Multiple sequence alignment - TraesCS5B01G224300

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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 TraesCS5B01G224300 chr5B 100.000 3561 0 0 1 3561 399780179 399776619 0.000000e+00 6577.0
1 TraesCS5B01G224300 chr5B 95.000 100 5 0 1167 1266 446421600 446421501 1.320000e-34 158.0
2 TraesCS5B01G224300 chr5B 93.204 103 7 0 1164 1266 447194770 447194872 6.160000e-33 152.0
3 TraesCS5B01G224300 chr5D 91.399 2953 146 54 294 3185 340746854 340743949 0.000000e+00 3947.0
4 TraesCS5B01G224300 chr5D 85.768 267 18 5 3295 3561 340743849 340743603 7.580000e-67 265.0
5 TraesCS5B01G224300 chr5A 91.255 2390 105 47 509 2832 441675416 441673065 0.000000e+00 3160.0
6 TraesCS5B01G224300 chr5A 88.321 411 14 8 130 512 441675849 441675445 2.500000e-126 462.0
7 TraesCS5B01G224300 chr5A 84.564 149 11 6 3049 3195 441671973 441671835 1.720000e-28 137.0
8 TraesCS5B01G224300 chr5A 100.000 38 0 0 2960 2997 441673027 441672990 1.770000e-08 71.3
9 TraesCS5B01G224300 chr5A 95.349 43 2 0 1800 1842 364148068 364148026 6.380000e-08 69.4
10 TraesCS5B01G224300 chr5A 100.000 31 0 0 75 105 441675881 441675851 1.380000e-04 58.4
11 TraesCS5B01G224300 chr1D 91.031 223 17 2 1728 1948 422597236 422597457 7.470000e-77 298.0
12 TraesCS5B01G224300 chr2D 92.903 155 11 0 1149 1303 624648667 624648821 3.580000e-55 226.0
13 TraesCS5B01G224300 chr2D 89.831 177 12 5 1774 1946 624648983 624649157 4.630000e-54 222.0
14 TraesCS5B01G224300 chr2D 97.727 44 1 0 1637 1680 624648884 624648927 3.810000e-10 76.8
15 TraesCS5B01G224300 chr7A 92.742 124 9 0 1203 1326 491964348 491964471 2.820000e-41 180.0
16 TraesCS5B01G224300 chr6D 91.525 118 8 1 1149 1266 409578590 409578705 1.020000e-35 161.0
17 TraesCS5B01G224300 chr6B 94.175 103 6 0 1164 1266 142988850 142988748 1.320000e-34 158.0
18 TraesCS5B01G224300 chr7D 91.743 109 9 0 1158 1266 609272691 609272583 6.160000e-33 152.0
19 TraesCS5B01G224300 chr4A 92.982 57 3 1 1376 1431 684087567 684087623 8.190000e-12 82.4


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 TraesCS5B01G224300 chr5B 399776619 399780179 3560 True 6577.00 6577 100.0000 1 3561 1 chr5B.!!$R1 3560
1 TraesCS5B01G224300 chr5D 340743603 340746854 3251 True 2106.00 3947 88.5835 294 3561 2 chr5D.!!$R1 3267
2 TraesCS5B01G224300 chr5A 441671835 441675881 4046 True 777.74 3160 92.8280 75 3195 5 chr5A.!!$R2 3120

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
810 890 0.257328 TTTTATCCTGGCCGCATGGA 59.743 50.0 8.66 8.66 37.49 3.41 F
860 941 0.320374 CCTGCCTTTCACACGGAGTA 59.680 55.0 0.00 0.00 41.61 2.59 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1867 1971 0.534412 CGATGGAGAGGTTGAGCAGT 59.466 55.0 0.0 0.0 0.0 4.40 R
2716 2847 1.165270 GTTAGCCATTGTTGCCGACT 58.835 50.0 0.0 0.0 0.0 4.18 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
24 25 6.829229 TGTACTCGTTTTTCTCTCCTATCA 57.171 37.500 0.00 0.00 0.00 2.15
25 26 7.223260 TGTACTCGTTTTTCTCTCCTATCAA 57.777 36.000 0.00 0.00 0.00 2.57
26 27 7.837863 TGTACTCGTTTTTCTCTCCTATCAAT 58.162 34.615 0.00 0.00 0.00 2.57
27 28 7.759886 TGTACTCGTTTTTCTCTCCTATCAATG 59.240 37.037 0.00 0.00 0.00 2.82
28 29 5.582665 ACTCGTTTTTCTCTCCTATCAATGC 59.417 40.000 0.00 0.00 0.00 3.56
29 30 5.487433 TCGTTTTTCTCTCCTATCAATGCA 58.513 37.500 0.00 0.00 0.00 3.96
30 31 5.937540 TCGTTTTTCTCTCCTATCAATGCAA 59.062 36.000 0.00 0.00 0.00 4.08
31 32 6.599244 TCGTTTTTCTCTCCTATCAATGCAAT 59.401 34.615 0.00 0.00 0.00 3.56
32 33 6.690098 CGTTTTTCTCTCCTATCAATGCAATG 59.310 38.462 0.00 0.00 0.00 2.82
33 34 7.414429 CGTTTTTCTCTCCTATCAATGCAATGA 60.414 37.037 6.97 6.97 0.00 2.57
34 35 8.411683 GTTTTTCTCTCCTATCAATGCAATGAT 58.588 33.333 20.55 20.55 42.52 2.45
35 36 9.631257 TTTTTCTCTCCTATCAATGCAATGATA 57.369 29.630 20.58 20.58 40.44 2.15
36 37 8.613060 TTTCTCTCCTATCAATGCAATGATAC 57.387 34.615 18.52 0.00 40.44 2.24
37 38 6.393171 TCTCTCCTATCAATGCAATGATACG 58.607 40.000 18.52 15.02 40.44 3.06
38 39 4.931601 TCTCCTATCAATGCAATGATACGC 59.068 41.667 18.52 0.00 40.44 4.42
39 40 4.002982 TCCTATCAATGCAATGATACGCC 58.997 43.478 18.52 0.00 40.44 5.68
40 41 3.752747 CCTATCAATGCAATGATACGCCA 59.247 43.478 18.52 2.61 40.44 5.69
41 42 4.397103 CCTATCAATGCAATGATACGCCAT 59.603 41.667 18.52 0.00 40.44 4.40
42 43 3.902261 TCAATGCAATGATACGCCATC 57.098 42.857 0.00 0.00 0.00 3.51
43 44 3.479489 TCAATGCAATGATACGCCATCT 58.521 40.909 0.00 0.00 34.46 2.90
44 45 3.884693 TCAATGCAATGATACGCCATCTT 59.115 39.130 0.00 0.00 34.46 2.40
45 46 5.062528 TCAATGCAATGATACGCCATCTTA 58.937 37.500 0.00 0.00 34.46 2.10
46 47 5.179929 TCAATGCAATGATACGCCATCTTAG 59.820 40.000 0.00 0.00 34.46 2.18
47 48 4.071961 TGCAATGATACGCCATCTTAGT 57.928 40.909 0.00 0.00 34.46 2.24
48 49 3.809279 TGCAATGATACGCCATCTTAGTG 59.191 43.478 0.00 0.00 34.46 2.74
49 50 3.809832 GCAATGATACGCCATCTTAGTGT 59.190 43.478 0.00 0.00 34.46 3.55
50 51 4.988540 GCAATGATACGCCATCTTAGTGTA 59.011 41.667 0.00 0.00 34.46 2.90
51 52 5.639506 GCAATGATACGCCATCTTAGTGTAT 59.360 40.000 0.00 0.00 42.17 2.29
52 53 6.147821 GCAATGATACGCCATCTTAGTGTATT 59.852 38.462 0.00 0.00 40.18 1.89
53 54 7.622256 GCAATGATACGCCATCTTAGTGTATTC 60.622 40.741 0.00 0.00 40.18 1.75
54 55 6.399639 TGATACGCCATCTTAGTGTATTCA 57.600 37.500 0.00 0.00 40.18 2.57
55 56 6.811954 TGATACGCCATCTTAGTGTATTCAA 58.188 36.000 0.00 0.00 40.18 2.69
56 57 6.700081 TGATACGCCATCTTAGTGTATTCAAC 59.300 38.462 0.00 0.00 40.18 3.18
57 58 4.827692 ACGCCATCTTAGTGTATTCAACA 58.172 39.130 0.00 0.00 35.06 3.33
58 59 5.242434 ACGCCATCTTAGTGTATTCAACAA 58.758 37.500 0.00 0.00 40.63 2.83
59 60 5.703592 ACGCCATCTTAGTGTATTCAACAAA 59.296 36.000 0.00 0.00 40.63 2.83
60 61 6.205853 ACGCCATCTTAGTGTATTCAACAAAA 59.794 34.615 0.00 0.00 40.63 2.44
61 62 7.081349 CGCCATCTTAGTGTATTCAACAAAAA 58.919 34.615 0.00 0.00 40.63 1.94
105 106 3.623060 TGCGCCTTTGAATCTGAATAGAC 59.377 43.478 4.18 0.00 35.34 2.59
114 115 8.640091 TTTGAATCTGAATAGACGATGAAGAG 57.360 34.615 0.00 0.00 35.34 2.85
115 116 7.573968 TGAATCTGAATAGACGATGAAGAGA 57.426 36.000 0.00 0.00 35.34 3.10
116 117 8.000780 TGAATCTGAATAGACGATGAAGAGAA 57.999 34.615 0.00 0.00 35.34 2.87
117 118 8.134261 TGAATCTGAATAGACGATGAAGAGAAG 58.866 37.037 0.00 0.00 35.34 2.85
118 119 7.581213 ATCTGAATAGACGATGAAGAGAAGT 57.419 36.000 0.00 0.00 35.34 3.01
119 120 7.397892 TCTGAATAGACGATGAAGAGAAGTT 57.602 36.000 0.00 0.00 0.00 2.66
120 121 7.831753 TCTGAATAGACGATGAAGAGAAGTTT 58.168 34.615 0.00 0.00 0.00 2.66
121 122 8.307483 TCTGAATAGACGATGAAGAGAAGTTTT 58.693 33.333 0.00 0.00 0.00 2.43
122 123 8.833231 TGAATAGACGATGAAGAGAAGTTTTT 57.167 30.769 0.00 0.00 0.00 1.94
153 154 7.171678 ACGATGAAGAGAAGTAAAGTGAAAAGG 59.828 37.037 0.00 0.00 0.00 3.11
212 213 4.650131 GGGATAGAGTAGTGTGCTTTACCT 59.350 45.833 0.00 0.00 0.00 3.08
222 223 1.246649 TGCTTTACCTGCACATGGTG 58.753 50.000 6.38 0.00 38.42 4.17
223 224 1.202867 TGCTTTACCTGCACATGGTGA 60.203 47.619 6.38 0.00 38.42 4.02
226 227 3.313526 GCTTTACCTGCACATGGTGATAG 59.686 47.826 6.38 2.70 38.42 2.08
242 261 7.832503 TGGTGATAGATGTATTAATCATGCG 57.167 36.000 0.00 0.00 31.49 4.73
269 288 8.956426 TGATAGATGTATTGATCATACGTGCTA 58.044 33.333 0.00 12.25 40.87 3.49
270 289 9.227490 GATAGATGTATTGATCATACGTGCTAC 57.773 37.037 0.00 2.13 40.87 3.58
271 290 6.981722 AGATGTATTGATCATACGTGCTACA 58.018 36.000 0.00 6.26 40.87 2.74
272 291 6.863645 AGATGTATTGATCATACGTGCTACAC 59.136 38.462 0.00 0.00 40.87 2.90
273 292 6.144078 TGTATTGATCATACGTGCTACACT 57.856 37.500 0.00 0.00 40.87 3.55
376 396 1.450312 CAATCAGCGGGAGTGGACC 60.450 63.158 1.62 0.00 37.93 4.46
491 520 2.066262 GCATGCACACAGTAACTACGT 58.934 47.619 14.21 0.00 0.00 3.57
492 521 3.247442 GCATGCACACAGTAACTACGTA 58.753 45.455 14.21 0.00 0.00 3.57
557 618 1.347320 GCCAGACTTTCGGAGTAACG 58.653 55.000 0.00 0.00 39.19 3.18
571 638 4.381292 CGGAGTAACGGAGATAAACCAACT 60.381 45.833 0.00 0.00 0.00 3.16
575 642 7.360691 GGAGTAACGGAGATAAACCAACTTTTC 60.361 40.741 0.00 0.00 0.00 2.29
648 721 6.487103 CCTGATCAAATACTTTTAACTCGCC 58.513 40.000 0.00 0.00 0.00 5.54
679 754 1.609208 GTCTGCAAATGACCTGGTGT 58.391 50.000 2.82 0.00 0.00 4.16
782 861 3.227948 CGTCCGGTTTTTAATTGTTCCG 58.772 45.455 0.00 0.00 38.05 4.30
783 862 2.981805 GTCCGGTTTTTAATTGTTCCGC 59.018 45.455 0.00 0.00 37.17 5.54
784 863 1.980156 CCGGTTTTTAATTGTTCCGCG 59.020 47.619 0.00 0.00 37.17 6.46
810 890 0.257328 TTTTATCCTGGCCGCATGGA 59.743 50.000 8.66 8.66 37.49 3.41
825 905 1.492133 ATGGACCCACCCTGTCAGTG 61.492 60.000 0.00 0.00 38.00 3.66
826 906 2.147387 GGACCCACCCTGTCAGTGT 61.147 63.158 0.00 0.00 34.36 3.55
858 939 2.328099 GCCTGCCTTTCACACGGAG 61.328 63.158 0.00 0.00 0.00 4.63
860 941 0.320374 CCTGCCTTTCACACGGAGTA 59.680 55.000 0.00 0.00 41.61 2.59
861 942 1.066143 CCTGCCTTTCACACGGAGTAT 60.066 52.381 0.00 0.00 41.61 2.12
862 943 2.167693 CCTGCCTTTCACACGGAGTATA 59.832 50.000 0.00 0.00 41.61 1.47
863 944 3.369052 CCTGCCTTTCACACGGAGTATAA 60.369 47.826 0.00 0.00 41.61 0.98
865 946 3.998341 TGCCTTTCACACGGAGTATAAAC 59.002 43.478 0.00 0.00 41.61 2.01
997 1089 2.666098 GCTGCGGTAGGGGAAGGAA 61.666 63.158 0.00 0.00 0.00 3.36
1092 1189 1.404851 CGGAGGAAGCTTCTTGAGGTC 60.405 57.143 25.05 12.12 34.30 3.85
1321 1424 3.849951 TCGCCGCCCTTCAGGATC 61.850 66.667 0.00 0.00 38.24 3.36
1584 1687 1.499502 GCGCTCCTCTGTTTCTTGC 59.500 57.895 0.00 0.00 0.00 4.01
1615 1719 1.372087 GGGTGCTCGGCTTCTGATTG 61.372 60.000 0.00 0.00 0.00 2.67
1951 2055 4.284860 CTCATCGCGGCCATCGGA 62.285 66.667 6.13 4.36 39.69 4.55
2086 2190 1.444553 GCTCAACTGGTCCGACGAG 60.445 63.158 8.86 8.86 0.00 4.18
2640 2769 6.264292 ACAATGGCAGTAACAAATACAGTTCA 59.736 34.615 0.00 0.00 36.94 3.18
2657 2786 5.140177 CAGTTCATCGCACTAGTTGTTTTC 58.860 41.667 0.00 0.00 0.00 2.29
2675 2804 1.275666 TCGTCAGTTGATCACCCCAT 58.724 50.000 0.00 0.00 0.00 4.00
2716 2847 2.653726 AGCATTTTGTCTGTCACCACA 58.346 42.857 0.00 0.00 0.00 4.17
2728 2866 0.179032 TCACCACAGTCGGCAACAAT 60.179 50.000 0.00 0.00 0.00 2.71
2780 2918 4.582240 GGGATTTTCCATCCTTGCTTCTAG 59.418 45.833 0.96 0.00 38.64 2.43
2868 3010 7.817962 TCTTGACAAATTAAGAGCTAGTGGTAC 59.182 37.037 0.00 0.00 0.00 3.34
2892 3040 0.179166 CCACACAACACAGCACACAC 60.179 55.000 0.00 0.00 0.00 3.82
2894 3042 0.672091 ACACAACACAGCACACACGA 60.672 50.000 0.00 0.00 0.00 4.35
2896 3044 0.391130 ACAACACAGCACACACGAGT 60.391 50.000 0.00 0.00 0.00 4.18
2925 3073 6.471976 ACTCGACCGGTTTAATAAAGAAAC 57.528 37.500 9.42 0.00 36.29 2.78
2947 3095 1.474077 GCAGTGTCATCCATTTCCCAC 59.526 52.381 0.00 0.00 0.00 4.61
2950 3098 3.441572 CAGTGTCATCCATTTCCCACTTC 59.558 47.826 0.00 0.00 31.19 3.01
3147 4263 0.771127 CTGGTCCAAAAGTCCTCCCA 59.229 55.000 0.00 0.00 0.00 4.37
3150 4266 0.402121 GTCCAAAAGTCCTCCCAGCT 59.598 55.000 0.00 0.00 0.00 4.24
3185 4301 0.246635 ACGCTCGCATTTGGACTACT 59.753 50.000 0.00 0.00 0.00 2.57
3186 4302 1.337823 ACGCTCGCATTTGGACTACTT 60.338 47.619 0.00 0.00 0.00 2.24
3190 4306 3.552294 GCTCGCATTTGGACTACTTCTAC 59.448 47.826 0.00 0.00 0.00 2.59
3196 4312 5.520649 GCATTTGGACTACTTCTACTACTGC 59.479 44.000 0.00 0.00 0.00 4.40
3197 4313 5.656213 TTTGGACTACTTCTACTACTGCC 57.344 43.478 0.00 0.00 0.00 4.85
3198 4314 4.311520 TGGACTACTTCTACTACTGCCA 57.688 45.455 0.00 0.00 0.00 4.92
3200 4316 5.269991 TGGACTACTTCTACTACTGCCATT 58.730 41.667 0.00 0.00 0.00 3.16
3202 4318 5.502153 ACTACTTCTACTACTGCCATTCG 57.498 43.478 0.00 0.00 0.00 3.34
3203 4319 3.166489 ACTTCTACTACTGCCATTCGC 57.834 47.619 0.00 0.00 38.31 4.70
3204 4320 2.159085 ACTTCTACTACTGCCATTCGCC 60.159 50.000 0.00 0.00 36.24 5.54
3206 4322 1.828595 TCTACTACTGCCATTCGCCAA 59.171 47.619 0.00 0.00 36.24 4.52
3207 4323 2.235155 TCTACTACTGCCATTCGCCAAA 59.765 45.455 0.00 0.00 36.24 3.28
3208 4324 1.165270 ACTACTGCCATTCGCCAAAC 58.835 50.000 0.00 0.00 36.24 2.93
3209 4325 1.164411 CTACTGCCATTCGCCAAACA 58.836 50.000 0.00 0.00 36.24 2.83
3210 4326 0.878416 TACTGCCATTCGCCAAACAC 59.122 50.000 0.00 0.00 36.24 3.32
3213 4329 1.361993 GCCATTCGCCAAACACACA 59.638 52.632 0.00 0.00 0.00 3.72
3215 4331 0.383590 CCATTCGCCAAACACACACA 59.616 50.000 0.00 0.00 0.00 3.72
3216 4332 1.476074 CATTCGCCAAACACACACAC 58.524 50.000 0.00 0.00 0.00 3.82
3220 4336 0.796491 CGCCAAACACACACACACAC 60.796 55.000 0.00 0.00 0.00 3.82
3221 4337 0.242286 GCCAAACACACACACACACA 59.758 50.000 0.00 0.00 0.00 3.72
3222 4338 1.975837 CCAAACACACACACACACAC 58.024 50.000 0.00 0.00 0.00 3.82
3223 4339 1.268079 CCAAACACACACACACACACA 59.732 47.619 0.00 0.00 0.00 3.72
3224 4340 2.315011 CAAACACACACACACACACAC 58.685 47.619 0.00 0.00 0.00 3.82
3229 4345 0.871057 CACACACACACACACACACA 59.129 50.000 0.00 0.00 0.00 3.72
3230 4346 0.871722 ACACACACACACACACACAC 59.128 50.000 0.00 0.00 0.00 3.82
3231 4347 0.871057 CACACACACACACACACACA 59.129 50.000 0.00 0.00 0.00 3.72
3234 4350 0.871722 ACACACACACACACACACAC 59.128 50.000 0.00 0.00 0.00 3.82
3235 4351 0.871057 CACACACACACACACACACA 59.129 50.000 0.00 0.00 0.00 3.72
3236 4352 0.871722 ACACACACACACACACACAC 59.128 50.000 0.00 0.00 0.00 3.82
3237 4353 0.871057 CACACACACACACACACACA 59.129 50.000 0.00 0.00 0.00 3.72
3238 4354 0.871722 ACACACACACACACACACAC 59.128 50.000 0.00 0.00 0.00 3.82
3240 4356 0.871722 ACACACACACACACACACAC 59.128 50.000 0.00 0.00 0.00 3.82
3241 4357 0.871057 CACACACACACACACACACA 59.129 50.000 0.00 0.00 0.00 3.72
3242 4358 0.871722 ACACACACACACACACACAC 59.128 50.000 0.00 0.00 0.00 3.82
3243 4359 0.871057 CACACACACACACACACACA 59.129 50.000 0.00 0.00 0.00 3.72
3244 4360 0.871722 ACACACACACACACACACAC 59.128 50.000 0.00 0.00 0.00 3.82
3246 4362 0.871722 ACACACACACACACACACAC 59.128 50.000 0.00 0.00 0.00 3.82
3247 4363 0.871057 CACACACACACACACACACA 59.129 50.000 0.00 0.00 0.00 3.72
3248 4364 0.871722 ACACACACACACACACACAC 59.128 50.000 0.00 0.00 0.00 3.82
3250 4366 0.871722 ACACACACACACACACACAC 59.128 50.000 0.00 0.00 0.00 3.82
3251 4367 0.871057 CACACACACACACACACACA 59.129 50.000 0.00 0.00 0.00 3.72
3252 4368 0.871722 ACACACACACACACACACAC 59.128 50.000 0.00 0.00 0.00 3.82
3254 4370 0.871722 ACACACACACACACACACAC 59.128 50.000 0.00 0.00 0.00 3.82
3255 4371 0.871057 CACACACACACACACACACA 59.129 50.000 0.00 0.00 0.00 3.72
3256 4372 0.871722 ACACACACACACACACACAC 59.128 50.000 0.00 0.00 0.00 3.82
3257 4373 0.871057 CACACACACACACACACACA 59.129 50.000 0.00 0.00 0.00 3.72
3258 4374 0.871722 ACACACACACACACACACAC 59.128 50.000 0.00 0.00 0.00 3.82
3262 4385 2.289133 ACACACACACACACACACACTA 60.289 45.455 0.00 0.00 0.00 2.74
3273 4396 1.699634 ACACACACTACTGCCCATCTT 59.300 47.619 0.00 0.00 0.00 2.40
3277 4400 1.065854 ACACTACTGCCCATCTTCTGC 60.066 52.381 0.00 0.00 0.00 4.26
3278 4401 1.065926 CACTACTGCCCATCTTCTGCA 60.066 52.381 0.00 0.00 0.00 4.41
3280 4403 1.209019 CTACTGCCCATCTTCTGCACT 59.791 52.381 0.00 0.00 0.00 4.40
3281 4404 1.279496 ACTGCCCATCTTCTGCACTA 58.721 50.000 0.00 0.00 0.00 2.74
3282 4405 1.209019 ACTGCCCATCTTCTGCACTAG 59.791 52.381 0.00 0.00 0.00 2.57
3283 4406 1.209019 CTGCCCATCTTCTGCACTAGT 59.791 52.381 0.00 0.00 0.00 2.57
3284 4407 2.432146 CTGCCCATCTTCTGCACTAGTA 59.568 50.000 0.00 0.00 0.00 1.82
3285 4408 2.168521 TGCCCATCTTCTGCACTAGTAC 59.831 50.000 0.00 0.00 0.00 2.73
3286 4409 2.432510 GCCCATCTTCTGCACTAGTACT 59.567 50.000 0.00 0.00 0.00 2.73
3287 4410 3.739519 GCCCATCTTCTGCACTAGTACTG 60.740 52.174 5.39 0.00 0.00 2.74
3288 4411 3.449018 CCCATCTTCTGCACTAGTACTGT 59.551 47.826 5.39 0.00 0.00 3.55
3289 4412 4.645136 CCCATCTTCTGCACTAGTACTGTA 59.355 45.833 5.39 0.00 0.00 2.74
3290 4413 5.303078 CCCATCTTCTGCACTAGTACTGTAT 59.697 44.000 5.39 0.00 0.00 2.29
3291 4414 6.183360 CCCATCTTCTGCACTAGTACTGTATT 60.183 42.308 5.39 0.00 0.00 1.89
3292 4415 6.699204 CCATCTTCTGCACTAGTACTGTATTG 59.301 42.308 5.39 0.00 0.00 1.90
3293 4416 5.651530 TCTTCTGCACTAGTACTGTATTGC 58.348 41.667 5.39 9.01 0.00 3.56
3294 4417 5.419155 TCTTCTGCACTAGTACTGTATTGCT 59.581 40.000 5.39 0.35 31.57 3.91
3295 4418 4.998788 TCTGCACTAGTACTGTATTGCTG 58.001 43.478 5.39 11.81 31.57 4.41
3296 4419 3.521560 TGCACTAGTACTGTATTGCTGC 58.478 45.455 5.39 0.00 31.57 5.25
3297 4420 3.056179 TGCACTAGTACTGTATTGCTGCA 60.056 43.478 5.39 0.00 31.57 4.41
3335 4458 5.470845 AGCAGATTAAAAGAAACCGATCG 57.529 39.130 8.51 8.51 0.00 3.69
3336 4459 5.175859 AGCAGATTAAAAGAAACCGATCGA 58.824 37.500 18.66 0.00 0.00 3.59
3337 4460 5.817816 AGCAGATTAAAAGAAACCGATCGAT 59.182 36.000 18.66 0.00 0.00 3.59
3338 4461 6.018669 AGCAGATTAAAAGAAACCGATCGATC 60.019 38.462 18.66 15.68 0.00 3.69
3344 4467 4.720649 AAGAAACCGATCGATCTCTGAA 57.279 40.909 22.43 0.00 0.00 3.02
3371 4494 9.265901 CCTGTTCTTGTATCAGGTGATATTAAG 57.734 37.037 14.65 14.65 42.42 1.85
3372 4495 9.265901 CTGTTCTTGTATCAGGTGATATTAAGG 57.734 37.037 17.77 5.68 39.03 2.69
3389 4512 1.448717 GGAGGAGAGGCGACTTTGC 60.449 63.158 0.00 0.00 44.43 3.68
3399 4522 0.040157 GCGACTTTGCTGCATGACAA 60.040 50.000 1.84 0.00 0.00 3.18
3402 4525 2.351060 CGACTTTGCTGCATGACAATGT 60.351 45.455 1.84 12.58 37.01 2.71
3410 4533 1.003851 GCATGACAATGTGCAATGGC 58.996 50.000 0.00 0.00 40.94 4.40
3411 4534 1.673329 GCATGACAATGTGCAATGGCA 60.673 47.619 6.42 6.42 40.07 4.92
3427 4550 2.253758 GCAGTGCAAGCGTTGGAGA 61.254 57.895 11.09 0.00 0.00 3.71
3458 4581 1.064906 CATCTCTTGGTGCCTGTGGAT 60.065 52.381 0.00 0.00 0.00 3.41
3461 4584 1.075482 CTTGGTGCCTGTGGATGGT 59.925 57.895 0.00 0.00 0.00 3.55
3463 4586 2.361610 GGTGCCTGTGGATGGTGG 60.362 66.667 0.00 0.00 0.00 4.61
3464 4587 2.756400 GTGCCTGTGGATGGTGGA 59.244 61.111 0.00 0.00 0.00 4.02
3465 4588 1.377725 GTGCCTGTGGATGGTGGAG 60.378 63.158 0.00 0.00 0.00 3.86
3466 4589 1.538629 TGCCTGTGGATGGTGGAGA 60.539 57.895 0.00 0.00 0.00 3.71
3469 4592 0.618680 CCTGTGGATGGTGGAGAGGA 60.619 60.000 0.00 0.00 0.00 3.71
3472 4595 1.685765 TGGATGGTGGAGAGGACGG 60.686 63.158 0.00 0.00 0.00 4.79
3473 4596 2.435693 GGATGGTGGAGAGGACGGG 61.436 68.421 0.00 0.00 0.00 5.28
3474 4597 3.083997 ATGGTGGAGAGGACGGGC 61.084 66.667 0.00 0.00 0.00 6.13
3475 4598 3.625632 ATGGTGGAGAGGACGGGCT 62.626 63.158 0.00 0.00 0.00 5.19
3500 4623 3.067742 GCTTGTTTATGCTCTGCCATGAT 59.932 43.478 0.00 0.00 0.00 2.45
3506 4629 1.897615 GCTCTGCCATGATGGAGCC 60.898 63.158 17.22 0.00 43.51 4.70
3556 4679 3.124636 GCGCCGAGATGTTTTTCTTTCTA 59.875 43.478 0.00 0.00 0.00 2.10
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 6.853720 TGATAGGAGAGAAAAACGAGTACAG 58.146 40.000 0.00 0.00 0.00 2.74
1 2 6.829229 TGATAGGAGAGAAAAACGAGTACA 57.171 37.500 0.00 0.00 0.00 2.90
2 3 7.254151 GCATTGATAGGAGAGAAAAACGAGTAC 60.254 40.741 0.00 0.00 0.00 2.73
3 4 6.757010 GCATTGATAGGAGAGAAAAACGAGTA 59.243 38.462 0.00 0.00 0.00 2.59
4 5 5.582665 GCATTGATAGGAGAGAAAAACGAGT 59.417 40.000 0.00 0.00 0.00 4.18
5 6 5.582269 TGCATTGATAGGAGAGAAAAACGAG 59.418 40.000 0.00 0.00 0.00 4.18
6 7 5.487433 TGCATTGATAGGAGAGAAAAACGA 58.513 37.500 0.00 0.00 0.00 3.85
7 8 5.801350 TGCATTGATAGGAGAGAAAAACG 57.199 39.130 0.00 0.00 0.00 3.60
8 9 7.765307 TCATTGCATTGATAGGAGAGAAAAAC 58.235 34.615 7.19 0.00 0.00 2.43
9 10 7.943079 TCATTGCATTGATAGGAGAGAAAAA 57.057 32.000 7.19 0.00 0.00 1.94
10 11 9.060347 GTATCATTGCATTGATAGGAGAGAAAA 57.940 33.333 24.60 5.67 38.83 2.29
11 12 7.386025 CGTATCATTGCATTGATAGGAGAGAAA 59.614 37.037 29.80 11.17 42.75 2.52
12 13 6.870439 CGTATCATTGCATTGATAGGAGAGAA 59.130 38.462 29.80 11.71 42.75 2.87
13 14 6.393171 CGTATCATTGCATTGATAGGAGAGA 58.607 40.000 29.80 12.27 42.75 3.10
14 15 5.063186 GCGTATCATTGCATTGATAGGAGAG 59.937 44.000 33.85 21.93 42.75 3.20
15 16 4.931601 GCGTATCATTGCATTGATAGGAGA 59.068 41.667 33.85 16.48 42.75 3.71
16 17 4.093998 GGCGTATCATTGCATTGATAGGAG 59.906 45.833 33.85 25.05 42.75 3.69
17 18 4.002982 GGCGTATCATTGCATTGATAGGA 58.997 43.478 33.85 17.02 42.75 2.94
18 19 3.752747 TGGCGTATCATTGCATTGATAGG 59.247 43.478 29.51 29.51 42.88 2.57
19 20 5.353400 AGATGGCGTATCATTGCATTGATAG 59.647 40.000 24.60 19.64 38.83 2.08
20 21 5.247862 AGATGGCGTATCATTGCATTGATA 58.752 37.500 21.66 21.66 38.31 2.15
21 22 4.077108 AGATGGCGTATCATTGCATTGAT 58.923 39.130 23.42 23.42 38.31 2.57
22 23 3.479489 AGATGGCGTATCATTGCATTGA 58.521 40.909 13.30 13.30 38.31 2.57
23 24 3.909776 AGATGGCGTATCATTGCATTG 57.090 42.857 2.08 2.08 38.31 2.82
24 25 5.049198 CACTAAGATGGCGTATCATTGCATT 60.049 40.000 0.00 0.00 38.31 3.56
25 26 4.453478 CACTAAGATGGCGTATCATTGCAT 59.547 41.667 0.00 0.00 38.31 3.96
26 27 3.809279 CACTAAGATGGCGTATCATTGCA 59.191 43.478 4.94 0.00 38.31 4.08
27 28 3.809832 ACACTAAGATGGCGTATCATTGC 59.190 43.478 4.94 0.00 38.31 3.56
28 29 7.384932 TGAATACACTAAGATGGCGTATCATTG 59.615 37.037 4.94 0.00 38.31 2.82
29 30 7.441836 TGAATACACTAAGATGGCGTATCATT 58.558 34.615 4.94 0.59 38.31 2.57
30 31 6.993079 TGAATACACTAAGATGGCGTATCAT 58.007 36.000 4.94 0.00 38.31 2.45
31 32 6.399639 TGAATACACTAAGATGGCGTATCA 57.600 37.500 4.94 0.00 38.31 2.15
32 33 6.700081 TGTTGAATACACTAAGATGGCGTATC 59.300 38.462 0.00 0.00 35.97 2.24
33 34 6.578944 TGTTGAATACACTAAGATGGCGTAT 58.421 36.000 0.00 0.00 0.00 3.06
34 35 5.968254 TGTTGAATACACTAAGATGGCGTA 58.032 37.500 0.00 0.00 0.00 4.42
35 36 4.827692 TGTTGAATACACTAAGATGGCGT 58.172 39.130 0.00 0.00 0.00 5.68
36 37 5.794687 TTGTTGAATACACTAAGATGGCG 57.205 39.130 0.00 0.00 36.21 5.69
59 60 5.643339 TTAAATCGTTGCGTGCAATTTTT 57.357 30.435 10.85 12.35 38.28 1.94
60 61 5.643339 TTTAAATCGTTGCGTGCAATTTT 57.357 30.435 10.85 12.65 38.28 1.82
61 62 5.607206 CATTTAAATCGTTGCGTGCAATTT 58.393 33.333 10.85 9.73 38.28 1.82
62 63 4.434067 GCATTTAAATCGTTGCGTGCAATT 60.434 37.500 10.85 3.65 38.28 2.32
63 64 3.060628 GCATTTAAATCGTTGCGTGCAAT 59.939 39.130 10.85 0.00 38.28 3.56
64 65 2.406691 GCATTTAAATCGTTGCGTGCAA 59.593 40.909 2.58 2.58 0.00 4.08
65 66 1.982223 GCATTTAAATCGTTGCGTGCA 59.018 42.857 0.00 0.00 0.00 4.57
66 67 2.676692 GCATTTAAATCGTTGCGTGC 57.323 45.000 0.00 0.00 0.00 5.34
70 71 1.908065 AGGCGCATTTAAATCGTTGC 58.092 45.000 10.83 10.29 0.00 4.17
71 72 3.917380 TCAAAGGCGCATTTAAATCGTTG 59.083 39.130 20.68 6.10 0.00 4.10
72 73 4.167554 TCAAAGGCGCATTTAAATCGTT 57.832 36.364 20.68 0.00 0.00 3.85
73 74 3.840890 TCAAAGGCGCATTTAAATCGT 57.159 38.095 20.68 0.00 0.00 3.73
119 120 7.703298 TTACTTCTCTTCATCGTTCGAAAAA 57.297 32.000 0.00 0.00 0.00 1.94
120 121 7.437267 ACTTTACTTCTCTTCATCGTTCGAAAA 59.563 33.333 0.00 0.00 0.00 2.29
121 122 6.921857 ACTTTACTTCTCTTCATCGTTCGAAA 59.078 34.615 0.00 0.00 0.00 3.46
122 123 6.362551 CACTTTACTTCTCTTCATCGTTCGAA 59.637 38.462 0.00 0.00 0.00 3.71
123 124 5.856986 CACTTTACTTCTCTTCATCGTTCGA 59.143 40.000 0.00 0.00 0.00 3.71
124 125 5.856986 TCACTTTACTTCTCTTCATCGTTCG 59.143 40.000 0.00 0.00 0.00 3.95
125 126 7.639162 TTCACTTTACTTCTCTTCATCGTTC 57.361 36.000 0.00 0.00 0.00 3.95
126 127 8.433421 TTTTCACTTTACTTCTCTTCATCGTT 57.567 30.769 0.00 0.00 0.00 3.85
127 128 7.171678 CCTTTTCACTTTACTTCTCTTCATCGT 59.828 37.037 0.00 0.00 0.00 3.73
128 129 7.385205 TCCTTTTCACTTTACTTCTCTTCATCG 59.615 37.037 0.00 0.00 0.00 3.84
129 130 8.608844 TCCTTTTCACTTTACTTCTCTTCATC 57.391 34.615 0.00 0.00 0.00 2.92
130 131 8.980481 TTCCTTTTCACTTTACTTCTCTTCAT 57.020 30.769 0.00 0.00 0.00 2.57
131 132 8.801882 TTTCCTTTTCACTTTACTTCTCTTCA 57.198 30.769 0.00 0.00 0.00 3.02
212 213 8.156165 TGATTAATACATCTATCACCATGTGCA 58.844 33.333 0.00 0.00 34.92 4.57
226 227 9.091784 ACATCTATCACGCATGATTAATACATC 57.908 33.333 0.00 0.00 43.40 3.06
242 261 7.757173 AGCACGTATGATCAATACATCTATCAC 59.243 37.037 0.00 0.00 41.20 3.06
291 310 4.559300 GCGCATTTGCTGATGGGTATTAAT 60.559 41.667 0.30 0.00 40.80 1.40
334 354 0.390124 TTGTCGGTATCATACGCCCC 59.610 55.000 0.00 0.00 0.00 5.80
355 375 2.825836 CACTCCCGCTGATTGGCC 60.826 66.667 0.00 0.00 0.00 5.36
376 396 3.487711 CGACAGAGAAGTCCAAGATACCG 60.488 52.174 0.00 0.00 35.07 4.02
469 498 2.159841 CGTAGTTACTGTGTGCATGCAC 60.160 50.000 38.00 38.00 46.33 4.57
491 520 0.741326 GCTGAGAGTGATGAGGCGTA 59.259 55.000 0.00 0.00 0.00 4.42
492 521 1.515020 GCTGAGAGTGATGAGGCGT 59.485 57.895 0.00 0.00 0.00 5.68
557 618 7.039313 AGTGTTGAAAAGTTGGTTTATCTCC 57.961 36.000 0.00 0.00 0.00 3.71
806 886 1.151810 ACTGACAGGGTGGGTCCAT 60.152 57.895 7.51 0.00 38.11 3.41
810 890 1.837090 GAACACTGACAGGGTGGGT 59.163 57.895 12.05 0.00 38.83 4.51
814 894 0.104304 GTCACGAACACTGACAGGGT 59.896 55.000 3.94 3.94 38.36 4.34
825 905 1.227853 AGGCAAGGTGGTCACGAAC 60.228 57.895 0.00 0.00 0.00 3.95
826 906 1.227823 CAGGCAAGGTGGTCACGAA 60.228 57.895 0.00 0.00 0.00 3.85
858 939 6.733145 CGTAGTAACAGAGAGGGGTTTATAC 58.267 44.000 0.00 0.00 0.00 1.47
859 940 5.300286 GCGTAGTAACAGAGAGGGGTTTATA 59.700 44.000 0.00 0.00 0.00 0.98
860 941 4.099113 GCGTAGTAACAGAGAGGGGTTTAT 59.901 45.833 0.00 0.00 0.00 1.40
861 942 3.445096 GCGTAGTAACAGAGAGGGGTTTA 59.555 47.826 0.00 0.00 0.00 2.01
862 943 2.233186 GCGTAGTAACAGAGAGGGGTTT 59.767 50.000 0.00 0.00 0.00 3.27
863 944 1.823610 GCGTAGTAACAGAGAGGGGTT 59.176 52.381 0.00 0.00 0.00 4.11
865 946 0.745468 GGCGTAGTAACAGAGAGGGG 59.255 60.000 0.00 0.00 0.00 4.79
933 1018 3.316573 GAGGGGGACACTTGGCGAG 62.317 68.421 0.00 0.00 0.00 5.03
981 1073 2.652095 CGTTCCTTCCCCTACCGCA 61.652 63.158 0.00 0.00 0.00 5.69
997 1089 2.347490 GCACCTGACCACCATCGT 59.653 61.111 0.00 0.00 0.00 3.73
1321 1424 2.182030 GGCAACGTCTCCCTCTCG 59.818 66.667 0.00 0.00 0.00 4.04
1562 1665 1.213013 GAAACAGAGGAGCGCGAGA 59.787 57.895 12.10 0.00 0.00 4.04
1563 1666 0.389166 AAGAAACAGAGGAGCGCGAG 60.389 55.000 12.10 0.00 0.00 5.03
1564 1667 0.667487 CAAGAAACAGAGGAGCGCGA 60.667 55.000 12.10 0.00 0.00 5.87
1565 1668 1.784062 CAAGAAACAGAGGAGCGCG 59.216 57.895 0.00 0.00 0.00 6.86
1566 1669 0.952984 AGCAAGAAACAGAGGAGCGC 60.953 55.000 0.00 0.00 0.00 5.92
1567 1670 0.795085 CAGCAAGAAACAGAGGAGCG 59.205 55.000 0.00 0.00 0.00 5.03
1568 1671 2.175878 TCAGCAAGAAACAGAGGAGC 57.824 50.000 0.00 0.00 0.00 4.70
1569 1672 3.933955 CTGATCAGCAAGAAACAGAGGAG 59.066 47.826 10.38 0.00 37.09 3.69
1570 1673 3.580022 TCTGATCAGCAAGAAACAGAGGA 59.420 43.478 18.36 0.00 38.15 3.71
1584 1687 1.269673 CGAGCACCCAGATCTGATCAG 60.270 57.143 24.62 17.07 0.00 2.90
1615 1719 2.983592 CCAAACACCTCCCCGCAC 60.984 66.667 0.00 0.00 0.00 5.34
1867 1971 0.534412 CGATGGAGAGGTTGAGCAGT 59.466 55.000 0.00 0.00 0.00 4.40
1936 2040 4.284860 TCTCCGATGGCCGCGATG 62.285 66.667 18.18 10.51 36.84 3.84
1942 2046 1.592669 CGACATGTCTCCGATGGCC 60.593 63.158 22.95 0.00 0.00 5.36
1951 2055 3.060000 TCCGACGCCGACATGTCT 61.060 61.111 22.95 4.58 38.22 3.41
2056 2160 2.022129 GTTGAGCACGTCCACGAGG 61.022 63.158 6.03 0.00 43.02 4.63
2359 2469 4.144727 TCCTCCTCCTCCTCGCCC 62.145 72.222 0.00 0.00 0.00 6.13
2360 2470 2.520741 CTCCTCCTCCTCCTCGCC 60.521 72.222 0.00 0.00 0.00 5.54
2361 2471 2.520741 CCTCCTCCTCCTCCTCGC 60.521 72.222 0.00 0.00 0.00 5.03
2362 2472 2.520741 GCCTCCTCCTCCTCCTCG 60.521 72.222 0.00 0.00 0.00 4.63
2363 2473 2.520741 CGCCTCCTCCTCCTCCTC 60.521 72.222 0.00 0.00 0.00 3.71
2364 2474 4.150454 CCGCCTCCTCCTCCTCCT 62.150 72.222 0.00 0.00 0.00 3.69
2577 2701 5.846203 AGGAATGTGGATGAACTTGTTTTG 58.154 37.500 0.00 0.00 0.00 2.44
2640 2769 3.386486 TGACGAAAACAACTAGTGCGAT 58.614 40.909 0.00 0.00 0.00 4.58
2657 2786 1.739466 CAATGGGGTGATCAACTGACG 59.261 52.381 11.29 0.00 0.00 4.35
2675 2804 4.455533 GCTACTCCAACATTGACATGACAA 59.544 41.667 12.85 12.85 34.11 3.18
2691 2820 3.437049 GGTGACAGACAAAATGCTACTCC 59.563 47.826 0.00 0.00 0.00 3.85
2692 2821 4.065088 TGGTGACAGACAAAATGCTACTC 58.935 43.478 0.00 0.00 35.01 2.59
2716 2847 1.165270 GTTAGCCATTGTTGCCGACT 58.835 50.000 0.00 0.00 0.00 4.18
2717 2848 1.165270 AGTTAGCCATTGTTGCCGAC 58.835 50.000 0.00 0.00 0.00 4.79
2718 2849 2.772077 TAGTTAGCCATTGTTGCCGA 57.228 45.000 0.00 0.00 0.00 5.54
2719 2850 3.057876 TGTTTAGTTAGCCATTGTTGCCG 60.058 43.478 0.00 0.00 0.00 5.69
2720 2851 4.513198 TGTTTAGTTAGCCATTGTTGCC 57.487 40.909 0.00 0.00 0.00 4.52
2721 2852 4.923281 CCTTGTTTAGTTAGCCATTGTTGC 59.077 41.667 0.00 0.00 0.00 4.17
2728 2866 8.325787 TGATTAGATTCCTTGTTTAGTTAGCCA 58.674 33.333 0.00 0.00 0.00 4.75
2762 2900 4.579869 GTGACTAGAAGCAAGGATGGAAA 58.420 43.478 0.00 0.00 0.00 3.13
2780 2918 3.496898 TCATCTGTGACAGCGTGAC 57.503 52.632 7.93 0.00 0.00 3.67
2835 2973 8.541133 AGCTCTTAATTTGTCAAGAGTAAGAC 57.459 34.615 14.32 0.00 46.25 3.01
2868 3010 1.867233 GTGCTGTGTTGTGTGGACTAG 59.133 52.381 0.00 0.00 0.00 2.57
2894 3042 0.826672 AACCGGTCGAGTTCTCCACT 60.827 55.000 8.04 0.00 39.07 4.00
2896 3044 1.619654 TAAACCGGTCGAGTTCTCCA 58.380 50.000 8.04 0.00 0.00 3.86
2897 3045 2.730550 TTAAACCGGTCGAGTTCTCC 57.269 50.000 8.04 0.00 0.00 3.71
2898 3046 6.095377 TCTTTATTAAACCGGTCGAGTTCTC 58.905 40.000 8.04 0.00 0.00 2.87
2901 3049 6.073058 GGTTTCTTTATTAAACCGGTCGAGTT 60.073 38.462 8.04 0.00 44.61 3.01
2902 3050 5.409520 GGTTTCTTTATTAAACCGGTCGAGT 59.590 40.000 8.04 0.00 44.61 4.18
2904 3052 5.861222 GGTTTCTTTATTAAACCGGTCGA 57.139 39.130 8.04 0.00 44.61 4.20
2925 3073 0.734889 GGAAATGGATGACACTGCGG 59.265 55.000 0.00 0.00 0.00 5.69
2928 3076 3.077484 AGTGGGAAATGGATGACACTG 57.923 47.619 0.00 0.00 37.74 3.66
3091 4204 1.903404 GGCCCAACACTGTTGGAGG 60.903 63.158 33.88 22.23 42.06 4.30
3093 4206 0.754957 CTTGGCCCAACACTGTTGGA 60.755 55.000 33.88 17.16 42.06 3.53
3147 4263 2.159043 CGTTATGATGTCCTGACCAGCT 60.159 50.000 0.00 0.00 0.00 4.24
3150 4266 1.831106 AGCGTTATGATGTCCTGACCA 59.169 47.619 0.00 0.00 0.00 4.02
3185 4301 2.596904 GGCGAATGGCAGTAGTAGAA 57.403 50.000 0.00 0.00 46.16 2.10
3196 4312 0.383590 TGTGTGTGTTTGGCGAATGG 59.616 50.000 0.00 0.00 0.00 3.16
3197 4313 1.202234 TGTGTGTGTGTTTGGCGAATG 60.202 47.619 0.00 0.00 0.00 2.67
3198 4314 1.098869 TGTGTGTGTGTTTGGCGAAT 58.901 45.000 0.00 0.00 0.00 3.34
3200 4316 0.955919 TGTGTGTGTGTGTTTGGCGA 60.956 50.000 0.00 0.00 0.00 5.54
3202 4318 0.242286 TGTGTGTGTGTGTGTTTGGC 59.758 50.000 0.00 0.00 0.00 4.52
3203 4319 1.268079 TGTGTGTGTGTGTGTGTTTGG 59.732 47.619 0.00 0.00 0.00 3.28
3204 4320 2.287248 TGTGTGTGTGTGTGTGTGTTTG 60.287 45.455 0.00 0.00 0.00 2.93
3206 4322 1.265635 GTGTGTGTGTGTGTGTGTGTT 59.734 47.619 0.00 0.00 0.00 3.32
3207 4323 0.871722 GTGTGTGTGTGTGTGTGTGT 59.128 50.000 0.00 0.00 0.00 3.72
3208 4324 0.871057 TGTGTGTGTGTGTGTGTGTG 59.129 50.000 0.00 0.00 0.00 3.82
3209 4325 0.871722 GTGTGTGTGTGTGTGTGTGT 59.128 50.000 0.00 0.00 0.00 3.72
3210 4326 0.871057 TGTGTGTGTGTGTGTGTGTG 59.129 50.000 0.00 0.00 0.00 3.82
3213 4329 0.871722 GTGTGTGTGTGTGTGTGTGT 59.128 50.000 0.00 0.00 0.00 3.72
3215 4331 0.871722 GTGTGTGTGTGTGTGTGTGT 59.128 50.000 0.00 0.00 0.00 3.72
3216 4332 0.871057 TGTGTGTGTGTGTGTGTGTG 59.129 50.000 0.00 0.00 0.00 3.82
3220 4336 0.871057 TGTGTGTGTGTGTGTGTGTG 59.129 50.000 0.00 0.00 0.00 3.82
3221 4337 0.871722 GTGTGTGTGTGTGTGTGTGT 59.128 50.000 0.00 0.00 0.00 3.72
3222 4338 0.871057 TGTGTGTGTGTGTGTGTGTG 59.129 50.000 0.00 0.00 0.00 3.82
3223 4339 0.871722 GTGTGTGTGTGTGTGTGTGT 59.128 50.000 0.00 0.00 0.00 3.72
3224 4340 0.871057 TGTGTGTGTGTGTGTGTGTG 59.129 50.000 0.00 0.00 0.00 3.82
3229 4345 0.871722 GTGTGTGTGTGTGTGTGTGT 59.128 50.000 0.00 0.00 0.00 3.72
3230 4346 0.871057 TGTGTGTGTGTGTGTGTGTG 59.129 50.000 0.00 0.00 0.00 3.82
3231 4347 0.871722 GTGTGTGTGTGTGTGTGTGT 59.128 50.000 0.00 0.00 0.00 3.72
3234 4350 0.871057 TGTGTGTGTGTGTGTGTGTG 59.129 50.000 0.00 0.00 0.00 3.82
3235 4351 0.871722 GTGTGTGTGTGTGTGTGTGT 59.128 50.000 0.00 0.00 0.00 3.72
3236 4352 0.871057 TGTGTGTGTGTGTGTGTGTG 59.129 50.000 0.00 0.00 0.00 3.82
3237 4353 0.871722 GTGTGTGTGTGTGTGTGTGT 59.128 50.000 0.00 0.00 0.00 3.72
3238 4354 0.871057 TGTGTGTGTGTGTGTGTGTG 59.129 50.000 0.00 0.00 0.00 3.82
3240 4356 0.871057 TGTGTGTGTGTGTGTGTGTG 59.129 50.000 0.00 0.00 0.00 3.82
3241 4357 0.871722 GTGTGTGTGTGTGTGTGTGT 59.128 50.000 0.00 0.00 0.00 3.72
3242 4358 1.155889 AGTGTGTGTGTGTGTGTGTG 58.844 50.000 0.00 0.00 0.00 3.82
3243 4359 2.028476 AGTAGTGTGTGTGTGTGTGTGT 60.028 45.455 0.00 0.00 0.00 3.72
3244 4360 2.348362 CAGTAGTGTGTGTGTGTGTGTG 59.652 50.000 0.00 0.00 0.00 3.82
3246 4362 1.327460 GCAGTAGTGTGTGTGTGTGTG 59.673 52.381 0.00 0.00 0.00 3.82
3247 4363 1.651987 GCAGTAGTGTGTGTGTGTGT 58.348 50.000 0.00 0.00 0.00 3.72
3248 4364 0.937304 GGCAGTAGTGTGTGTGTGTG 59.063 55.000 0.00 0.00 0.00 3.82
3250 4366 0.179059 TGGGCAGTAGTGTGTGTGTG 60.179 55.000 0.00 0.00 0.00 3.82
3251 4367 0.764890 ATGGGCAGTAGTGTGTGTGT 59.235 50.000 0.00 0.00 0.00 3.72
3252 4368 1.002430 AGATGGGCAGTAGTGTGTGTG 59.998 52.381 0.00 0.00 0.00 3.82
3254 4370 2.027745 AGAAGATGGGCAGTAGTGTGTG 60.028 50.000 0.00 0.00 0.00 3.82
3255 4371 2.027745 CAGAAGATGGGCAGTAGTGTGT 60.028 50.000 0.00 0.00 0.00 3.72
3256 4372 2.625737 CAGAAGATGGGCAGTAGTGTG 58.374 52.381 0.00 0.00 0.00 3.82
3257 4373 1.065854 GCAGAAGATGGGCAGTAGTGT 60.066 52.381 0.00 0.00 0.00 3.55
3258 4374 1.065926 TGCAGAAGATGGGCAGTAGTG 60.066 52.381 0.00 0.00 32.95 2.74
3262 4385 1.209019 CTAGTGCAGAAGATGGGCAGT 59.791 52.381 0.00 0.00 43.20 4.40
3273 4396 4.678044 GCAGCAATACAGTACTAGTGCAGA 60.678 45.833 17.59 0.00 39.62 4.26
3277 4400 5.007039 CCAATGCAGCAATACAGTACTAGTG 59.993 44.000 5.39 0.00 0.00 2.74
3278 4401 5.104941 TCCAATGCAGCAATACAGTACTAGT 60.105 40.000 0.00 0.00 0.00 2.57
3280 4403 5.351948 TCCAATGCAGCAATACAGTACTA 57.648 39.130 0.00 0.00 0.00 1.82
3281 4404 4.220693 TCCAATGCAGCAATACAGTACT 57.779 40.909 0.00 0.00 0.00 2.73
3282 4405 5.505173 AATCCAATGCAGCAATACAGTAC 57.495 39.130 0.00 0.00 0.00 2.73
3283 4406 6.118852 TGTAATCCAATGCAGCAATACAGTA 58.881 36.000 0.00 0.00 0.00 2.74
3284 4407 4.949238 TGTAATCCAATGCAGCAATACAGT 59.051 37.500 0.00 0.00 0.00 3.55
3285 4408 5.503662 TGTAATCCAATGCAGCAATACAG 57.496 39.130 0.00 0.00 0.00 2.74
3286 4409 6.468333 AATGTAATCCAATGCAGCAATACA 57.532 33.333 0.00 3.34 0.00 2.29
3287 4410 7.775397 AAAATGTAATCCAATGCAGCAATAC 57.225 32.000 0.00 0.00 0.00 1.89
3288 4411 9.531942 CTAAAAATGTAATCCAATGCAGCAATA 57.468 29.630 0.00 0.00 0.00 1.90
3289 4412 7.011669 GCTAAAAATGTAATCCAATGCAGCAAT 59.988 33.333 0.00 0.00 0.00 3.56
3290 4413 6.313411 GCTAAAAATGTAATCCAATGCAGCAA 59.687 34.615 0.00 0.00 0.00 3.91
3291 4414 5.811613 GCTAAAAATGTAATCCAATGCAGCA 59.188 36.000 0.00 0.00 0.00 4.41
3292 4415 5.811613 TGCTAAAAATGTAATCCAATGCAGC 59.188 36.000 0.00 0.00 0.00 5.25
3293 4416 7.259882 TCTGCTAAAAATGTAATCCAATGCAG 58.740 34.615 0.00 0.00 42.70 4.41
3294 4417 7.167924 TCTGCTAAAAATGTAATCCAATGCA 57.832 32.000 0.00 0.00 0.00 3.96
3295 4418 8.652810 AATCTGCTAAAAATGTAATCCAATGC 57.347 30.769 0.00 0.00 0.00 3.56
3325 4448 3.117046 GGTTCAGAGATCGATCGGTTTC 58.883 50.000 19.33 13.41 0.00 2.78
3335 4458 6.634805 TGATACAAGAACAGGTTCAGAGATC 58.365 40.000 14.06 10.91 41.84 2.75
3336 4459 6.351711 CCTGATACAAGAACAGGTTCAGAGAT 60.352 42.308 14.06 2.91 44.06 2.75
3337 4460 5.047021 CCTGATACAAGAACAGGTTCAGAGA 60.047 44.000 14.06 0.00 44.06 3.10
3338 4461 5.174395 CCTGATACAAGAACAGGTTCAGAG 58.826 45.833 14.06 6.08 44.06 3.35
3362 4485 3.827302 GTCGCCTCTCCTCCTTAATATCA 59.173 47.826 0.00 0.00 0.00 2.15
3363 4486 4.083565 AGTCGCCTCTCCTCCTTAATATC 58.916 47.826 0.00 0.00 0.00 1.63
3364 4487 4.120946 AGTCGCCTCTCCTCCTTAATAT 57.879 45.455 0.00 0.00 0.00 1.28
3365 4488 3.596940 AGTCGCCTCTCCTCCTTAATA 57.403 47.619 0.00 0.00 0.00 0.98
3366 4489 2.463047 AGTCGCCTCTCCTCCTTAAT 57.537 50.000 0.00 0.00 0.00 1.40
3367 4490 2.233305 AAGTCGCCTCTCCTCCTTAA 57.767 50.000 0.00 0.00 0.00 1.85
3368 4491 1.825474 CAAAGTCGCCTCTCCTCCTTA 59.175 52.381 0.00 0.00 0.00 2.69
3369 4492 0.610687 CAAAGTCGCCTCTCCTCCTT 59.389 55.000 0.00 0.00 0.00 3.36
3370 4493 1.893919 GCAAAGTCGCCTCTCCTCCT 61.894 60.000 0.00 0.00 0.00 3.69
3371 4494 1.448717 GCAAAGTCGCCTCTCCTCC 60.449 63.158 0.00 0.00 0.00 4.30
3372 4495 0.739112 CAGCAAAGTCGCCTCTCCTC 60.739 60.000 0.00 0.00 0.00 3.71
3399 4522 3.780357 TGCACTGCCATTGCACAT 58.220 50.000 5.53 0.00 45.06 3.21
3410 4533 1.571460 GTCTCCAACGCTTGCACTG 59.429 57.895 0.00 0.00 0.00 3.66
3411 4534 1.598130 GGTCTCCAACGCTTGCACT 60.598 57.895 0.00 0.00 0.00 4.40
3427 4550 1.765314 CCAAGAGATGAGATTCCCGGT 59.235 52.381 0.00 0.00 0.00 5.28
3458 4581 2.238319 ATAGCCCGTCCTCTCCACCA 62.238 60.000 0.00 0.00 0.00 4.17
3461 4584 2.134287 GCATAGCCCGTCCTCTCCA 61.134 63.158 0.00 0.00 0.00 3.86
3463 4586 0.249657 CAAGCATAGCCCGTCCTCTC 60.250 60.000 0.00 0.00 0.00 3.20
3464 4587 0.978146 ACAAGCATAGCCCGTCCTCT 60.978 55.000 0.00 0.00 0.00 3.69
3465 4588 0.107654 AACAAGCATAGCCCGTCCTC 60.108 55.000 0.00 0.00 0.00 3.71
3466 4589 0.328258 AAACAAGCATAGCCCGTCCT 59.672 50.000 0.00 0.00 0.00 3.85
3469 4592 1.676006 GCATAAACAAGCATAGCCCGT 59.324 47.619 0.00 0.00 0.00 5.28
3472 4595 3.549625 GCAGAGCATAAACAAGCATAGCC 60.550 47.826 0.00 0.00 0.00 3.93
3473 4596 3.549625 GGCAGAGCATAAACAAGCATAGC 60.550 47.826 0.00 0.00 0.00 2.97
3474 4597 3.628942 TGGCAGAGCATAAACAAGCATAG 59.371 43.478 0.00 0.00 0.00 2.23
3475 4598 3.619419 TGGCAGAGCATAAACAAGCATA 58.381 40.909 0.00 0.00 0.00 3.14
3517 4640 4.201679 CCCGTCTGCCGATGCGTA 62.202 66.667 0.00 0.00 41.78 4.42


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

AutoCloner maintained by Alex Coulton.