490 66.667 16.57 1.03 37.74 5.19
2107 2839 0.798776 GAACCGCTGACATGTCTTGG 59.201 55.000 25.55 23.53 0.00 3.61
2169 2901 3.712907 TACCTTGCCCAGTCCGCC 61.713 66.667 0.00 0.00 0.00 6.13
2265 2997 1.849039 ACCTCTCTCCCCATCCAATTG 59.151 52.381 0.00 0.00 0.00 2.32
2270 3002 1.341156 CCACACCTCTCTCCCCATCC 61.341 65.000 0.00 0.00 0.00 3.51
2343 3075 0.107654 GGATGTAGTCCACCACCAGC 60.108 60.000 0.00 0.00 46.96 4.85
2372 3104 1.492993 AAAGAGCCTGAGGTCACCCC 61.493 60.000 0.00 0.00 43.21 4.95
2393 3125 3.127533 GGCTGTCGTGGTCATGGC 61.128 66.667 0.00 0.00 0.00 4.40
2394 3126 1.003355 AAGGCTGTCGTGGTCATGG 60.003 57.895 0.00 0.00 0.00 3.66
2395 3127 0.603707 ACAAGGCTGTCGTGGTCATG 60.604 55.000 0.00 0.00 0.00 3.07
2554 3286 1.467678 ATCCGCTTATGCTCCTCGCT 61.468 55.000 0.00 0.00 40.11 4.93
2555 3287 1.005630 ATCCGCTTATGCTCCTCGC 60.006 57.895 0.00 0.00 36.97 5.03
2556 3288 0.315251 TCATCCGCTTATGCTCCTCG 59.685 55.000 0.00 0.00 36.97 4.63
2566 3304 2.185350 CGCCTCACTCATCCGCTT 59.815 61.111 0.00 0.00 0.00 4.68
2569 3307 2.105128 GACCGCCTCACTCATCCG 59.895 66.667 0.00 0.00 0.00 4.18
2570 3308 2.303549 CTGGACCGCCTCACTCATCC 62.304 65.000 0.00 0.00 34.31 3.51
2573 3311 2.997315 CCTGGACCGCCTCACTCA 60.997 66.667 0.00 0.00 34.31 3.41
2574 3312 4.459089 GCCTGGACCGCCTCACTC 62.459 72.222 0.00 0.00 34.31 3.51
2741 3718 1.375013 GCTTGGCATGGCAAAGTGG 60.375 57.895 31.42 21.79 41.30 4.00
2824 3801 5.278266 CCTCTTGCTGTTTCAACGGAATTTA 60.278 40.000 2.50 0.00 37.48 1.40
2842 3823 4.148825 CCTCGTCCCCGCCTCTTG 62.149 72.222 0.00 0.00 0.00 3.02
2894 3901 7.592885 ATGATTTCATCCCTGTTAATGGAAG 57.407 36.000 0.00 0.00 33.54 3.46
2913 3970 2.894126 CCGGGAGCACTAGTAGATGATT 59.106 50.000 3.59 0.00 0.00 2.57
2981 4038 8.880878 ACACACATGCATATAAAATACTCGTA 57.119 30.769 0.00 0.00 0.00 3.43
2982 4039 7.306574 CGACACACATGCATATAAAATACTCGT 60.307 37.037 0.00 0.00 0.00 4.18
2983 4040 7.003648 CGACACACATGCATATAAAATACTCG 58.996 38.462 0.00 0.00 0.00 4.18
2984 4041 7.170828 TCCGACACACATGCATATAAAATACTC 59.829 37.037 0.00 0.00 0.00 2.59
2985 4042 6.989759 TCCGACACACATGCATATAAAATACT 59.010 34.615 0.00 0.00 0.00 2.12
2986 4043 7.184800 TCCGACACACATGCATATAAAATAC 57.815 36.000 0.00 0.00 0.00 1.89
3014 4071 2.354510 CCTGCACAAACTCAAGTCGAAA 59.645 45.455 0.00 0.00 0.00 3.46
3015 4072 1.939934 CCTGCACAAACTCAAGTCGAA 59.060 47.619 0.00 0.00 0.00 3.71
3016 4073 1.581934 CCTGCACAAACTCAAGTCGA 58.418 50.000 0.00 0.00 0.00 4.20
3017 4074 0.588252 CCCTGCACAAACTCAAGTCG 59.412 55.000 0.00 0.00 0.00 4.18
3018 4075 1.876156 CTCCCTGCACAAACTCAAGTC 59.124 52.381 0.00 0.00 0.00 3.01
3019 4076 1.490490 TCTCCCTGCACAAACTCAAGT 59.510 47.619 0.00 0.00 0.00 3.16
3020 4077 2.149578 CTCTCCCTGCACAAACTCAAG 58.850 52.381 0.00 0.00 0.00 3.02
3021 4078 1.202806 CCTCTCCCTGCACAAACTCAA 60.203 52.381 0.00 0.00 0.00 3.02
3022 4079 0.397941 CCTCTCCCTGCACAAACTCA 59.602 55.000 0.00 0.00 0.00 3.41
3023 4080 0.687354 TCCTCTCCCTGCACAAACTC 59.313 55.000 0.00 0.00 0.00 3.01
3024 4081 1.366319 ATCCTCTCCCTGCACAAACT 58.634 50.000 0.00 0.00 0.00 2.66
3025 4082 2.237392 ACTATCCTCTCCCTGCACAAAC 59.763 50.000 0.00 0.00 0.00 2.93
3026 4083 2.501723 GACTATCCTCTCCCTGCACAAA 59.498 50.000 0.00 0.00 0.00 2.83
3027 4084 2.111384 GACTATCCTCTCCCTGCACAA 58.889 52.381 0.00 0.00 0.00 3.33
3028 4085 1.781786 GACTATCCTCTCCCTGCACA 58.218 55.000 0.00 0.00 0.00 4.57
3029 4086 0.671251 CGACTATCCTCTCCCTGCAC 59.329 60.000 0.00 0.00 0.00 4.57
3030 4087 1.109920 GCGACTATCCTCTCCCTGCA 61.110 60.000 0.00 0.00 0.00 4.41
3031 4088 0.825840 AGCGACTATCCTCTCCCTGC 60.826 60.000 0.00 0.00 0.00 4.85
3032 4089 0.958091 CAGCGACTATCCTCTCCCTG 59.042 60.000 0.00 0.00 0.00 4.45
3033 4090 0.553819 ACAGCGACTATCCTCTCCCT 59.446 55.000 0.00 0.00 0.00 4.20
3034 4091 1.067821 CAACAGCGACTATCCTCTCCC 59.932 57.143 0.00 0.00 0.00 4.30
3035 4092 1.067821 CCAACAGCGACTATCCTCTCC 59.932 57.143 0.00 0.00 0.00 3.71
3036 4093 1.537135 GCCAACAGCGACTATCCTCTC 60.537 57.143 0.00 0.00 0.00 3.20
3037 4094 0.461961 GCCAACAGCGACTATCCTCT 59.538 55.000 0.00 0.00 0.00 3.69
3038 4095 2.979130 GCCAACAGCGACTATCCTC 58.021 57.895 0.00 0.00 0.00 3.71
3048 4105 0.955919 AAAGTCTAGCCGCCAACAGC 60.956 55.000 0.00 0.00 38.52 4.40
3049 4106 1.079503 GAAAGTCTAGCCGCCAACAG 58.920 55.000 0.00 0.00 0.00 3.16
3050 4107 0.685097 AGAAAGTCTAGCCGCCAACA 59.315 50.000 0.00 0.00 0.00 3.33
3051 4108 1.732809 GAAGAAAGTCTAGCCGCCAAC 59.267 52.381 0.00 0.00 0.00 3.77
3052 4109 1.623811 AGAAGAAAGTCTAGCCGCCAA 59.376 47.619 0.00 0.00 0.00 4.52
3053 4110 1.267121 AGAAGAAAGTCTAGCCGCCA 58.733 50.000 0.00 0.00 0.00 5.69
3054 4111 2.688958 TCTAGAAGAAAGTCTAGCCGCC 59.311 50.000 4.66 0.00 44.62 6.13
3055 4112 4.577834 ATCTAGAAGAAAGTCTAGCCGC 57.422 45.455 0.00 0.00 44.62 6.53
3056 4113 7.209471 ACATATCTAGAAGAAAGTCTAGCCG 57.791 40.000 0.00 0.00 44.62 5.52
3057 4114 7.870445 CCAACATATCTAGAAGAAAGTCTAGCC 59.130 40.741 0.00 0.00 44.62 3.93
3058 4115 8.417884 ACCAACATATCTAGAAGAAAGTCTAGC 58.582 37.037 0.00 0.00 44.62 3.42
3061 4118 7.550906 GCAACCAACATATCTAGAAGAAAGTCT 59.449 37.037 0.00 0.00 0.00 3.24
3062 4119 7.550906 AGCAACCAACATATCTAGAAGAAAGTC 59.449 37.037 0.00 0.00 0.00 3.01
3063 4120 7.335422 CAGCAACCAACATATCTAGAAGAAAGT 59.665 37.037 0.00 0.00 0.00 2.66
3064 4121 7.201679 CCAGCAACCAACATATCTAGAAGAAAG 60.202 40.741 0.00 0.00 0.00 2.62
3065 4122 6.599244 CCAGCAACCAACATATCTAGAAGAAA 59.401 38.462 0.00 0.00 0.00 2.52
3066 4123 6.115446 CCAGCAACCAACATATCTAGAAGAA 58.885 40.000 0.00 0.00 0.00 2.52
3067 4124 5.674525 CCAGCAACCAACATATCTAGAAGA 58.325 41.667 0.00 0.00 0.00 2.87
3068 4125 4.274459 GCCAGCAACCAACATATCTAGAAG 59.726 45.833 0.00 0.00 0.00 2.85
3069 4126 4.080356 AGCCAGCAACCAACATATCTAGAA 60.080 41.667 0.00 0.00 0.00 2.10
3070 4127 3.455910 AGCCAGCAACCAACATATCTAGA 59.544 43.478 0.00 0.00 0.00 2.43
3071 4128 3.562973 CAGCCAGCAACCAACATATCTAG 59.437 47.826 0.00 0.00 0.00 2.43
3072 4129 3.544684 CAGCCAGCAACCAACATATCTA 58.455 45.455 0.00 0.00 0.00 1.98
3073 4130 2.372264 CAGCCAGCAACCAACATATCT 58.628 47.619 0.00 0.00 0.00 1.98
3074 4131 1.406539 CCAGCCAGCAACCAACATATC 59.593 52.381 0.00 0.00 0.00 1.63
3075 4132 1.477553 CCAGCCAGCAACCAACATAT 58.522 50.000 0.00 0.00 0.00 1.78
3076 4133 1.250154 GCCAGCCAGCAACCAACATA 61.250 55.000 0.00 0.00 0.00 2.29
3077 4134 2.576832 GCCAGCCAGCAACCAACAT 61.577 57.895 0.00 0.00 0.00 2.71
3078 4135 3.225798 GCCAGCCAGCAACCAACA 61.226 61.111 0.00 0.00 0.00 3.33
3079 4136 2.501602 AAGCCAGCCAGCAACCAAC 61.502 57.895 0.00 0.00 34.23 3.77
3080 4137 2.123338 AAGCCAGCCAGCAACCAA 60.123 55.556 0.00 0.00 34.23 3.67
3081 4138 2.350511 TACAAGCCAGCCAGCAACCA 62.351 55.000 0.00 0.00 34.23 3.67
3082 4139 1.178534 TTACAAGCCAGCCAGCAACC 61.179 55.000 0.00 0.00 34.23 3.77
3083 4140 0.039165 GTTACAAGCCAGCCAGCAAC 60.039 55.000 0.00 0.00 34.23 4.17
3084 4141 0.467106 TGTTACAAGCCAGCCAGCAA 60.467 50.000 0.00 0.00 34.23 3.91
3085 4142 0.890542 CTGTTACAAGCCAGCCAGCA 60.891 55.000 0.00 0.00 34.23 4.41
3086 4143 0.606401 TCTGTTACAAGCCAGCCAGC 60.606 55.000 0.00 0.00 0.00 4.85
3087 4144 1.160137 GTCTGTTACAAGCCAGCCAG 58.840 55.000 0.00 0.00 0.00 4.85
3088 4145 0.764890 AGTCTGTTACAAGCCAGCCA 59.235 50.000 0.00 0.00 0.00 4.75
3089 4146 1.443802 GAGTCTGTTACAAGCCAGCC 58.556 55.000 0.00 0.00 0.00 4.85
3090 4147 1.071605 CGAGTCTGTTACAAGCCAGC 58.928 55.000 0.00 0.00 0.00 4.85
3091 4148 2.440539 ACGAGTCTGTTACAAGCCAG 57.559 50.000 0.00 0.00 0.00 4.85
3092 4149 2.352421 GCTACGAGTCTGTTACAAGCCA 60.352 50.000 0.00 0.00 0.00 4.75
3093 4150 2.094649 AGCTACGAGTCTGTTACAAGCC 60.095 50.000 0.00 0.00 0.00 4.35
3094 4151 3.119779 AGAGCTACGAGTCTGTTACAAGC 60.120 47.826 0.00 0.00 0.00 4.01
3095 4152 4.154375 TCAGAGCTACGAGTCTGTTACAAG 59.846 45.833 0.00 0.00 40.97 3.16
3096 4153 4.070009 TCAGAGCTACGAGTCTGTTACAA 58.930 43.478 0.00 0.00 40.97 2.41
3097 4154 3.671716 TCAGAGCTACGAGTCTGTTACA 58.328 45.455 0.00 0.00 40.97 2.41
3098 4155 4.405196 GTTCAGAGCTACGAGTCTGTTAC 58.595 47.826 0.00 0.00 40.97 2.50
3099 4156 3.439476 GGTTCAGAGCTACGAGTCTGTTA 59.561 47.826 0.00 0.00 40.97 2.41
3100 4157 2.229302 GGTTCAGAGCTACGAGTCTGTT 59.771 50.000 0.00 0.00 40.97 3.16
3101 4158 1.813786 GGTTCAGAGCTACGAGTCTGT 59.186 52.381 0.00 0.00 40.97 3.41
3102 4159 2.088423 AGGTTCAGAGCTACGAGTCTG 58.912 52.381 0.00 0.00 41.44 3.51
3103 4160 2.500392 AGGTTCAGAGCTACGAGTCT 57.500 50.000 0.00 0.00 0.00 3.24
3104 4161 3.246619 CAAAGGTTCAGAGCTACGAGTC 58.753 50.000 0.00 0.00 32.23 3.36
3105 4162 2.028930 CCAAAGGTTCAGAGCTACGAGT 60.029 50.000 0.00 0.00 32.23 4.18
3106 4163 2.611518 CCAAAGGTTCAGAGCTACGAG 58.388 52.381 0.00 0.00 32.23 4.18
3107 4164 1.337823 GCCAAAGGTTCAGAGCTACGA 60.338 52.381 0.00 0.00 32.23 3.43
3108 4165 1.079503 GCCAAAGGTTCAGAGCTACG 58.920 55.000 0.00 0.00 32.23 3.51
3109 4166 2.481289 AGCCAAAGGTTCAGAGCTAC 57.519 50.000 0.00 0.00 32.23 3.58
3110 4167 2.553028 CCAAGCCAAAGGTTCAGAGCTA 60.553 50.000 0.00 0.00 32.23 3.32
3111 4168 1.613836 CAAGCCAAAGGTTCAGAGCT 58.386 50.000 0.00 0.00 34.43 4.09
3112 4169 0.600057 CCAAGCCAAAGGTTCAGAGC 59.400 55.000 0.00 0.00 0.00 4.09
3113 4170 1.986882 ACCAAGCCAAAGGTTCAGAG 58.013 50.000 0.00 0.00 33.39 3.35
3114 4171 2.452600 AACCAAGCCAAAGGTTCAGA 57.547 45.000 0.00 0.00 44.51 3.27
3115 4172 2.695147 AGAAACCAAGCCAAAGGTTCAG 59.305 45.455 0.00 0.00 46.92 3.02
3116 4173 2.430332 CAGAAACCAAGCCAAAGGTTCA 59.570 45.455 0.00 0.00 46.92 3.18
3117 4174 2.430694 ACAGAAACCAAGCCAAAGGTTC 59.569 45.455 0.00 0.00 46.92 3.62
3119 4176 2.159179 ACAGAAACCAAGCCAAAGGT 57.841 45.000 0.00 0.00 40.61 3.50
3120 4177 4.559153 CATTACAGAAACCAAGCCAAAGG 58.441 43.478 0.00 0.00 0.00 3.11
3121 4178 3.989817 GCATTACAGAAACCAAGCCAAAG 59.010 43.478 0.00 0.00 0.00 2.77
3122 4179 3.386078 TGCATTACAGAAACCAAGCCAAA 59.614 39.130 0.00 0.00 0.00 3.28
3123 4180 2.961741 TGCATTACAGAAACCAAGCCAA 59.038 40.909 0.00 0.00 0.00 4.52
3124 4181 2.591923 TGCATTACAGAAACCAAGCCA 58.408 42.857 0.00 0.00 0.00 4.75
3125 4182 3.658757 TTGCATTACAGAAACCAAGCC 57.341 42.857 0.00 0.00 0.00 4.35
3126 4183 5.229423 TGATTTGCATTACAGAAACCAAGC 58.771 37.500 0.00 0.00 0.00 4.01
3127 4184 6.680810 TCTGATTTGCATTACAGAAACCAAG 58.319 36.000 12.53 0.00 36.63 3.61
3128 4185 6.294675 CCTCTGATTTGCATTACAGAAACCAA 60.295 38.462 14.72 0.00 38.60 3.67
3129 4186 5.183713 CCTCTGATTTGCATTACAGAAACCA 59.816 40.000 14.72 0.00 38.60 3.67
3130 4187 5.393461 CCCTCTGATTTGCATTACAGAAACC 60.393 44.000 14.72 0.00 38.60 3.27
3131 4188 5.393461 CCCCTCTGATTTGCATTACAGAAAC 60.393 44.000 14.72 0.00 38.60 2.78
3132 4189 4.706476 CCCCTCTGATTTGCATTACAGAAA 59.294 41.667 14.72 0.00 38.60 2.52
3133 4190 4.018506 TCCCCTCTGATTTGCATTACAGAA 60.019 41.667 14.72 0.00 38.60 3.02
3134 4191 3.523157 TCCCCTCTGATTTGCATTACAGA 59.477 43.478 13.67 13.67 37.71 3.41
3135 4192 3.889815 TCCCCTCTGATTTGCATTACAG 58.110 45.455 7.81 7.81 0.00 2.74
3136 4193 4.314522 TTCCCCTCTGATTTGCATTACA 57.685 40.909 0.00 0.00 0.00 2.41
3137 4194 4.142160 GGTTTCCCCTCTGATTTGCATTAC 60.142 45.833 0.00 0.00 0.00 1.89
3138 4195 4.023291 GGTTTCCCCTCTGATTTGCATTA 58.977 43.478 0.00 0.00 0.00 1.90
3139 4196 2.833943 GGTTTCCCCTCTGATTTGCATT 59.166 45.455 0.00 0.00 0.00 3.56
3140 4197 2.460669 GGTTTCCCCTCTGATTTGCAT 58.539 47.619 0.00 0.00 0.00 3.96
3141 4198 1.923356 GGTTTCCCCTCTGATTTGCA 58.077 50.000 0.00 0.00 0.00 4.08
3169 4226 4.320935 GCACCATATTCCGACACACTTTTT 60.321 41.667 0.00 0.00 0.00 1.94
3170 4227 3.190535 GCACCATATTCCGACACACTTTT 59.809 43.478 0.00 0.00 0.00 2.27
3171 4228 2.747446 GCACCATATTCCGACACACTTT 59.253 45.455 0.00 0.00 0.00 2.66
3172 4229 2.027192 AGCACCATATTCCGACACACTT 60.027 45.455 0.00 0.00 0.00 3.16
3173 4230 1.555075 AGCACCATATTCCGACACACT 59.445 47.619 0.00 0.00 0.00 3.55
3174 4231 2.024176 AGCACCATATTCCGACACAC 57.976 50.000 0.00 0.00 0.00 3.82
3175 4232 3.897141 TTAGCACCATATTCCGACACA 57.103 42.857 0.00 0.00 0.00 3.72
3176 4233 4.495844 GCTTTTAGCACCATATTCCGACAC 60.496 45.833 0.00 0.00 41.89 3.67
3177 4234 3.625764 GCTTTTAGCACCATATTCCGACA 59.374 43.478 0.00 0.00 41.89 4.35
3178 4235 4.210832 GCTTTTAGCACCATATTCCGAC 57.789 45.455 0.00 0.00 41.89 4.79
3226 4283 1.594862 GTGATGGCGTCTCAATGTAGC 59.405 52.381 8.40 0.00 0.00 3.58
3258 4315 1.439353 CTGCATGCCCGCTTCGTAAT 61.439 55.000 16.68 0.00 0.00 1.89
3263 4320 4.189188 CAGCTGCATGCCCGCTTC 62.189 66.667 23.94 4.72 44.23 3.86
3277 4334 2.774439 TTCCAAGACGCTTTTTCAGC 57.226 45.000 0.00 0.00 46.31 4.26
3279 4336 2.540769 CGCTTTCCAAGACGCTTTTTCA 60.541 45.455 0.00 0.00 0.00 2.69
3404 4462 9.543018 GTTTACGGACTCAAAAATGATCTTTAG 57.457 33.333 0.00 0.00 0.00 1.85
3408 4466 7.687941 ATGTTTACGGACTCAAAAATGATCT 57.312 32.000 0.00 0.00 0.00 2.75
3409 4467 8.742554 AAATGTTTACGGACTCAAAAATGATC 57.257 30.769 0.00 0.00 0.00 2.92
3539 4598 9.565213 GTCAGTGAATTTGAAATTATTCCTGAG 57.435 33.333 15.28 0.66 37.96 3.35
3543 4602 9.696917 AAGTGTCAGTGAATTTGAAATTATTCC 57.303 29.630 2.71 0.00 34.49 3.01


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

AutoCloner maintained by Alex Coulton.