Multiple sequence alignment - TraesCS1D01G072200

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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 TraesCS1D01G072200 chr1D 100.000 3830 0 0 1 3830 52578005 52574176 0.000000e+00 7073.0
1 TraesCS1D01G072200 chr1D 100.000 151 0 0 3021 3171 351259973 351260123 2.910000e-71 279.0
2 TraesCS1D01G072200 chr1B 92.636 3042 148 44 11 3020 83641698 83638701 0.000000e+00 4307.0
3 TraesCS1D01G072200 chr1B 91.851 589 16 11 3265 3830 83638133 83637554 0.000000e+00 793.0
4 TraesCS1D01G072200 chr1B 76.490 302 65 6 11 308 83642373 83642074 3.960000e-35 159.0
5 TraesCS1D01G072200 chr1B 87.692 65 0 5 3164 3227 83638717 83638660 6.870000e-08 69.4
6 TraesCS1D01G072200 chr1A 97.573 2101 43 3 925 3020 52238256 52236159 0.000000e+00 3591.0
7 TraesCS1D01G072200 chr1A 86.876 922 75 22 11 904 52239471 52238568 0.000000e+00 990.0
8 TraesCS1D01G072200 chr1A 89.883 682 40 17 3171 3830 52236168 52235494 0.000000e+00 850.0
9 TraesCS1D01G072200 chr3B 85.827 381 44 9 1609 1983 822832864 822833240 2.770000e-106 396.0
10 TraesCS1D01G072200 chr5B 80.840 381 66 7 1573 1950 141574543 141574167 3.740000e-75 292.0
11 TraesCS1D01G072200 chr5D 80.577 381 67 7 1573 1950 129478244 129477868 1.740000e-73 287.0
12 TraesCS1D01G072200 chr5D 99.346 153 1 0 3021 3173 410492090 410491938 1.050000e-70 278.0
13 TraesCS1D01G072200 chr5A 80.577 381 67 7 1573 1950 144707953 144707577 1.740000e-73 287.0
14 TraesCS1D01G072200 chr5A 100.000 151 0 0 3021 3171 650133660 650133810 2.910000e-71 279.0
15 TraesCS1D01G072200 chr4A 100.000 152 0 0 3021 3172 593348447 593348598 8.100000e-72 281.0
16 TraesCS1D01G072200 chr4B 99.351 154 1 0 3021 3174 43229712 43229865 2.910000e-71 279.0
17 TraesCS1D01G072200 chr2B 99.329 149 1 0 3021 3169 286979953 286979805 1.750000e-68 270.0
18 TraesCS1D01G072200 chr2B 78.453 362 64 14 1575 1929 221087802 221088156 1.380000e-54 224.0
19 TraesCS1D01G072200 chr2A 97.484 159 3 1 3014 3171 602456805 602456963 1.750000e-68 270.0
20 TraesCS1D01G072200 chr2A 78.442 385 69 14 1575 1952 172537714 172538091 4.940000e-59 239.0
21 TraesCS1D01G072200 chr6B 98.052 154 3 0 3018 3171 156075672 156075825 6.310000e-68 268.0
22 TraesCS1D01G072200 chr6A 98.026 152 3 0 3020 3171 31392264 31392415 8.160000e-67 265.0
23 TraesCS1D01G072200 chr2D 78.571 364 68 10 1575 1933 161900584 161900942 8.270000e-57 231.0


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 TraesCS1D01G072200 chr1D 52574176 52578005 3829 True 7073.000000 7073 100.00000 1 3830 1 chr1D.!!$R1 3829
1 TraesCS1D01G072200 chr1B 83637554 83642373 4819 True 1332.100000 4307 87.16725 11 3830 4 chr1B.!!$R1 3819
2 TraesCS1D01G072200 chr1A 52235494 52239471 3977 True 1810.333333 3591 91.44400 11 3830 3 chr1A.!!$R1 3819

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
165 833 0.036164 ACGCAACCACAGCCTCAATA 59.964 50.0 0.00 0.00 0.00 1.90 F
188 856 0.036388 TGGAATCGGGTTCACTGCTC 60.036 55.0 3.03 0.00 38.64 4.26 F
270 938 0.393077 ACGCCTTTATCCTGGATCCG 59.607 55.0 13.54 11.35 0.00 4.18 F
576 1261 0.615850 AAGCGGAGGAGGGAAAGAAG 59.384 55.0 0.00 0.00 0.00 2.85 F
741 1456 0.778083 ACTTCCTTTTCTCCACCCCC 59.222 55.0 0.00 0.00 0.00 5.40 F
877 1600 0.845102 TTTCCCCTCCTCTTGTCCCC 60.845 60.0 0.00 0.00 0.00 4.81 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1599 2614 4.373116 TTGAGGTCCGGCAGCGTC 62.373 66.667 0.00 1.29 0.00 5.19 R
2235 3250 2.625823 CGGCATGTTTCTTGCGGGT 61.626 57.895 0.00 0.00 41.07 5.28 R
2241 3256 2.423577 GTGTAGTCCGGCATGTTTCTT 58.576 47.619 0.00 0.00 0.00 2.52 R
2556 3571 1.524002 CCAGTCGGTGAGCATGGAT 59.476 57.895 0.00 0.00 32.55 3.41 R
2640 3655 3.385384 TGCAGCTCGTCTCCCTGG 61.385 66.667 0.00 0.00 0.00 4.45 R
2942 3963 8.019669 AGCATATATGTACGTACTAAAGAACCG 58.980 37.037 25.12 7.90 0.00 4.44 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
20 686 2.191400 CCCTCTCAACCTCTCAATCCA 58.809 52.381 0.00 0.00 0.00 3.41
41 707 5.103000 CCATATCGATCTTACCACGAATCC 58.897 45.833 0.00 0.00 39.38 3.01
58 724 6.927936 CACGAATCCAATATCACATTCTCTCT 59.072 38.462 0.00 0.00 0.00 3.10
82 748 1.170442 TGTCGCTAGTGATTCGTCCA 58.830 50.000 9.64 0.00 0.00 4.02
106 773 1.755179 AAGATGAAGCAACCATCGGG 58.245 50.000 0.00 0.00 43.73 5.14
144 812 1.085893 TGGCAACATGTATGCGACAG 58.914 50.000 19.68 0.00 46.17 3.51
165 833 0.036164 ACGCAACCACAGCCTCAATA 59.964 50.000 0.00 0.00 0.00 1.90
166 834 0.447801 CGCAACCACAGCCTCAATAC 59.552 55.000 0.00 0.00 0.00 1.89
186 854 1.017387 GATGGAATCGGGTTCACTGC 58.983 55.000 3.03 0.00 38.64 4.40
188 856 0.036388 TGGAATCGGGTTCACTGCTC 60.036 55.000 3.03 0.00 38.64 4.26
195 863 1.067821 CGGGTTCACTGCTCTCTATCC 59.932 57.143 0.00 0.00 0.00 2.59
206 874 1.465387 CTCTCTATCCCGAATCGACCG 59.535 57.143 3.36 0.00 0.00 4.79
265 933 3.469008 TCACATACGCCTTTATCCTGG 57.531 47.619 0.00 0.00 0.00 4.45
270 938 0.393077 ACGCCTTTATCCTGGATCCG 59.607 55.000 13.54 11.35 0.00 4.18
306 984 4.081695 AGGGAGAAAATACCACCTCTCT 57.918 45.455 0.00 0.00 35.64 3.10
329 1007 6.485313 TCTCAAGATAACCACACGAAACATTT 59.515 34.615 0.00 0.00 0.00 2.32
331 1009 5.622770 AGATAACCACACGAAACATTTCC 57.377 39.130 0.00 0.00 33.68 3.13
340 1018 5.748152 CACACGAAACATTTCCAACATTTCT 59.252 36.000 0.00 0.00 33.68 2.52
357 1035 8.586273 CAACATTTCTACACACACAAAAGAAAG 58.414 33.333 0.00 0.00 38.98 2.62
367 1047 7.278868 ACACACACAAAAGAAAGAAAAACACAA 59.721 29.630 0.00 0.00 0.00 3.33
431 1116 0.972983 TACCTGCAGCTCCACTCCTC 60.973 60.000 8.66 0.00 0.00 3.71
434 1119 0.971959 CTGCAGCTCCACTCCTCTCT 60.972 60.000 0.00 0.00 0.00 3.10
508 1193 3.579626 GACTTGTGCGCGTTGGCTC 62.580 63.158 8.43 0.00 36.88 4.70
524 1209 1.377333 CTCGCCCTCCTTTTGACCC 60.377 63.158 0.00 0.00 0.00 4.46
528 1213 2.757077 CCTCCTTTTGACCCGGCT 59.243 61.111 0.00 0.00 0.00 5.52
544 1229 2.314647 GCTACCGCAGCGACACAAA 61.315 57.895 18.75 0.00 41.37 2.83
566 1251 2.286365 AACAATTGGAAAGCGGAGGA 57.714 45.000 10.83 0.00 0.00 3.71
568 1253 1.098050 CAATTGGAAAGCGGAGGAGG 58.902 55.000 0.00 0.00 0.00 4.30
576 1261 0.615850 AAGCGGAGGAGGGAAAGAAG 59.384 55.000 0.00 0.00 0.00 2.85
585 1270 3.834813 AGGAGGGAAAGAAGGCATTTTTC 59.165 43.478 9.01 9.01 0.00 2.29
587 1272 4.322273 GGAGGGAAAGAAGGCATTTTTCTG 60.322 45.833 14.06 0.00 35.20 3.02
588 1273 4.226384 AGGGAAAGAAGGCATTTTTCTGT 58.774 39.130 14.06 0.00 35.20 3.41
679 1390 1.996191 GACCATCACAGCTTCTTCGTC 59.004 52.381 0.00 0.00 0.00 4.20
680 1391 1.620819 ACCATCACAGCTTCTTCGTCT 59.379 47.619 0.00 0.00 0.00 4.18
681 1392 2.266554 CCATCACAGCTTCTTCGTCTC 58.733 52.381 0.00 0.00 0.00 3.36
682 1393 1.916651 CATCACAGCTTCTTCGTCTCG 59.083 52.381 0.00 0.00 0.00 4.04
683 1394 0.952280 TCACAGCTTCTTCGTCTCGT 59.048 50.000 0.00 0.00 0.00 4.18
724 1439 1.371467 TCATCAATCCCACCACCACT 58.629 50.000 0.00 0.00 0.00 4.00
734 1449 2.230660 CCACCACCACTTCCTTTTCTC 58.769 52.381 0.00 0.00 0.00 2.87
735 1450 2.230660 CACCACCACTTCCTTTTCTCC 58.769 52.381 0.00 0.00 0.00 3.71
736 1451 1.850345 ACCACCACTTCCTTTTCTCCA 59.150 47.619 0.00 0.00 0.00 3.86
737 1452 2.230660 CCACCACTTCCTTTTCTCCAC 58.769 52.381 0.00 0.00 0.00 4.02
738 1453 2.230660 CACCACTTCCTTTTCTCCACC 58.769 52.381 0.00 0.00 0.00 4.61
739 1454 1.145119 ACCACTTCCTTTTCTCCACCC 59.855 52.381 0.00 0.00 0.00 4.61
740 1455 1.547901 CCACTTCCTTTTCTCCACCCC 60.548 57.143 0.00 0.00 0.00 4.95
741 1456 0.778083 ACTTCCTTTTCTCCACCCCC 59.222 55.000 0.00 0.00 0.00 5.40
742 1457 1.076438 CTTCCTTTTCTCCACCCCCT 58.924 55.000 0.00 0.00 0.00 4.79
743 1458 1.004862 CTTCCTTTTCTCCACCCCCTC 59.995 57.143 0.00 0.00 0.00 4.30
763 1478 1.425448 CCCTCCACCTCCATTATTCCC 59.575 57.143 0.00 0.00 0.00 3.97
807 1530 3.596956 TCCCTCTCTACATATACCCCTCC 59.403 52.174 0.00 0.00 0.00 4.30
808 1531 3.598782 CCCTCTCTACATATACCCCTCCT 59.401 52.174 0.00 0.00 0.00 3.69
811 1534 4.524312 TCTCTACATATACCCCTCCTCCT 58.476 47.826 0.00 0.00 0.00 3.69
814 1537 1.437547 ACATATACCCCTCCTCCTCCC 59.562 57.143 0.00 0.00 0.00 4.30
841 1564 1.605058 CTACCCACCTCACCCACTCG 61.605 65.000 0.00 0.00 0.00 4.18
842 1565 3.706373 CCCACCTCACCCACTCGG 61.706 72.222 0.00 0.00 37.81 4.63
843 1566 2.603473 CCACCTCACCCACTCGGA 60.603 66.667 0.00 0.00 34.64 4.55
844 1567 2.650116 CCACCTCACCCACTCGGAG 61.650 68.421 2.83 2.83 34.64 4.63
847 1570 3.775654 CTCACCCACTCGGAGCCC 61.776 72.222 4.58 0.00 34.64 5.19
877 1600 0.845102 TTTCCCCTCCTCTTGTCCCC 60.845 60.000 0.00 0.00 0.00 4.81
920 1930 7.062957 TGGAAGAAGAAGAACCAAGAAAGAAT 58.937 34.615 0.00 0.00 0.00 2.40
1179 2194 2.030562 GGATCGTGGTATGGGCCG 59.969 66.667 0.00 0.00 0.00 6.13
1599 2614 3.834799 GAGTACCCGCCGGACCTG 61.835 72.222 5.05 0.00 0.00 4.00
2280 3295 2.586792 GACCTGCTCGGCTCCATT 59.413 61.111 0.00 0.00 35.61 3.16
2640 3655 4.021925 AAGCTGGACTGGGGCGTC 62.022 66.667 0.00 0.00 0.00 5.19
3026 4047 3.430473 TGGATGCCCAAACGAAACT 57.570 47.368 0.00 0.00 40.09 2.66
3027 4048 0.958091 TGGATGCCCAAACGAAACTG 59.042 50.000 0.00 0.00 40.09 3.16
3028 4049 0.388520 GGATGCCCAAACGAAACTGC 60.389 55.000 0.00 0.00 0.00 4.40
3029 4050 0.598065 GATGCCCAAACGAAACTGCT 59.402 50.000 0.00 0.00 0.00 4.24
3030 4051 0.314935 ATGCCCAAACGAAACTGCTG 59.685 50.000 0.00 0.00 0.00 4.41
3031 4052 1.034838 TGCCCAAACGAAACTGCTGT 61.035 50.000 0.00 0.00 0.00 4.40
3032 4053 0.948678 GCCCAAACGAAACTGCTGTA 59.051 50.000 0.00 0.00 0.00 2.74
3033 4054 1.335496 GCCCAAACGAAACTGCTGTAA 59.665 47.619 0.00 0.00 0.00 2.41
3034 4055 2.223618 GCCCAAACGAAACTGCTGTAAA 60.224 45.455 0.00 0.00 0.00 2.01
3035 4056 3.628017 CCCAAACGAAACTGCTGTAAAG 58.372 45.455 0.00 0.00 0.00 1.85
3036 4057 3.314080 CCCAAACGAAACTGCTGTAAAGA 59.686 43.478 0.00 0.00 0.00 2.52
3037 4058 4.279659 CCAAACGAAACTGCTGTAAAGAC 58.720 43.478 0.00 0.00 0.00 3.01
3038 4059 3.854286 AACGAAACTGCTGTAAAGACG 57.146 42.857 0.00 2.16 0.00 4.18
3039 4060 3.088194 ACGAAACTGCTGTAAAGACGA 57.912 42.857 0.00 0.00 0.00 4.20
3040 4061 3.650139 ACGAAACTGCTGTAAAGACGAT 58.350 40.909 0.00 0.00 0.00 3.73
3041 4062 4.801891 ACGAAACTGCTGTAAAGACGATA 58.198 39.130 0.00 0.00 0.00 2.92
3042 4063 4.620184 ACGAAACTGCTGTAAAGACGATAC 59.380 41.667 0.00 0.00 0.00 2.24
3043 4064 4.857588 CGAAACTGCTGTAAAGACGATACT 59.142 41.667 0.00 0.00 0.00 2.12
3044 4065 5.220043 CGAAACTGCTGTAAAGACGATACTG 60.220 44.000 0.00 0.00 0.00 2.74
3045 4066 3.512680 ACTGCTGTAAAGACGATACTGC 58.487 45.455 12.42 12.42 44.02 4.40
3046 4067 2.526077 TGCTGTAAAGACGATACTGCG 58.474 47.619 13.61 0.00 45.61 5.18
3047 4068 2.094906 TGCTGTAAAGACGATACTGCGT 60.095 45.455 13.61 0.00 45.61 5.24
3048 4069 2.279136 GCTGTAAAGACGATACTGCGTG 59.721 50.000 0.00 0.00 45.72 5.34
3049 4070 2.256174 TGTAAAGACGATACTGCGTGC 58.744 47.619 0.00 0.00 45.72 5.34
3050 4071 2.256174 GTAAAGACGATACTGCGTGCA 58.744 47.619 0.00 0.00 45.72 4.57
3051 4072 1.068474 AAAGACGATACTGCGTGCAC 58.932 50.000 6.82 6.82 45.72 4.57
3052 4073 1.071019 AAGACGATACTGCGTGCACG 61.071 55.000 34.01 34.01 45.72 5.34
3053 4074 1.513373 GACGATACTGCGTGCACGA 60.513 57.895 41.19 24.37 45.72 4.35
3054 4075 1.730593 GACGATACTGCGTGCACGAC 61.731 60.000 41.19 30.17 45.72 4.34
3055 4076 1.799916 CGATACTGCGTGCACGACA 60.800 57.895 41.19 32.66 43.02 4.35
3056 4077 1.341369 CGATACTGCGTGCACGACAA 61.341 55.000 41.19 23.94 43.02 3.18
3057 4078 0.366871 GATACTGCGTGCACGACAAG 59.633 55.000 41.19 32.17 43.02 3.16
3058 4079 1.014044 ATACTGCGTGCACGACAAGG 61.014 55.000 41.19 25.94 43.02 3.61
3059 4080 2.077821 TACTGCGTGCACGACAAGGA 62.078 55.000 41.19 27.15 43.02 3.36
3060 4081 2.661537 TGCGTGCACGACAAGGAG 60.662 61.111 41.19 11.65 43.02 3.69
3061 4082 2.355837 GCGTGCACGACAAGGAGA 60.356 61.111 41.19 0.00 43.02 3.71
3062 4083 2.658707 GCGTGCACGACAAGGAGAC 61.659 63.158 41.19 17.19 43.02 3.36
3063 4084 2.365068 CGTGCACGACAAGGAGACG 61.365 63.158 34.93 1.26 43.02 4.18
3064 4085 1.007734 GTGCACGACAAGGAGACGA 60.008 57.895 0.00 0.00 38.73 4.20
3065 4086 1.007734 TGCACGACAAGGAGACGAC 60.008 57.895 0.00 0.00 38.73 4.34
3066 4087 2.081212 GCACGACAAGGAGACGACG 61.081 63.158 0.00 0.00 38.73 5.12
3067 4088 1.442184 CACGACAAGGAGACGACGG 60.442 63.158 0.00 0.00 38.73 4.79
3068 4089 2.504244 CGACAAGGAGACGACGGC 60.504 66.667 0.00 0.00 37.60 5.68
3069 4090 2.126031 GACAAGGAGACGACGGCC 60.126 66.667 0.00 0.00 0.00 6.13
3070 4091 2.915659 ACAAGGAGACGACGGCCA 60.916 61.111 2.24 0.00 0.00 5.36
3071 4092 2.342279 CAAGGAGACGACGGCCAA 59.658 61.111 2.24 0.00 0.00 4.52
3072 4093 1.301401 CAAGGAGACGACGGCCAAA 60.301 57.895 2.24 0.00 0.00 3.28
3073 4094 0.673644 CAAGGAGACGACGGCCAAAT 60.674 55.000 2.24 0.00 0.00 2.32
3074 4095 0.391263 AAGGAGACGACGGCCAAATC 60.391 55.000 2.24 0.00 0.00 2.17
3075 4096 1.814169 GGAGACGACGGCCAAATCC 60.814 63.158 2.24 0.00 0.00 3.01
3076 4097 1.079405 GAGACGACGGCCAAATCCA 60.079 57.895 2.24 0.00 0.00 3.41
3077 4098 1.079127 AGACGACGGCCAAATCCAG 60.079 57.895 2.24 0.00 0.00 3.86
3078 4099 2.746277 ACGACGGCCAAATCCAGC 60.746 61.111 2.24 0.00 0.00 4.85
3079 4100 3.508840 CGACGGCCAAATCCAGCC 61.509 66.667 2.24 0.00 46.17 4.85
3083 4104 2.044946 GGCCAAATCCAGCCGTCT 60.045 61.111 0.00 0.00 39.87 4.18
3084 4105 2.409870 GGCCAAATCCAGCCGTCTG 61.410 63.158 0.00 0.00 39.87 3.51
3085 4106 3.056313 GCCAAATCCAGCCGTCTGC 62.056 63.158 0.00 0.00 39.00 4.26
3096 4117 1.797025 GCCGTCTGCTTCACTTTACT 58.203 50.000 0.00 0.00 36.87 2.24
3097 4118 1.461127 GCCGTCTGCTTCACTTTACTG 59.539 52.381 0.00 0.00 36.87 2.74
3098 4119 2.755650 CCGTCTGCTTCACTTTACTGT 58.244 47.619 0.00 0.00 0.00 3.55
3099 4120 3.131396 CCGTCTGCTTCACTTTACTGTT 58.869 45.455 0.00 0.00 0.00 3.16
3100 4121 3.059597 CCGTCTGCTTCACTTTACTGTTG 60.060 47.826 0.00 0.00 0.00 3.33
3101 4122 3.555956 CGTCTGCTTCACTTTACTGTTGT 59.444 43.478 0.00 0.00 0.00 3.32
3102 4123 4.550831 CGTCTGCTTCACTTTACTGTTGTG 60.551 45.833 0.00 0.00 0.00 3.33
3103 4124 3.312421 TCTGCTTCACTTTACTGTTGTGC 59.688 43.478 0.00 0.00 0.00 4.57
3104 4125 3.013219 TGCTTCACTTTACTGTTGTGCA 58.987 40.909 0.00 0.00 0.00 4.57
3105 4126 3.631686 TGCTTCACTTTACTGTTGTGCAT 59.368 39.130 0.00 0.00 0.00 3.96
3106 4127 3.976942 GCTTCACTTTACTGTTGTGCATG 59.023 43.478 0.00 0.00 0.00 4.06
3107 4128 4.539870 CTTCACTTTACTGTTGTGCATGG 58.460 43.478 0.00 0.00 0.00 3.66
3108 4129 3.814625 TCACTTTACTGTTGTGCATGGA 58.185 40.909 0.00 0.00 0.00 3.41
3109 4130 4.397420 TCACTTTACTGTTGTGCATGGAT 58.603 39.130 0.00 0.00 0.00 3.41
3110 4131 4.216042 TCACTTTACTGTTGTGCATGGATG 59.784 41.667 0.00 0.00 0.00 3.51
3111 4132 4.216042 CACTTTACTGTTGTGCATGGATGA 59.784 41.667 0.00 0.00 0.00 2.92
3112 4133 4.456911 ACTTTACTGTTGTGCATGGATGAG 59.543 41.667 0.00 0.00 0.00 2.90
3113 4134 2.574006 ACTGTTGTGCATGGATGAGT 57.426 45.000 0.00 0.00 0.00 3.41
3114 4135 2.867624 ACTGTTGTGCATGGATGAGTT 58.132 42.857 0.00 0.00 0.00 3.01
3115 4136 2.555325 ACTGTTGTGCATGGATGAGTTG 59.445 45.455 0.00 0.00 0.00 3.16
3116 4137 2.815503 CTGTTGTGCATGGATGAGTTGA 59.184 45.455 0.00 0.00 0.00 3.18
3117 4138 3.423749 TGTTGTGCATGGATGAGTTGAT 58.576 40.909 0.00 0.00 0.00 2.57
3118 4139 3.441222 TGTTGTGCATGGATGAGTTGATC 59.559 43.478 0.00 0.00 0.00 2.92
3119 4140 3.639672 TGTGCATGGATGAGTTGATCT 57.360 42.857 0.00 0.00 0.00 2.75
3120 4141 3.275999 TGTGCATGGATGAGTTGATCTG 58.724 45.455 0.00 0.00 0.00 2.90
3121 4142 2.033049 GTGCATGGATGAGTTGATCTGC 59.967 50.000 0.00 0.00 0.00 4.26
3122 4143 1.263484 GCATGGATGAGTTGATCTGCG 59.737 52.381 0.00 0.00 0.00 5.18
3123 4144 2.558378 CATGGATGAGTTGATCTGCGT 58.442 47.619 0.00 0.00 0.00 5.24
3124 4145 2.768253 TGGATGAGTTGATCTGCGTT 57.232 45.000 0.00 0.00 0.00 4.84
3125 4146 3.885724 TGGATGAGTTGATCTGCGTTA 57.114 42.857 0.00 0.00 0.00 3.18
3126 4147 4.406648 TGGATGAGTTGATCTGCGTTAT 57.593 40.909 0.00 0.00 0.00 1.89
3127 4148 4.371786 TGGATGAGTTGATCTGCGTTATC 58.628 43.478 0.00 0.00 0.00 1.75
3128 4149 3.426859 GGATGAGTTGATCTGCGTTATCG 59.573 47.826 0.00 0.00 40.37 2.92
3129 4150 3.503827 TGAGTTGATCTGCGTTATCGT 57.496 42.857 0.00 0.00 39.49 3.73
3130 4151 3.845178 TGAGTTGATCTGCGTTATCGTT 58.155 40.909 0.00 0.00 39.49 3.85
3131 4152 3.857665 TGAGTTGATCTGCGTTATCGTTC 59.142 43.478 0.00 0.00 39.49 3.95
3132 4153 3.845178 AGTTGATCTGCGTTATCGTTCA 58.155 40.909 0.00 0.00 39.49 3.18
3133 4154 3.859961 AGTTGATCTGCGTTATCGTTCAG 59.140 43.478 0.00 0.00 39.49 3.02
3134 4155 2.809446 TGATCTGCGTTATCGTTCAGG 58.191 47.619 0.00 0.00 39.49 3.86
3135 4156 2.425668 TGATCTGCGTTATCGTTCAGGA 59.574 45.455 0.00 0.00 39.49 3.86
3136 4157 3.119280 TGATCTGCGTTATCGTTCAGGAA 60.119 43.478 0.00 0.00 39.49 3.36
3137 4158 3.520290 TCTGCGTTATCGTTCAGGAAT 57.480 42.857 0.00 0.00 39.49 3.01
3138 4159 3.444916 TCTGCGTTATCGTTCAGGAATC 58.555 45.455 0.00 0.00 39.49 2.52
3139 4160 2.190161 TGCGTTATCGTTCAGGAATCG 58.810 47.619 0.00 0.00 39.49 3.34
3140 4161 2.190981 GCGTTATCGTTCAGGAATCGT 58.809 47.619 0.00 0.00 39.49 3.73
3141 4162 2.215812 GCGTTATCGTTCAGGAATCGTC 59.784 50.000 0.00 0.00 39.49 4.20
3142 4163 2.787680 CGTTATCGTTCAGGAATCGTCC 59.212 50.000 0.00 0.00 45.35 4.79
3151 4172 3.551259 GGAATCGTCCACACACCAT 57.449 52.632 0.00 0.00 44.26 3.55
3152 4173 1.369625 GGAATCGTCCACACACCATC 58.630 55.000 0.00 0.00 44.26 3.51
3153 4174 0.999406 GAATCGTCCACACACCATCG 59.001 55.000 0.00 0.00 0.00 3.84
3154 4175 0.320374 AATCGTCCACACACCATCGT 59.680 50.000 0.00 0.00 0.00 3.73
3155 4176 0.389817 ATCGTCCACACACCATCGTG 60.390 55.000 0.00 0.00 46.11 4.35
3166 4187 1.860950 CACCATCGTGTGTATAGCAGC 59.139 52.381 0.00 0.00 35.10 5.25
3167 4188 1.131771 CCATCGTGTGTATAGCAGCG 58.868 55.000 0.00 0.00 0.00 5.18
3168 4189 0.504384 CATCGTGTGTATAGCAGCGC 59.496 55.000 0.00 0.00 0.00 5.92
3169 4190 0.385751 ATCGTGTGTATAGCAGCGCT 59.614 50.000 2.64 2.64 43.41 5.92
3219 4240 8.587608 TGATGAAGAAAGAACAGCCAATATTTT 58.412 29.630 0.00 0.00 0.00 1.82
3221 4242 9.860898 ATGAAGAAAGAACAGCCAATATTTTAC 57.139 29.630 0.00 0.00 0.00 2.01
3222 4243 9.077885 TGAAGAAAGAACAGCCAATATTTTACT 57.922 29.630 0.00 0.00 0.00 2.24
3356 4864 4.276926 GTGTGCTTCCTTGTCTCTTGATTT 59.723 41.667 0.00 0.00 0.00 2.17
3369 4877 7.874940 TGTCTCTTGATTTATCAAACTTGTGG 58.125 34.615 6.61 0.00 45.26 4.17
3401 4913 6.299805 ACTCTTCTCATGCCAAAGTACATA 57.700 37.500 0.00 0.00 0.00 2.29
3402 4914 6.893583 ACTCTTCTCATGCCAAAGTACATAT 58.106 36.000 0.00 0.00 0.00 1.78
3464 4987 1.350351 CCTCCATGATCACATCTCCCC 59.650 57.143 0.00 0.00 34.15 4.81
3467 4990 3.125656 TCCATGATCACATCTCCCCTTT 58.874 45.455 0.00 0.00 34.15 3.11
3512 5040 7.493743 CATTCTCCAAAAGAGTGGATCATAG 57.506 40.000 0.00 0.00 46.66 2.23
3604 5149 4.156008 GCAATCACAGGTTAGTTTAGTGGG 59.844 45.833 0.00 0.00 0.00 4.61
3694 5239 1.368209 CATGCACCCAAAGCAAGCA 59.632 52.632 0.00 0.00 46.27 3.91
3697 5245 1.592400 GCACCCAAAGCAAGCACAC 60.592 57.895 0.00 0.00 0.00 3.82
3715 5266 6.947464 AGCACACAGAGTAGGTAATTATTGT 58.053 36.000 0.00 0.00 0.00 2.71
3716 5267 7.394816 AGCACACAGAGTAGGTAATTATTGTT 58.605 34.615 0.00 0.00 0.00 2.83
3717 5268 8.537016 AGCACACAGAGTAGGTAATTATTGTTA 58.463 33.333 0.00 0.00 0.00 2.41
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
1 2 5.566429 CGATATGGATTGAGAGGTTGAGAGG 60.566 48.000 0.00 0.00 0.00 3.69
6 7 6.035368 AGATCGATATGGATTGAGAGGTTG 57.965 41.667 0.00 0.00 0.00 3.77
7 8 6.678568 AAGATCGATATGGATTGAGAGGTT 57.321 37.500 0.00 0.00 0.00 3.50
8 9 6.153680 GGTAAGATCGATATGGATTGAGAGGT 59.846 42.308 0.00 0.00 0.00 3.85
9 10 6.153510 TGGTAAGATCGATATGGATTGAGAGG 59.846 42.308 0.00 0.00 0.00 3.69
10 11 7.032580 GTGGTAAGATCGATATGGATTGAGAG 58.967 42.308 0.00 0.00 0.00 3.20
12 13 5.802451 CGTGGTAAGATCGATATGGATTGAG 59.198 44.000 0.00 0.00 0.00 3.02
20 686 5.977489 TGGATTCGTGGTAAGATCGATAT 57.023 39.130 0.00 0.00 33.72 1.63
41 707 6.118170 ACAACCCAGAGAGAATGTGATATTG 58.882 40.000 0.00 0.00 0.00 1.90
58 724 1.403647 CGAATCACTAGCGACAACCCA 60.404 52.381 0.00 0.00 0.00 4.51
82 748 1.317613 TGGTTGCTTCATCTTTGCGT 58.682 45.000 0.00 0.00 0.00 5.24
106 773 0.745845 ATGAGGTGGAGATTGTGCGC 60.746 55.000 0.00 0.00 0.00 6.09
144 812 4.030452 GAGGCTGTGGTTGCGTGC 62.030 66.667 0.00 0.00 0.00 5.34
186 854 1.465387 CGGTCGATTCGGGATAGAGAG 59.535 57.143 6.18 0.00 0.00 3.20
188 856 0.109689 GCGGTCGATTCGGGATAGAG 60.110 60.000 6.18 0.00 0.00 2.43
195 863 2.358193 TATGGTGGCGGTCGATTCGG 62.358 60.000 6.18 0.00 0.00 4.30
206 874 0.030369 CGACCTACGACTATGGTGGC 59.970 60.000 0.00 0.00 45.77 5.01
265 933 2.202974 GTTACCCGGTGGCGGATC 60.203 66.667 0.00 0.00 33.59 3.36
270 938 2.360726 CCTTGGTTACCCGGTGGC 60.361 66.667 0.00 0.00 33.59 5.01
306 984 6.293735 GGAAATGTTTCGTGTGGTTATCTTGA 60.294 38.462 0.00 0.00 38.06 3.02
329 1007 6.375736 TCTTTTGTGTGTGTAGAAATGTTGGA 59.624 34.615 0.00 0.00 0.00 3.53
331 1009 8.459521 TTTCTTTTGTGTGTGTAGAAATGTTG 57.540 30.769 0.00 0.00 31.82 3.33
340 1018 7.921214 TGTGTTTTTCTTTCTTTTGTGTGTGTA 59.079 29.630 0.00 0.00 0.00 2.90
357 1035 7.867445 TGTGTTTCTTCTCTTTGTGTTTTTC 57.133 32.000 0.00 0.00 0.00 2.29
367 1047 2.887152 GGGTGCATGTGTTTCTTCTCTT 59.113 45.455 0.00 0.00 0.00 2.85
416 1096 0.543883 AAGAGAGGAGTGGAGCTGCA 60.544 55.000 2.72 2.72 38.09 4.41
449 1134 8.964420 TTTCGCCTCTAATAATTTGTTTTCTG 57.036 30.769 0.00 0.00 0.00 3.02
456 1141 7.308229 CCCTCTCATTTCGCCTCTAATAATTTG 60.308 40.741 0.00 0.00 0.00 2.32
461 1146 4.480115 TCCCTCTCATTTCGCCTCTAATA 58.520 43.478 0.00 0.00 0.00 0.98
462 1147 3.309296 TCCCTCTCATTTCGCCTCTAAT 58.691 45.455 0.00 0.00 0.00 1.73
464 1149 2.454336 TCCCTCTCATTTCGCCTCTA 57.546 50.000 0.00 0.00 0.00 2.43
468 1153 0.107459 AGCTTCCCTCTCATTTCGCC 60.107 55.000 0.00 0.00 0.00 5.54
469 1154 2.205911 GTAGCTTCCCTCTCATTTCGC 58.794 52.381 0.00 0.00 0.00 4.70
508 1193 2.746277 CGGGTCAAAAGGAGGGCG 60.746 66.667 0.00 0.00 0.00 6.13
528 1213 2.691571 TTTTTGTGTCGCTGCGGTA 58.308 47.368 23.03 8.65 0.00 4.02
544 1229 3.386402 TCCTCCGCTTTCCAATTGTTTTT 59.614 39.130 4.43 0.00 0.00 1.94
554 1239 0.393132 CTTTCCCTCCTCCGCTTTCC 60.393 60.000 0.00 0.00 0.00 3.13
566 1251 4.226384 ACAGAAAAATGCCTTCTTTCCCT 58.774 39.130 0.00 0.00 30.58 4.20
568 1253 7.494298 TGTTTAACAGAAAAATGCCTTCTTTCC 59.506 33.333 0.00 0.00 30.58 3.13
576 1261 5.181056 CCCCATTGTTTAACAGAAAAATGCC 59.819 40.000 0.00 0.00 0.00 4.40
585 1270 3.979101 ATTGCCCCCATTGTTTAACAG 57.021 42.857 0.00 0.00 0.00 3.16
587 1272 3.776340 CGTATTGCCCCCATTGTTTAAC 58.224 45.455 0.00 0.00 0.00 2.01
588 1273 2.166664 GCGTATTGCCCCCATTGTTTAA 59.833 45.455 0.00 0.00 37.76 1.52
630 1320 2.290641 CTCGCCTTTCTCTCTCTAGCTC 59.709 54.545 0.00 0.00 0.00 4.09
679 1390 3.073356 AGATAAGGGAGGTAGGAGACGAG 59.927 52.174 0.00 0.00 0.00 4.18
680 1391 3.054576 AGATAAGGGAGGTAGGAGACGA 58.945 50.000 0.00 0.00 0.00 4.20
681 1392 3.073356 AGAGATAAGGGAGGTAGGAGACG 59.927 52.174 0.00 0.00 0.00 4.18
682 1393 4.734843 AGAGATAAGGGAGGTAGGAGAC 57.265 50.000 0.00 0.00 0.00 3.36
683 1394 5.195960 TGAAAGAGATAAGGGAGGTAGGAGA 59.804 44.000 0.00 0.00 0.00 3.71
724 1439 1.073098 GAGGGGGTGGAGAAAAGGAA 58.927 55.000 0.00 0.00 0.00 3.36
735 1450 4.354943 AGGTGGAGGGAGGGGGTG 62.355 72.222 0.00 0.00 0.00 4.61
736 1451 4.026357 GAGGTGGAGGGAGGGGGT 62.026 72.222 0.00 0.00 0.00 4.95
737 1452 4.825679 GGAGGTGGAGGGAGGGGG 62.826 77.778 0.00 0.00 0.00 5.40
738 1453 2.865183 AATGGAGGTGGAGGGAGGGG 62.865 65.000 0.00 0.00 0.00 4.79
739 1454 0.030092 TAATGGAGGTGGAGGGAGGG 60.030 60.000 0.00 0.00 0.00 4.30
740 1455 2.124560 ATAATGGAGGTGGAGGGAGG 57.875 55.000 0.00 0.00 0.00 4.30
741 1456 2.373502 GGAATAATGGAGGTGGAGGGAG 59.626 54.545 0.00 0.00 0.00 4.30
742 1457 2.418669 GGAATAATGGAGGTGGAGGGA 58.581 52.381 0.00 0.00 0.00 4.20
743 1458 1.425448 GGGAATAATGGAGGTGGAGGG 59.575 57.143 0.00 0.00 0.00 4.30
780 1503 4.274978 GGTATATGTAGAGAGGGAGAGGC 58.725 52.174 0.00 0.00 0.00 4.70
807 1530 1.196012 GGTAGTGTGGAAGGGAGGAG 58.804 60.000 0.00 0.00 0.00 3.69
808 1531 0.252558 GGGTAGTGTGGAAGGGAGGA 60.253 60.000 0.00 0.00 0.00 3.71
811 1534 0.838987 GGTGGGTAGTGTGGAAGGGA 60.839 60.000 0.00 0.00 0.00 4.20
814 1537 1.002087 GTGAGGTGGGTAGTGTGGAAG 59.998 57.143 0.00 0.00 0.00 3.46
847 1570 2.258748 GAGGGGAAAGAAGCGAGGGG 62.259 65.000 0.00 0.00 0.00 4.79
853 1576 1.352687 ACAAGAGGAGGGGAAAGAAGC 59.647 52.381 0.00 0.00 0.00 3.86
854 1577 2.026729 GGACAAGAGGAGGGGAAAGAAG 60.027 54.545 0.00 0.00 0.00 2.85
856 1579 1.657804 GGACAAGAGGAGGGGAAAGA 58.342 55.000 0.00 0.00 0.00 2.52
857 1580 0.621082 GGGACAAGAGGAGGGGAAAG 59.379 60.000 0.00 0.00 0.00 2.62
858 1581 0.845102 GGGGACAAGAGGAGGGGAAA 60.845 60.000 0.00 0.00 0.00 3.13
859 1582 1.229853 GGGGACAAGAGGAGGGGAA 60.230 63.158 0.00 0.00 0.00 3.97
860 1583 2.454941 GGGGACAAGAGGAGGGGA 59.545 66.667 0.00 0.00 0.00 4.81
877 1600 5.869344 TCTTCCAGTACGTTCTTGATTGATG 59.131 40.000 0.00 0.00 0.00 3.07
1599 2614 4.373116 TTGAGGTCCGGCAGCGTC 62.373 66.667 0.00 1.29 0.00 5.19
2235 3250 2.625823 CGGCATGTTTCTTGCGGGT 61.626 57.895 0.00 0.00 41.07 5.28
2241 3256 2.423577 GTGTAGTCCGGCATGTTTCTT 58.576 47.619 0.00 0.00 0.00 2.52
2280 3295 3.785859 GAGAGCATGGCCGGGTCA 61.786 66.667 23.28 2.64 35.30 4.02
2517 3532 2.125912 GGCGACATGAGTGAGCGT 60.126 61.111 0.00 0.00 34.89 5.07
2523 3538 4.760047 GTGGCCGGCGACATGAGT 62.760 66.667 33.44 0.00 0.00 3.41
2556 3571 1.524002 CCAGTCGGTGAGCATGGAT 59.476 57.895 0.00 0.00 32.55 3.41
2640 3655 3.385384 TGCAGCTCGTCTCCCTGG 61.385 66.667 0.00 0.00 0.00 4.45
2942 3963 8.019669 AGCATATATGTACGTACTAAAGAACCG 58.980 37.037 25.12 7.90 0.00 4.44
3010 4031 0.598065 AGCAGTTTCGTTTGGGCATC 59.402 50.000 0.00 0.00 0.00 3.91
3011 4032 0.314935 CAGCAGTTTCGTTTGGGCAT 59.685 50.000 0.00 0.00 0.00 4.40
3012 4033 1.034838 ACAGCAGTTTCGTTTGGGCA 61.035 50.000 0.00 0.00 0.00 5.36
3013 4034 0.948678 TACAGCAGTTTCGTTTGGGC 59.051 50.000 0.00 0.00 0.00 5.36
3014 4035 3.314080 TCTTTACAGCAGTTTCGTTTGGG 59.686 43.478 0.00 0.00 0.00 4.12
3015 4036 4.279659 GTCTTTACAGCAGTTTCGTTTGG 58.720 43.478 0.00 0.00 0.00 3.28
3016 4037 3.960002 CGTCTTTACAGCAGTTTCGTTTG 59.040 43.478 0.00 0.00 0.00 2.93
3017 4038 3.866910 TCGTCTTTACAGCAGTTTCGTTT 59.133 39.130 0.00 0.00 0.00 3.60
3018 4039 3.450578 TCGTCTTTACAGCAGTTTCGTT 58.549 40.909 0.00 0.00 0.00 3.85
3019 4040 3.088194 TCGTCTTTACAGCAGTTTCGT 57.912 42.857 0.00 0.00 0.00 3.85
3020 4041 4.857588 AGTATCGTCTTTACAGCAGTTTCG 59.142 41.667 0.00 0.00 0.00 3.46
3021 4042 5.444745 GCAGTATCGTCTTTACAGCAGTTTC 60.445 44.000 0.00 0.00 33.67 2.78
3022 4043 4.389077 GCAGTATCGTCTTTACAGCAGTTT 59.611 41.667 0.00 0.00 33.67 2.66
3023 4044 3.927142 GCAGTATCGTCTTTACAGCAGTT 59.073 43.478 0.00 0.00 33.67 3.16
3024 4045 3.512680 GCAGTATCGTCTTTACAGCAGT 58.487 45.455 0.00 0.00 33.67 4.40
3025 4046 2.531912 CGCAGTATCGTCTTTACAGCAG 59.468 50.000 0.00 0.00 33.22 4.24
3026 4047 2.094906 ACGCAGTATCGTCTTTACAGCA 60.095 45.455 0.00 0.00 41.94 4.41
3027 4048 2.279136 CACGCAGTATCGTCTTTACAGC 59.721 50.000 0.00 0.00 41.61 4.40
3028 4049 2.279136 GCACGCAGTATCGTCTTTACAG 59.721 50.000 0.00 0.00 41.61 2.74
3029 4050 2.256174 GCACGCAGTATCGTCTTTACA 58.744 47.619 0.00 0.00 41.61 2.41
3030 4051 2.027688 GTGCACGCAGTATCGTCTTTAC 59.972 50.000 0.00 0.00 41.61 2.01
3031 4052 2.256174 GTGCACGCAGTATCGTCTTTA 58.744 47.619 0.00 0.00 41.61 1.85
3032 4053 1.068474 GTGCACGCAGTATCGTCTTT 58.932 50.000 0.00 0.00 41.61 2.52
3033 4054 1.071019 CGTGCACGCAGTATCGTCTT 61.071 55.000 28.16 0.00 41.61 3.01
3034 4055 1.514228 CGTGCACGCAGTATCGTCT 60.514 57.895 28.16 0.00 41.61 4.18
3035 4056 1.513373 TCGTGCACGCAGTATCGTC 60.513 57.895 33.63 0.00 41.61 4.20
3036 4057 1.800315 GTCGTGCACGCAGTATCGT 60.800 57.895 33.63 0.00 41.61 3.73
3037 4058 1.341369 TTGTCGTGCACGCAGTATCG 61.341 55.000 33.63 8.67 41.61 2.92
3038 4059 0.366871 CTTGTCGTGCACGCAGTATC 59.633 55.000 33.63 17.93 41.61 2.24
3039 4060 1.014044 CCTTGTCGTGCACGCAGTAT 61.014 55.000 33.63 0.00 41.61 2.12
3040 4061 1.663388 CCTTGTCGTGCACGCAGTA 60.663 57.895 33.63 14.65 41.61 2.74
3042 4063 2.661537 TCCTTGTCGTGCACGCAG 60.662 61.111 33.63 25.63 39.60 5.18
3043 4064 2.661537 CTCCTTGTCGTGCACGCA 60.662 61.111 33.63 28.85 39.60 5.24
3044 4065 2.355837 TCTCCTTGTCGTGCACGC 60.356 61.111 33.63 26.73 39.60 5.34
3045 4066 2.365068 CGTCTCCTTGTCGTGCACG 61.365 63.158 32.76 32.76 41.45 5.34
3046 4067 1.007734 TCGTCTCCTTGTCGTGCAC 60.008 57.895 6.82 6.82 0.00 4.57
3047 4068 1.007734 GTCGTCTCCTTGTCGTGCA 60.008 57.895 0.00 0.00 0.00 4.57
3048 4069 2.081212 CGTCGTCTCCTTGTCGTGC 61.081 63.158 0.00 0.00 0.00 5.34
3049 4070 1.442184 CCGTCGTCTCCTTGTCGTG 60.442 63.158 0.00 0.00 0.00 4.35
3050 4071 2.952245 CCGTCGTCTCCTTGTCGT 59.048 61.111 0.00 0.00 0.00 4.34
3051 4072 2.504244 GCCGTCGTCTCCTTGTCG 60.504 66.667 0.00 0.00 0.00 4.35
3052 4073 2.126031 GGCCGTCGTCTCCTTGTC 60.126 66.667 0.00 0.00 0.00 3.18
3053 4074 2.035237 TTTGGCCGTCGTCTCCTTGT 62.035 55.000 0.00 0.00 0.00 3.16
3054 4075 0.673644 ATTTGGCCGTCGTCTCCTTG 60.674 55.000 0.00 0.00 0.00 3.61
3055 4076 0.391263 GATTTGGCCGTCGTCTCCTT 60.391 55.000 0.00 0.00 0.00 3.36
3056 4077 1.218316 GATTTGGCCGTCGTCTCCT 59.782 57.895 0.00 0.00 0.00 3.69
3057 4078 1.814169 GGATTTGGCCGTCGTCTCC 60.814 63.158 0.00 0.00 0.00 3.71
3058 4079 1.079405 TGGATTTGGCCGTCGTCTC 60.079 57.895 0.00 0.00 0.00 3.36
3059 4080 1.079127 CTGGATTTGGCCGTCGTCT 60.079 57.895 0.00 0.00 0.00 4.18
3060 4081 2.750888 GCTGGATTTGGCCGTCGTC 61.751 63.158 0.00 0.00 0.00 4.20
3061 4082 2.746277 GCTGGATTTGGCCGTCGT 60.746 61.111 0.00 0.00 0.00 4.34
3062 4083 3.508840 GGCTGGATTTGGCCGTCG 61.509 66.667 0.00 0.00 38.91 5.12
3066 4087 2.044946 AGACGGCTGGATTTGGCC 60.045 61.111 0.00 0.00 44.43 5.36
3067 4088 3.056313 GCAGACGGCTGGATTTGGC 62.056 63.158 22.33 0.00 42.53 4.52
3068 4089 3.190878 GCAGACGGCTGGATTTGG 58.809 61.111 22.33 0.00 42.53 3.28
3077 4098 1.461127 CAGTAAAGTGAAGCAGACGGC 59.539 52.381 0.00 0.00 45.30 5.68
3078 4099 2.755650 ACAGTAAAGTGAAGCAGACGG 58.244 47.619 0.00 0.00 0.00 4.79
3079 4100 3.555956 ACAACAGTAAAGTGAAGCAGACG 59.444 43.478 0.00 0.00 0.00 4.18
3080 4101 4.786609 GCACAACAGTAAAGTGAAGCAGAC 60.787 45.833 0.00 0.00 35.33 3.51
3081 4102 3.312421 GCACAACAGTAAAGTGAAGCAGA 59.688 43.478 0.00 0.00 35.33 4.26
3082 4103 3.065233 TGCACAACAGTAAAGTGAAGCAG 59.935 43.478 0.00 0.00 35.33 4.24
3083 4104 3.013219 TGCACAACAGTAAAGTGAAGCA 58.987 40.909 0.00 0.00 35.33 3.91
3084 4105 3.691049 TGCACAACAGTAAAGTGAAGC 57.309 42.857 0.00 0.00 35.33 3.86
3085 4106 4.275689 TCCATGCACAACAGTAAAGTGAAG 59.724 41.667 0.00 0.00 35.33 3.02
3086 4107 4.203226 TCCATGCACAACAGTAAAGTGAA 58.797 39.130 0.00 0.00 35.33 3.18
3087 4108 3.814625 TCCATGCACAACAGTAAAGTGA 58.185 40.909 0.00 0.00 35.33 3.41
3088 4109 4.216042 TCATCCATGCACAACAGTAAAGTG 59.784 41.667 0.00 0.00 36.39 3.16
3089 4110 4.397420 TCATCCATGCACAACAGTAAAGT 58.603 39.130 0.00 0.00 0.00 2.66
3090 4111 4.456911 ACTCATCCATGCACAACAGTAAAG 59.543 41.667 0.00 0.00 0.00 1.85
3091 4112 4.397420 ACTCATCCATGCACAACAGTAAA 58.603 39.130 0.00 0.00 0.00 2.01
3092 4113 4.019792 ACTCATCCATGCACAACAGTAA 57.980 40.909 0.00 0.00 0.00 2.24
3093 4114 3.701205 ACTCATCCATGCACAACAGTA 57.299 42.857 0.00 0.00 0.00 2.74
3094 4115 2.555325 CAACTCATCCATGCACAACAGT 59.445 45.455 0.00 0.00 0.00 3.55
3095 4116 2.815503 TCAACTCATCCATGCACAACAG 59.184 45.455 0.00 0.00 0.00 3.16
3096 4117 2.861274 TCAACTCATCCATGCACAACA 58.139 42.857 0.00 0.00 0.00 3.33
3097 4118 3.693085 AGATCAACTCATCCATGCACAAC 59.307 43.478 0.00 0.00 0.00 3.32
3098 4119 3.692593 CAGATCAACTCATCCATGCACAA 59.307 43.478 0.00 0.00 0.00 3.33
3099 4120 3.275999 CAGATCAACTCATCCATGCACA 58.724 45.455 0.00 0.00 0.00 4.57
3100 4121 2.033049 GCAGATCAACTCATCCATGCAC 59.967 50.000 0.00 0.00 32.79 4.57
3101 4122 2.294979 GCAGATCAACTCATCCATGCA 58.705 47.619 0.00 0.00 32.79 3.96
3102 4123 1.263484 CGCAGATCAACTCATCCATGC 59.737 52.381 0.00 0.00 0.00 4.06
3103 4124 2.558378 ACGCAGATCAACTCATCCATG 58.442 47.619 0.00 0.00 0.00 3.66
3104 4125 2.996249 ACGCAGATCAACTCATCCAT 57.004 45.000 0.00 0.00 0.00 3.41
3105 4126 2.768253 AACGCAGATCAACTCATCCA 57.232 45.000 0.00 0.00 0.00 3.41
3106 4127 3.426859 CGATAACGCAGATCAACTCATCC 59.573 47.826 0.00 0.00 0.00 3.51
3107 4128 4.045104 ACGATAACGCAGATCAACTCATC 58.955 43.478 0.00 0.00 43.96 2.92
3108 4129 4.046938 ACGATAACGCAGATCAACTCAT 57.953 40.909 0.00 0.00 43.96 2.90
3109 4130 3.503827 ACGATAACGCAGATCAACTCA 57.496 42.857 0.00 0.00 43.96 3.41
3110 4131 3.857665 TGAACGATAACGCAGATCAACTC 59.142 43.478 0.00 0.00 43.96 3.01
3111 4132 3.845178 TGAACGATAACGCAGATCAACT 58.155 40.909 0.00 0.00 43.96 3.16
3112 4133 3.000322 CCTGAACGATAACGCAGATCAAC 60.000 47.826 0.00 0.00 43.96 3.18
3113 4134 3.119280 TCCTGAACGATAACGCAGATCAA 60.119 43.478 0.00 0.00 43.96 2.57
3114 4135 2.425668 TCCTGAACGATAACGCAGATCA 59.574 45.455 0.00 0.00 43.96 2.92
3115 4136 3.079960 TCCTGAACGATAACGCAGATC 57.920 47.619 0.00 0.00 43.96 2.75
3116 4137 3.520290 TTCCTGAACGATAACGCAGAT 57.480 42.857 0.00 0.00 43.96 2.90
3117 4138 3.444916 GATTCCTGAACGATAACGCAGA 58.555 45.455 0.00 0.00 43.96 4.26
3118 4139 2.216488 CGATTCCTGAACGATAACGCAG 59.784 50.000 0.00 0.00 43.96 5.18
3119 4140 2.190161 CGATTCCTGAACGATAACGCA 58.810 47.619 0.00 0.00 43.96 5.24
3120 4141 2.190981 ACGATTCCTGAACGATAACGC 58.809 47.619 0.00 0.00 43.96 4.84
3121 4142 2.787680 GGACGATTCCTGAACGATAACG 59.212 50.000 0.00 0.00 41.19 3.18
3122 4143 3.550678 GTGGACGATTCCTGAACGATAAC 59.449 47.826 0.00 0.00 43.31 1.89
3123 4144 3.193903 TGTGGACGATTCCTGAACGATAA 59.806 43.478 0.00 0.00 43.31 1.75
3124 4145 2.756207 TGTGGACGATTCCTGAACGATA 59.244 45.455 0.00 0.00 43.31 2.92
3125 4146 1.548719 TGTGGACGATTCCTGAACGAT 59.451 47.619 0.00 0.00 43.31 3.73
3126 4147 0.963225 TGTGGACGATTCCTGAACGA 59.037 50.000 0.00 0.00 43.31 3.85
3127 4148 1.068474 GTGTGGACGATTCCTGAACG 58.932 55.000 0.00 0.00 43.31 3.95
3128 4149 1.798813 GTGTGTGGACGATTCCTGAAC 59.201 52.381 0.00 0.00 43.31 3.18
3129 4150 1.270625 GGTGTGTGGACGATTCCTGAA 60.271 52.381 0.00 0.00 43.31 3.02
3130 4151 0.320374 GGTGTGTGGACGATTCCTGA 59.680 55.000 0.00 0.00 43.31 3.86
3131 4152 0.034756 TGGTGTGTGGACGATTCCTG 59.965 55.000 0.00 0.00 43.31 3.86
3132 4153 0.984230 ATGGTGTGTGGACGATTCCT 59.016 50.000 0.00 0.00 43.31 3.36
3133 4154 1.369625 GATGGTGTGTGGACGATTCC 58.630 55.000 0.00 0.00 43.19 3.01
3134 4155 0.999406 CGATGGTGTGTGGACGATTC 59.001 55.000 0.00 0.00 0.00 2.52
3135 4156 0.320374 ACGATGGTGTGTGGACGATT 59.680 50.000 0.00 0.00 0.00 3.34
3136 4157 0.389817 CACGATGGTGTGTGGACGAT 60.390 55.000 0.00 0.00 39.38 3.73
3137 4158 1.006688 CACGATGGTGTGTGGACGA 60.007 57.895 0.00 0.00 39.38 4.20
3138 4159 3.549467 CACGATGGTGTGTGGACG 58.451 61.111 0.00 0.00 39.38 4.79
3147 4168 1.536072 CGCTGCTATACACACGATGGT 60.536 52.381 0.00 0.00 0.00 3.55
3148 4169 1.131771 CGCTGCTATACACACGATGG 58.868 55.000 0.00 0.00 0.00 3.51
3149 4170 0.504384 GCGCTGCTATACACACGATG 59.496 55.000 0.00 0.00 0.00 3.84
3150 4171 0.385751 AGCGCTGCTATACACACGAT 59.614 50.000 10.39 0.00 36.99 3.73
3151 4172 0.525455 CAGCGCTGCTATACACACGA 60.525 55.000 26.68 0.00 36.40 4.35
3152 4173 0.525455 TCAGCGCTGCTATACACACG 60.525 55.000 32.44 4.42 36.40 4.49
3153 4174 1.524355 CATCAGCGCTGCTATACACAC 59.476 52.381 32.44 0.00 36.40 3.82
3154 4175 1.856802 CATCAGCGCTGCTATACACA 58.143 50.000 32.44 13.24 36.40 3.72
3155 4176 0.510359 GCATCAGCGCTGCTATACAC 59.490 55.000 32.44 12.84 36.40 2.90
3156 4177 0.601046 GGCATCAGCGCTGCTATACA 60.601 55.000 32.44 14.85 43.41 2.29
3157 4178 2.157421 GGCATCAGCGCTGCTATAC 58.843 57.895 32.44 15.91 43.41 1.47
3158 4179 4.681421 GGCATCAGCGCTGCTATA 57.319 55.556 32.44 16.07 43.41 1.31
3166 4187 2.045045 TCCCTTTGGGCATCAGCG 60.045 61.111 0.00 0.00 43.94 5.18
3167 4188 2.421399 GCTCCCTTTGGGCATCAGC 61.421 63.158 0.00 0.00 43.94 4.26
3168 4189 1.755783 GGCTCCCTTTGGGCATCAG 60.756 63.158 0.00 0.00 43.94 2.90
3169 4190 1.803453 AAGGCTCCCTTTGGGCATCA 61.803 55.000 0.00 0.00 41.69 3.07
3219 4240 3.013984 AGGGAAGGGGGAAAAGAAGTA 57.986 47.619 0.00 0.00 0.00 2.24
3220 4241 1.848174 AGGGAAGGGGGAAAAGAAGT 58.152 50.000 0.00 0.00 0.00 3.01
3221 4242 2.808919 GAAGGGAAGGGGGAAAAGAAG 58.191 52.381 0.00 0.00 0.00 2.85
3222 4243 1.074889 CGAAGGGAAGGGGGAAAAGAA 59.925 52.381 0.00 0.00 0.00 2.52
3369 4877 7.792374 TTGGCATGAGAAGAGTACAATATTC 57.208 36.000 0.00 0.00 0.00 1.75
3401 4913 2.821969 GCTGGTGAACACTTCCATTGAT 59.178 45.455 4.96 0.00 0.00 2.57
3402 4914 2.229792 GCTGGTGAACACTTCCATTGA 58.770 47.619 4.96 0.00 0.00 2.57
3464 4987 7.784037 TGGAATGGACATGGAATCAAATAAAG 58.216 34.615 0.00 0.00 0.00 1.85
3467 4990 7.785985 AGAATGGAATGGACATGGAATCAAATA 59.214 33.333 0.00 0.00 0.00 1.40
3512 5040 3.665745 ATCAAATTGTGCCAGTGGTTC 57.334 42.857 11.74 4.93 0.00 3.62
3604 5149 2.182842 GTGCATGACGCCTCCATCC 61.183 63.158 0.00 0.00 41.33 3.51
3715 5266 2.356741 GCCTAACCCACAGCCAGAATAA 60.357 50.000 0.00 0.00 0.00 1.40
3716 5267 1.211949 GCCTAACCCACAGCCAGAATA 59.788 52.381 0.00 0.00 0.00 1.75
3717 5268 0.034089 GCCTAACCCACAGCCAGAAT 60.034 55.000 0.00 0.00 0.00 2.40


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

AutoCloner maintained by Alex Coulton.