Multiple sequence alignment - TraesCS6A01G406600

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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 TraesCS6A01G406600 chr6A 100.000 6376 0 0 1 6376 611850596 611856971 0.000000e+00 11775.0
1 TraesCS6A01G406600 chr6D 93.384 2509 94 28 662 3152 465202854 465205308 0.000000e+00 3648.0
2 TraesCS6A01G406600 chr6D 96.386 1909 55 9 3159 5055 465205368 465207274 0.000000e+00 3131.0
3 TraesCS6A01G406600 chr6D 91.625 991 33 18 5060 6018 465207316 465208288 0.000000e+00 1325.0
4 TraesCS6A01G406600 chr6D 89.636 357 31 5 6019 6370 465208248 465208603 3.510000e-122 449.0
5 TraesCS6A01G406600 chr6D 83.333 360 50 8 6019 6370 78819455 78819812 2.220000e-84 324.0
6 TraesCS6A01G406600 chr6D 76.515 396 37 27 180 541 465202254 465202627 1.420000e-36 165.0
7 TraesCS6A01G406600 chr6B 92.371 2176 87 31 101 2266 710096039 710098145 0.000000e+00 3025.0
8 TraesCS6A01G406600 chr6B 85.971 1447 109 41 4410 5827 710100268 710101649 0.000000e+00 1461.0
9 TraesCS6A01G406600 chr6B 90.605 1107 56 21 2913 3977 710098767 710099867 0.000000e+00 1424.0
10 TraesCS6A01G406600 chr6B 91.694 602 40 3 2259 2854 710098169 710098766 0.000000e+00 826.0
11 TraesCS6A01G406600 chr6B 90.314 382 26 7 4040 4413 710099862 710100240 2.070000e-134 490.0
12 TraesCS6A01G406600 chr3D 87.151 358 36 9 6019 6370 283311610 283311257 1.290000e-106 398.0
13 TraesCS6A01G406600 chr5D 86.034 358 41 6 6019 6370 509543061 509542707 6.040000e-100 375.0
14 TraesCS6A01G406600 chr5D 85.359 362 39 10 6019 6370 350373953 350373596 4.700000e-96 363.0
15 TraesCS6A01G406600 chr5D 91.379 58 4 1 5958 6015 278283951 278283895 1.910000e-10 78.7
16 TraesCS6A01G406600 chr5D 88.710 62 4 3 5957 6018 511950723 511950665 8.870000e-09 73.1
17 TraesCS6A01G406600 chr7D 86.111 324 38 5 6019 6336 102958925 102958603 6.120000e-90 342.0
18 TraesCS6A01G406600 chr7D 88.732 71 4 4 5948 6018 11680339 11680273 4.100000e-12 84.2
19 TraesCS6A01G406600 chr7D 89.394 66 4 3 5952 6017 72176913 72176975 5.300000e-11 80.5
20 TraesCS6A01G406600 chr7B 83.844 359 50 7 6019 6370 181408271 181407914 1.020000e-87 335.0
21 TraesCS6A01G406600 chr3B 83.889 360 46 9 6019 6370 377420060 377419705 3.680000e-87 333.0
22 TraesCS6A01G406600 chr4A 83.799 358 46 11 6019 6370 550136879 550137230 4.770000e-86 329.0
23 TraesCS6A01G406600 chr1A 83.486 218 34 1 3430 3647 556588654 556588439 1.080000e-47 202.0
24 TraesCS6A01G406600 chr2B 85.965 171 24 0 2965 3135 697709314 697709144 3.930000e-42 183.0
25 TraesCS6A01G406600 chr2D 85.380 171 25 0 2965 3135 579758953 579758783 1.830000e-40 178.0
26 TraesCS6A01G406600 chr2D 90.164 61 3 2 5957 6017 628591558 628591501 6.850000e-10 76.8
27 TraesCS6A01G406600 chr2A 85.380 171 25 0 2965 3135 717386746 717386576 1.830000e-40 178.0
28 TraesCS6A01G406600 chr7A 100.000 94 0 0 5549 5642 321668389 321668482 2.360000e-39 174.0
29 TraesCS6A01G406600 chr7A 92.647 68 2 3 5952 6019 77168368 77168432 1.890000e-15 95.3
30 TraesCS6A01G406600 chr1D 93.651 63 1 3 5957 6019 270617818 270617877 2.450000e-14 91.6
31 TraesCS6A01G406600 chr4D 91.045 67 2 3 5952 6018 495893741 495893679 3.170000e-13 87.9
32 TraesCS6A01G406600 chr5B 94.340 53 2 1 5952 6004 340615700 340615649 5.300000e-11 80.5


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 TraesCS6A01G406600 chr6A 611850596 611856971 6375 False 11775.0 11775 100.0000 1 6376 1 chr6A.!!$F1 6375
1 TraesCS6A01G406600 chr6D 465202254 465208603 6349 False 1743.6 3648 89.5092 180 6370 5 chr6D.!!$F2 6190
2 TraesCS6A01G406600 chr6B 710096039 710101649 5610 False 1445.2 3025 90.1910 101 5827 5 chr6B.!!$F1 5726

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
56 57 0.032130 CCGGTGTGATAGATCGGTGG 59.968 60.000 0.00 0.0 36.38 4.61 F
245 254 0.179936 CTCCTCCATCACTTGGCCTC 59.820 60.000 3.32 0.0 46.01 4.70 F
1155 1325 0.310854 CTTCAGGAACAAACACCGGC 59.689 55.000 0.00 0.0 0.00 6.13 F
1312 1482 1.244019 GCATGGGCAAGGAAAGACGT 61.244 55.000 0.00 0.0 40.72 4.34 F
1356 1526 3.845259 GGCGAGTATGCCGGTGGA 61.845 66.667 1.90 0.0 46.75 4.02 F
1533 1703 4.081697 GGAAAGTACACATGGGAAAATGGG 60.082 45.833 0.00 0.0 36.98 4.00 F
3137 3356 2.673368 GGAAATCTGAAGTGCAGGTACG 59.327 50.000 0.00 0.0 44.98 3.67 F
4592 4913 0.322187 ATAACCCAACAGACCCGTGC 60.322 55.000 0.00 0.0 0.00 5.34 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1599 1769 0.457166 TGCCTTCGTACGAATCACCG 60.457 55.000 29.25 17.46 33.28 4.94 R
1641 1811 5.892119 ACTCCATGTATAGATACCATACCCG 59.108 44.000 0.00 0.00 32.33 5.28 R
2401 2602 0.995728 GCTAGCACAGCGAAGTCTTC 59.004 55.000 10.63 2.18 41.37 2.87 R
2881 3088 3.428870 AGCAGAAATAACTTCACGACGTG 59.571 43.478 21.88 21.88 36.40 4.49 R
2882 3089 3.650139 AGCAGAAATAACTTCACGACGT 58.350 40.909 0.00 0.00 36.40 4.34 R
3446 3724 3.249917 ACAACAAAACGGAACTGCAAAG 58.750 40.909 0.00 0.00 0.00 2.77 R
5055 5383 0.107456 AAGCTCCCACTCTGTGTGTG 59.893 55.000 8.81 0.00 44.81 3.82 R
5654 6061 0.040058 TTCCAGATGCCCAGCACATT 59.960 50.000 0.00 0.00 43.04 2.71 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 21 3.469008 AATGTTTCCTCGCGGATATCA 57.531 42.857 6.13 0.00 39.58 2.15
21 22 2.971660 TGTTTCCTCGCGGATATCAA 57.028 45.000 6.13 0.00 39.58 2.57
22 23 2.546778 TGTTTCCTCGCGGATATCAAC 58.453 47.619 6.13 0.00 39.58 3.18
23 24 2.093921 TGTTTCCTCGCGGATATCAACA 60.094 45.455 6.13 5.52 39.58 3.33
24 25 2.933906 GTTTCCTCGCGGATATCAACAA 59.066 45.455 6.13 0.00 39.58 2.83
25 26 2.971660 TCCTCGCGGATATCAACAAA 57.028 45.000 6.13 0.00 33.30 2.83
26 27 3.469008 TCCTCGCGGATATCAACAAAT 57.531 42.857 6.13 0.00 33.30 2.32
27 28 4.594123 TCCTCGCGGATATCAACAAATA 57.406 40.909 6.13 0.00 33.30 1.40
28 29 5.147330 TCCTCGCGGATATCAACAAATAT 57.853 39.130 6.13 0.00 33.30 1.28
29 30 5.547465 TCCTCGCGGATATCAACAAATATT 58.453 37.500 6.13 0.00 33.30 1.28
30 31 5.408299 TCCTCGCGGATATCAACAAATATTG 59.592 40.000 6.13 0.00 33.30 1.90
31 32 5.390885 CCTCGCGGATATCAACAAATATTGG 60.391 44.000 6.13 0.00 34.12 3.16
32 33 5.060506 TCGCGGATATCAACAAATATTGGT 58.939 37.500 6.13 0.00 34.12 3.67
33 34 5.529430 TCGCGGATATCAACAAATATTGGTT 59.471 36.000 6.13 2.11 34.12 3.67
34 35 5.624900 CGCGGATATCAACAAATATTGGTTG 59.375 40.000 24.33 24.33 44.35 3.77
35 36 5.920273 GCGGATATCAACAAATATTGGTTGG 59.080 40.000 27.82 15.81 43.44 3.77
36 37 6.460953 GCGGATATCAACAAATATTGGTTGGT 60.461 38.462 27.82 25.09 43.44 3.67
37 38 7.138736 CGGATATCAACAAATATTGGTTGGTC 58.861 38.462 27.82 22.51 43.44 4.02
38 39 7.433680 GGATATCAACAAATATTGGTTGGTCC 58.566 38.462 27.82 25.73 43.44 4.46
39 40 4.775058 TCAACAAATATTGGTTGGTCCG 57.225 40.909 27.82 9.13 43.44 4.79
40 41 3.508012 TCAACAAATATTGGTTGGTCCGG 59.492 43.478 27.82 8.52 43.44 5.14
41 42 3.163616 ACAAATATTGGTTGGTCCGGT 57.836 42.857 0.00 0.00 39.52 5.28
42 43 2.823154 ACAAATATTGGTTGGTCCGGTG 59.177 45.455 0.00 0.00 39.52 4.94
43 44 2.823154 CAAATATTGGTTGGTCCGGTGT 59.177 45.455 0.00 0.00 39.52 4.16
44 45 2.122783 ATATTGGTTGGTCCGGTGTG 57.877 50.000 0.00 0.00 39.52 3.82
45 46 1.057471 TATTGGTTGGTCCGGTGTGA 58.943 50.000 0.00 0.00 39.52 3.58
46 47 0.404040 ATTGGTTGGTCCGGTGTGAT 59.596 50.000 0.00 0.00 39.52 3.06
47 48 1.057471 TTGGTTGGTCCGGTGTGATA 58.943 50.000 0.00 0.00 39.52 2.15
48 49 0.611200 TGGTTGGTCCGGTGTGATAG 59.389 55.000 0.00 0.00 39.52 2.08
49 50 0.899720 GGTTGGTCCGGTGTGATAGA 59.100 55.000 0.00 0.00 0.00 1.98
50 51 1.485066 GGTTGGTCCGGTGTGATAGAT 59.515 52.381 0.00 0.00 0.00 1.98
51 52 2.483188 GGTTGGTCCGGTGTGATAGATC 60.483 54.545 0.00 0.00 0.00 2.75
52 53 1.029681 TGGTCCGGTGTGATAGATCG 58.970 55.000 0.00 0.00 0.00 3.69
53 54 0.314302 GGTCCGGTGTGATAGATCGG 59.686 60.000 0.00 0.00 41.80 4.18
54 55 1.030457 GTCCGGTGTGATAGATCGGT 58.970 55.000 0.00 0.00 41.27 4.69
55 56 1.029681 TCCGGTGTGATAGATCGGTG 58.970 55.000 0.00 0.00 41.27 4.94
56 57 0.032130 CCGGTGTGATAGATCGGTGG 59.968 60.000 0.00 0.00 36.38 4.61
57 58 0.744874 CGGTGTGATAGATCGGTGGT 59.255 55.000 0.00 0.00 0.00 4.16
58 59 1.536072 CGGTGTGATAGATCGGTGGTG 60.536 57.143 0.00 0.00 0.00 4.17
59 60 1.202533 GGTGTGATAGATCGGTGGTGG 60.203 57.143 0.00 0.00 0.00 4.61
60 61 1.119684 TGTGATAGATCGGTGGTGGG 58.880 55.000 0.00 0.00 0.00 4.61
61 62 0.249911 GTGATAGATCGGTGGTGGGC 60.250 60.000 0.00 0.00 0.00 5.36
62 63 1.371558 GATAGATCGGTGGTGGGCC 59.628 63.158 0.00 0.00 0.00 5.80
63 64 1.074471 ATAGATCGGTGGTGGGCCT 60.074 57.895 4.53 0.00 35.27 5.19
64 65 1.122019 ATAGATCGGTGGTGGGCCTC 61.122 60.000 4.53 0.00 35.27 4.70
65 66 4.176752 GATCGGTGGTGGGCCTCC 62.177 72.222 17.79 17.79 43.26 4.30
68 69 4.489771 CGGTGGTGGGCCTCCATC 62.490 72.222 28.57 26.68 46.16 3.51
71 72 2.204136 TGGTGGGCCTCCATCACT 60.204 61.111 23.02 0.00 46.55 3.41
72 73 1.852157 TGGTGGGCCTCCATCACTT 60.852 57.895 23.02 0.00 46.55 3.16
73 74 1.379044 GGTGGGCCTCCATCACTTG 60.379 63.158 19.59 0.00 46.09 3.16
74 75 1.379044 GTGGGCCTCCATCACTTGG 60.379 63.158 4.53 0.00 46.09 3.61
75 76 2.440980 GGGCCTCCATCACTTGGC 60.441 66.667 0.84 0.00 46.01 4.52
76 77 2.679716 GGCCTCCATCACTTGGCT 59.320 61.111 0.00 0.00 46.01 4.75
77 78 1.452833 GGCCTCCATCACTTGGCTC 60.453 63.158 0.00 0.00 46.01 4.70
78 79 1.452833 GCCTCCATCACTTGGCTCC 60.453 63.158 0.00 0.00 46.01 4.70
79 80 1.993653 CCTCCATCACTTGGCTCCA 59.006 57.895 0.00 0.00 46.01 3.86
80 81 0.549950 CCTCCATCACTTGGCTCCAT 59.450 55.000 0.00 0.00 46.01 3.41
81 82 1.676746 CTCCATCACTTGGCTCCATG 58.323 55.000 0.79 0.79 46.01 3.66
82 83 0.994247 TCCATCACTTGGCTCCATGT 59.006 50.000 2.01 2.01 46.01 3.21
83 84 1.065199 TCCATCACTTGGCTCCATGTC 60.065 52.381 4.66 0.00 46.01 3.06
84 85 1.064906 CCATCACTTGGCTCCATGTCT 60.065 52.381 4.66 0.00 39.09 3.41
85 86 2.171237 CCATCACTTGGCTCCATGTCTA 59.829 50.000 4.66 0.00 39.09 2.59
86 87 3.181447 CCATCACTTGGCTCCATGTCTAT 60.181 47.826 4.66 0.56 39.09 1.98
87 88 4.458397 CATCACTTGGCTCCATGTCTATT 58.542 43.478 4.66 0.00 32.98 1.73
88 89 4.574674 TCACTTGGCTCCATGTCTATTT 57.425 40.909 4.66 0.00 32.98 1.40
89 90 4.922206 TCACTTGGCTCCATGTCTATTTT 58.078 39.130 4.66 0.00 32.98 1.82
90 91 6.061022 TCACTTGGCTCCATGTCTATTTTA 57.939 37.500 4.66 0.00 32.98 1.52
91 92 6.115446 TCACTTGGCTCCATGTCTATTTTAG 58.885 40.000 4.66 0.00 32.98 1.85
92 93 4.884164 ACTTGGCTCCATGTCTATTTTAGC 59.116 41.667 2.01 0.00 29.96 3.09
93 94 4.778213 TGGCTCCATGTCTATTTTAGCT 57.222 40.909 0.00 0.00 0.00 3.32
94 95 4.708177 TGGCTCCATGTCTATTTTAGCTC 58.292 43.478 0.00 0.00 0.00 4.09
95 96 4.068599 GGCTCCATGTCTATTTTAGCTCC 58.931 47.826 0.00 0.00 0.00 4.70
96 97 4.202409 GGCTCCATGTCTATTTTAGCTCCT 60.202 45.833 0.00 0.00 0.00 3.69
97 98 5.372373 GCTCCATGTCTATTTTAGCTCCTT 58.628 41.667 0.00 0.00 0.00 3.36
98 99 5.238214 GCTCCATGTCTATTTTAGCTCCTTG 59.762 44.000 0.00 0.00 0.00 3.61
99 100 6.313519 TCCATGTCTATTTTAGCTCCTTGT 57.686 37.500 0.00 0.00 0.00 3.16
115 116 1.427895 TTGTTTCCGTCCATGGGGGA 61.428 55.000 18.27 18.27 45.89 4.81
144 145 5.006153 TCTGGATGACCACTAACAATACG 57.994 43.478 0.00 0.00 41.77 3.06
156 157 8.019094 ACCACTAACAATACGCTTTAATGTTTC 58.981 33.333 0.00 0.00 35.89 2.78
157 158 7.483691 CCACTAACAATACGCTTTAATGTTTCC 59.516 37.037 0.00 0.00 35.89 3.13
159 160 8.736244 ACTAACAATACGCTTTAATGTTTCCAT 58.264 29.630 0.00 0.00 35.89 3.41
164 165 5.957842 ACGCTTTAATGTTTCCATTCAGA 57.042 34.783 0.00 0.00 41.50 3.27
167 168 6.071952 ACGCTTTAATGTTTCCATTCAGACAT 60.072 34.615 0.00 0.00 41.50 3.06
169 170 7.967854 CGCTTTAATGTTTCCATTCAGACATAA 59.032 33.333 0.00 0.00 41.50 1.90
170 171 9.076596 GCTTTAATGTTTCCATTCAGACATAAC 57.923 33.333 0.00 0.00 41.50 1.89
173 174 9.513906 TTAATGTTTCCATTCAGACATAACTGA 57.486 29.630 0.00 0.00 43.83 3.41
174 175 8.585471 AATGTTTCCATTCAGACATAACTGAT 57.415 30.769 0.00 0.00 44.67 2.90
215 216 2.129785 GGATTGCTGGATGGGTGGC 61.130 63.158 0.00 0.00 0.00 5.01
240 249 1.202463 CCTACGCTCCTCCATCACTTG 60.202 57.143 0.00 0.00 0.00 3.16
242 251 1.817099 CGCTCCTCCATCACTTGGC 60.817 63.158 0.00 0.00 46.01 4.52
243 252 1.452833 GCTCCTCCATCACTTGGCC 60.453 63.158 0.00 0.00 46.01 5.36
244 253 1.919600 GCTCCTCCATCACTTGGCCT 61.920 60.000 3.32 0.00 46.01 5.19
245 254 0.179936 CTCCTCCATCACTTGGCCTC 59.820 60.000 3.32 0.00 46.01 4.70
253 262 1.303643 CACTTGGCCTCCCCTGTTC 60.304 63.158 3.32 0.00 0.00 3.18
385 421 4.660938 GGTGGGTGGTGGACCTGC 62.661 72.222 0.00 0.00 45.33 4.85
389 425 2.363975 GGGTGGTGGACCTGCGATA 61.364 63.158 0.00 0.00 45.33 2.92
405 441 4.183865 TGCGATACTCCATTCAGTTCAAG 58.816 43.478 0.00 0.00 0.00 3.02
406 442 3.001736 GCGATACTCCATTCAGTTCAAGC 59.998 47.826 0.00 0.00 0.00 4.01
421 457 0.679321 CAAGCCCCCTCTGCTTTCTC 60.679 60.000 0.00 0.00 46.47 2.87
423 459 1.223211 GCCCCCTCTGCTTTCTCTC 59.777 63.158 0.00 0.00 0.00 3.20
443 479 8.596781 TCTCTCTACCTAGCTATTTGTTTTCT 57.403 34.615 0.00 0.00 0.00 2.52
453 489 5.239525 AGCTATTTGTTTTCTTCTTCTGCGT 59.760 36.000 0.00 0.00 0.00 5.24
484 520 2.315925 TCCGTGCTCTGGATTTGATC 57.684 50.000 0.00 0.00 0.00 2.92
500 536 2.329267 TGATCCATTCCCTCGCTACAT 58.671 47.619 0.00 0.00 0.00 2.29
506 542 2.890808 TTCCCTCGCTACATCATCAC 57.109 50.000 0.00 0.00 0.00 3.06
621 782 3.932545 TTTTTATGCTGGATTGTGCGT 57.067 38.095 0.00 0.00 0.00 5.24
624 785 0.451383 TATGCTGGATTGTGCGTTGC 59.549 50.000 0.00 0.00 0.00 4.17
625 786 1.525718 ATGCTGGATTGTGCGTTGCA 61.526 50.000 0.00 0.00 35.60 4.08
645 813 3.274288 CAGCCCTATCTCTTGGTTTGAC 58.726 50.000 0.00 0.00 0.00 3.18
657 825 0.958876 GGTTTGACTTCCGCCCGATT 60.959 55.000 0.00 0.00 0.00 3.34
744 914 2.212652 TCAGACATGTGTGTTGTGCTC 58.787 47.619 21.18 0.00 39.09 4.26
756 926 4.511454 TGTGTTGTGCTCTTGTACAGATTC 59.489 41.667 0.00 0.00 39.77 2.52
770 940 3.416156 ACAGATTCTGCTGAGGGTTTTC 58.584 45.455 13.64 0.00 39.20 2.29
771 941 3.181440 ACAGATTCTGCTGAGGGTTTTCA 60.181 43.478 13.64 0.00 39.20 2.69
772 942 3.190118 CAGATTCTGCTGAGGGTTTTCAC 59.810 47.826 0.00 0.00 38.14 3.18
773 943 3.073650 AGATTCTGCTGAGGGTTTTCACT 59.926 43.478 0.00 0.00 35.53 3.41
774 944 3.297134 TTCTGCTGAGGGTTTTCACTT 57.703 42.857 0.00 0.00 31.31 3.16
819 989 2.563179 AGCCTCGATGTACACTCAAGTT 59.437 45.455 0.00 0.00 0.00 2.66
842 1012 9.084533 AGTTTTCACCCTATGACTATCTCTATC 57.915 37.037 0.00 0.00 36.92 2.08
843 1013 9.084533 GTTTTCACCCTATGACTATCTCTATCT 57.915 37.037 0.00 0.00 36.92 1.98
866 1036 7.711846 TCTTCATGAGAATGTTTTCCGAAAAA 58.288 30.769 7.88 0.40 32.31 1.94
867 1037 8.359642 TCTTCATGAGAATGTTTTCCGAAAAAT 58.640 29.630 7.88 2.54 33.56 1.82
868 1038 8.519492 TTCATGAGAATGTTTTCCGAAAAATC 57.481 30.769 7.88 7.34 36.77 2.17
870 1040 8.359642 TCATGAGAATGTTTTCCGAAAAATCTT 58.640 29.630 7.88 2.78 36.77 2.40
872 1042 9.626045 ATGAGAATGTTTTCCGAAAAATCTTAC 57.374 29.630 7.88 0.00 36.77 2.34
873 1043 8.846211 TGAGAATGTTTTCCGAAAAATCTTACT 58.154 29.630 7.88 4.10 36.77 2.24
874 1044 9.118236 GAGAATGTTTTCCGAAAAATCTTACTG 57.882 33.333 7.88 0.00 36.77 2.74
875 1045 8.630037 AGAATGTTTTCCGAAAAATCTTACTGT 58.370 29.630 7.88 0.00 36.77 3.55
877 1047 8.797266 ATGTTTTCCGAAAAATCTTACTGTTC 57.203 30.769 7.88 0.00 36.77 3.18
878 1048 6.908284 TGTTTTCCGAAAAATCTTACTGTTCG 59.092 34.615 7.88 0.00 40.47 3.95
882 1052 4.149396 CCGAAAAATCTTACTGTTCGTCGT 59.851 41.667 0.00 0.00 39.45 4.34
918 1088 9.254133 CCAGATGTTAAGTATTACTCACTGATG 57.746 37.037 0.00 0.00 0.00 3.07
919 1089 9.809096 CAGATGTTAAGTATTACTCACTGATGT 57.191 33.333 0.00 0.00 0.00 3.06
967 1137 4.651503 TGTGGTCTGAATCTATCTTCTCCC 59.348 45.833 0.00 0.00 0.00 4.30
991 1161 3.385384 TGGGCGAGTCCTGCTCTG 61.385 66.667 0.00 0.00 41.98 3.35
1050 1220 0.490017 TACAGGGGGTCTCCAGTTCA 59.510 55.000 0.00 0.00 37.22 3.18
1155 1325 0.310854 CTTCAGGAACAAACACCGGC 59.689 55.000 0.00 0.00 0.00 6.13
1312 1482 1.244019 GCATGGGCAAGGAAAGACGT 61.244 55.000 0.00 0.00 40.72 4.34
1326 1496 4.636435 ACGTTGTGGCCTTCCGGG 62.636 66.667 3.32 0.00 38.36 5.73
1356 1526 3.845259 GGCGAGTATGCCGGTGGA 61.845 66.667 1.90 0.00 46.75 4.02
1533 1703 4.081697 GGAAAGTACACATGGGAAAATGGG 60.082 45.833 0.00 0.00 36.98 4.00
1599 1769 7.225931 GGAAAGGGAACATTTACTTGGAAAAAC 59.774 37.037 0.00 0.00 0.00 2.43
2373 2574 8.183830 TCTAGCAAAAGTTTGACAACAAATTG 57.816 30.769 7.96 0.00 45.71 2.32
2401 2602 4.380531 TCTCTGCTGAAAAGTAACAGTGG 58.619 43.478 0.00 0.00 36.62 4.00
2500 2705 5.121811 CCTCTTAGGAACTGATGGAACATG 58.878 45.833 0.00 0.00 42.54 3.21
2552 2757 4.281435 TGTTGAAACATCAGGCATTCACAT 59.719 37.500 0.00 0.00 33.17 3.21
2888 3095 8.598075 GTTATTTGGACTTATAAATCACGTCGT 58.402 33.333 0.00 0.00 0.00 4.34
2894 3101 6.309737 GGACTTATAAATCACGTCGTGAAGTT 59.690 38.462 30.05 26.00 45.96 2.66
2895 3102 7.485913 GGACTTATAAATCACGTCGTGAAGTTA 59.514 37.037 30.05 27.04 45.96 2.24
2896 3103 8.922058 ACTTATAAATCACGTCGTGAAGTTAT 57.078 30.769 30.37 30.37 45.96 1.89
2901 3108 5.763444 ATCACGTCGTGAAGTTATTTCTG 57.237 39.130 30.05 0.00 45.96 3.02
2902 3109 3.427528 TCACGTCGTGAAGTTATTTCTGC 59.572 43.478 25.13 0.00 39.78 4.26
2903 3110 3.428870 CACGTCGTGAAGTTATTTCTGCT 59.571 43.478 20.75 0.00 35.23 4.24
2904 3111 3.673809 ACGTCGTGAAGTTATTTCTGCTC 59.326 43.478 0.00 0.00 36.71 4.26
2905 3112 3.673338 CGTCGTGAAGTTATTTCTGCTCA 59.327 43.478 0.00 0.00 36.71 4.26
2907 3114 5.163953 CGTCGTGAAGTTATTTCTGCTCATT 60.164 40.000 0.00 0.00 36.71 2.57
2908 3115 6.034577 CGTCGTGAAGTTATTTCTGCTCATTA 59.965 38.462 0.00 0.00 36.71 1.90
2909 3116 7.254117 CGTCGTGAAGTTATTTCTGCTCATTAT 60.254 37.037 0.00 0.00 36.71 1.28
3000 3219 3.380637 AGATGTTCAAGATTGATGCTGCC 59.619 43.478 0.00 0.00 37.00 4.85
3137 3356 2.673368 GGAAATCTGAAGTGCAGGTACG 59.327 50.000 0.00 0.00 44.98 3.67
3153 3372 4.868734 CAGGTACGTTTTTCTATCTGGACC 59.131 45.833 0.00 0.00 0.00 4.46
3156 3375 5.105432 GGTACGTTTTTCTATCTGGACCTCT 60.105 44.000 0.00 0.00 0.00 3.69
3159 3378 5.187967 ACGTTTTTCTATCTGGACCTCTCAT 59.812 40.000 0.00 0.00 0.00 2.90
3160 3379 6.109359 CGTTTTTCTATCTGGACCTCTCATT 58.891 40.000 0.00 0.00 0.00 2.57
3161 3380 7.093465 ACGTTTTTCTATCTGGACCTCTCATTA 60.093 37.037 0.00 0.00 0.00 1.90
3162 3381 7.928706 CGTTTTTCTATCTGGACCTCTCATTAT 59.071 37.037 0.00 0.00 0.00 1.28
3179 3453 9.755804 CTCTCATTATATAAGCTTGTTCAGTGA 57.244 33.333 9.86 6.25 0.00 3.41
3213 3487 7.542025 TCTATATATCATGCAGTGCTAGTGTG 58.458 38.462 17.60 7.56 0.00 3.82
3359 3635 7.563724 ACCTTCTAGTGGTCAAAAGGTAATA 57.436 36.000 7.76 0.00 45.96 0.98
3370 3646 9.967451 TGGTCAAAAGGTAATAATCATCAACTA 57.033 29.630 0.00 0.00 0.00 2.24
3379 3655 8.076178 GGTAATAATCATCAACTAATGCACACC 58.924 37.037 0.00 0.00 0.00 4.16
3383 3659 4.910195 TCATCAACTAATGCACACCTCTT 58.090 39.130 0.00 0.00 0.00 2.85
3404 3682 6.987386 TCTTTTGAGGTTTTTCTTGTTCACA 58.013 32.000 0.00 0.00 0.00 3.58
3446 3724 7.245419 ACAATCCTTGTTTATTGTTTGCAAC 57.755 32.000 0.00 0.00 42.22 4.17
3564 3842 7.957484 CGTTCTACTGACAAAATTGAAATCGAT 59.043 33.333 0.00 0.00 0.00 3.59
3600 3878 7.127032 ACTCTGAAGGATTTGGATCTGAACTAT 59.873 37.037 0.00 0.00 32.66 2.12
3621 3899 8.164057 ACTATTCCTTTTATCTGGAACCTTCT 57.836 34.615 0.00 0.00 44.02 2.85
3931 4214 7.597743 GTCATTTTTCAGATTTCTGTGCAGAAT 59.402 33.333 14.43 6.14 45.78 2.40
3932 4215 8.145767 TCATTTTTCAGATTTCTGTGCAGAATT 58.854 29.630 14.43 11.29 45.78 2.17
4043 4326 3.107402 TCTCCCTGAGAGCACTTATGT 57.893 47.619 0.00 0.00 42.90 2.29
4445 4765 2.167900 GGGTGTCATAGTGTCACTACCC 59.832 54.545 20.33 20.33 36.79 3.69
4563 4883 3.260475 TGTGGTTCATGATCCTAACCG 57.740 47.619 20.87 0.00 44.62 4.44
4592 4913 0.322187 ATAACCCAACAGACCCGTGC 60.322 55.000 0.00 0.00 0.00 5.34
5018 5346 2.503356 CAGCTAGGTGAGGGTCATTTCT 59.497 50.000 17.08 0.00 0.00 2.52
5026 5354 5.364157 AGGTGAGGGTCATTTCTATCACTAC 59.636 44.000 0.00 0.00 37.71 2.73
5031 5359 5.600484 AGGGTCATTTCTATCACTACTCCTG 59.400 44.000 0.00 0.00 0.00 3.86
5035 5363 7.921745 GGTCATTTCTATCACTACTCCTGTAAC 59.078 40.741 0.00 0.00 0.00 2.50
5038 5366 8.687242 CATTTCTATCACTACTCCTGTAACAGA 58.313 37.037 0.00 0.00 32.44 3.41
5039 5367 8.824756 TTTCTATCACTACTCCTGTAACAGAT 57.175 34.615 0.00 0.00 32.44 2.90
5051 5379 5.053145 CCTGTAACAGATATGGCTCTGAAC 58.947 45.833 9.00 7.19 44.48 3.18
5055 5383 3.878778 ACAGATATGGCTCTGAACCAAC 58.121 45.455 3.56 0.00 44.48 3.77
5056 5384 3.264193 ACAGATATGGCTCTGAACCAACA 59.736 43.478 3.56 0.00 44.48 3.33
5057 5385 3.624861 CAGATATGGCTCTGAACCAACAC 59.375 47.826 3.56 0.00 44.48 3.32
5058 5386 3.264193 AGATATGGCTCTGAACCAACACA 59.736 43.478 3.56 0.00 41.49 3.72
5063 5428 1.331756 GCTCTGAACCAACACACACAG 59.668 52.381 0.00 0.00 0.00 3.66
5089 5454 1.109323 AGCTTTTGGTGACTGGGCAC 61.109 55.000 0.00 0.00 38.05 5.01
5138 5503 2.751436 CTGGGGGTGAACATGCCG 60.751 66.667 0.00 0.00 0.00 5.69
5294 5659 0.589229 CGATGCAGTACGACTCGGTC 60.589 60.000 2.98 0.00 0.00 4.79
5398 5779 2.819595 CGGCCAACCATCACTCCG 60.820 66.667 2.24 0.00 34.57 4.63
5400 5781 3.134127 GCCAACCATCACTCCGGC 61.134 66.667 0.00 0.00 0.00 6.13
5418 5800 4.785453 GAACGCTCCAGCCCCAGG 62.785 72.222 0.00 0.00 37.91 4.45
5505 5895 2.119495 GTCTTCTGGAGGGCTGGATTA 58.881 52.381 0.00 0.00 0.00 1.75
5573 5964 0.825010 GCATGGCTGGGTTATGGAGG 60.825 60.000 0.00 0.00 0.00 4.30
5654 6061 1.077716 TCCGTCGAGATCAGGAGCA 60.078 57.895 0.00 0.00 0.00 4.26
5846 6253 2.231478 CTCTACCGTTCTTGCAAGAGGA 59.769 50.000 31.16 17.17 36.22 3.71
5847 6254 2.832129 TCTACCGTTCTTGCAAGAGGAT 59.168 45.455 31.16 20.67 36.22 3.24
5848 6255 1.813513 ACCGTTCTTGCAAGAGGATG 58.186 50.000 31.16 21.94 36.22 3.51
5849 6256 0.449388 CCGTTCTTGCAAGAGGATGC 59.551 55.000 27.02 15.35 46.58 3.91
5921 6328 2.031333 GCAGGAAGAACTTGAGCTGTTG 60.031 50.000 0.00 0.00 0.00 3.33
5947 6354 7.593644 GTGTAAGCACCCAAAACTAAATAACAG 59.406 37.037 0.00 0.00 39.61 3.16
5973 6389 0.748005 CAGATTTGTAGCACCCGGGG 60.748 60.000 27.92 12.73 0.00 5.73
5974 6390 1.205460 AGATTTGTAGCACCCGGGGT 61.205 55.000 27.92 14.51 35.62 4.95
5992 6408 2.550830 GTGCTCCACACCCCTATATG 57.449 55.000 0.00 0.00 44.02 1.78
5993 6409 2.047061 GTGCTCCACACCCCTATATGA 58.953 52.381 0.00 0.00 44.02 2.15
5994 6410 2.438021 GTGCTCCACACCCCTATATGAA 59.562 50.000 0.00 0.00 44.02 2.57
5995 6411 2.438021 TGCTCCACACCCCTATATGAAC 59.562 50.000 0.00 0.00 0.00 3.18
5996 6412 2.438021 GCTCCACACCCCTATATGAACA 59.562 50.000 0.00 0.00 0.00 3.18
5997 6413 3.073062 GCTCCACACCCCTATATGAACAT 59.927 47.826 0.00 0.00 0.00 2.71
5998 6414 4.446311 GCTCCACACCCCTATATGAACATT 60.446 45.833 0.00 0.00 0.00 2.71
5999 6415 5.221843 GCTCCACACCCCTATATGAACATTA 60.222 44.000 0.00 0.00 0.00 1.90
6000 6416 6.690460 GCTCCACACCCCTATATGAACATTAA 60.690 42.308 0.00 0.00 0.00 1.40
6001 6417 7.214460 TCCACACCCCTATATGAACATTAAA 57.786 36.000 0.00 0.00 0.00 1.52
6002 6418 7.821566 TCCACACCCCTATATGAACATTAAAT 58.178 34.615 0.00 0.00 0.00 1.40
6003 6419 8.285891 TCCACACCCCTATATGAACATTAAATT 58.714 33.333 0.00 0.00 0.00 1.82
6004 6420 8.923270 CCACACCCCTATATGAACATTAAATTT 58.077 33.333 0.00 0.00 0.00 1.82
6029 6445 0.323087 AAAATACCGCTCCACACCCC 60.323 55.000 0.00 0.00 0.00 4.95
6047 6463 7.716123 CCACACCCCTATACGAACATTAAATTA 59.284 37.037 0.00 0.00 0.00 1.40
6117 6536 0.398098 GGGGTCCCGATCTACTTCCA 60.398 60.000 0.48 0.00 0.00 3.53
6123 6542 3.132289 GTCCCGATCTACTTCCATGTGAA 59.868 47.826 0.00 0.00 0.00 3.18
6134 6553 8.717821 TCTACTTCCATGTGAAATTTCGTTAAG 58.282 33.333 13.34 11.93 31.06 1.85
6161 6582 4.160065 TCCATGAAACATATTGGTGGCAAG 59.840 41.667 0.00 0.00 0.00 4.01
6164 6585 5.798125 TGAAACATATTGGTGGCAAGAAA 57.202 34.783 0.00 0.00 0.00 2.52
6232 6653 9.203421 GATTTTTGTTCGGACAATATTTCCTTT 57.797 29.630 10.76 0.00 44.71 3.11
6237 6658 4.277476 TCGGACAATATTTCCTTTGCCAT 58.723 39.130 12.12 0.00 0.00 4.40
6239 6660 4.142182 CGGACAATATTTCCTTTGCCATGT 60.142 41.667 12.12 0.00 0.00 3.21
6244 6665 8.532186 ACAATATTTCCTTTGCCATGTATACA 57.468 30.769 8.27 8.27 0.00 2.29
6255 6676 6.199557 TGCCATGTATACATTTCCTGGTAT 57.800 37.500 15.85 0.00 33.61 2.73
6314 6735 3.068024 CCCACGTTTCATATCCCCAAATG 59.932 47.826 0.00 0.00 0.00 2.32
6326 6747 9.354673 TCATATCCCCAAATGTTAGATTCTTTC 57.645 33.333 0.00 0.00 0.00 2.62
6327 6748 8.579863 CATATCCCCAAATGTTAGATTCTTTCC 58.420 37.037 0.00 0.00 0.00 3.13
6329 6750 6.502138 TCCCCAAATGTTAGATTCTTTCCAT 58.498 36.000 0.00 0.00 0.00 3.41
6330 6751 6.959366 TCCCCAAATGTTAGATTCTTTCCATT 59.041 34.615 0.00 0.00 0.00 3.16
6331 6752 7.457535 TCCCCAAATGTTAGATTCTTTCCATTT 59.542 33.333 9.98 9.98 33.97 2.32
6332 6753 8.102676 CCCCAAATGTTAGATTCTTTCCATTTT 58.897 33.333 11.85 0.00 32.00 1.82
6333 6754 9.506018 CCCAAATGTTAGATTCTTTCCATTTTT 57.494 29.630 11.85 0.00 32.00 1.94
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
8 9 5.179368 ACCAATATTTGTTGATATCCGCGAG 59.821 40.000 8.23 0.00 0.00 5.03
9 10 5.060506 ACCAATATTTGTTGATATCCGCGA 58.939 37.500 8.23 0.00 0.00 5.87
10 11 5.356882 ACCAATATTTGTTGATATCCGCG 57.643 39.130 0.00 0.00 0.00 6.46
11 12 5.920273 CCAACCAATATTTGTTGATATCCGC 59.080 40.000 26.05 0.00 0.00 5.54
12 13 7.038154 ACCAACCAATATTTGTTGATATCCG 57.962 36.000 26.05 14.59 0.00 4.18
13 14 7.433680 GGACCAACCAATATTTGTTGATATCC 58.566 38.462 26.05 23.31 38.79 2.59
14 15 7.138736 CGGACCAACCAATATTTGTTGATATC 58.861 38.462 26.05 20.07 38.90 1.63
15 16 6.040391 CCGGACCAACCAATATTTGTTGATAT 59.960 38.462 26.05 14.97 38.90 1.63
16 17 5.358442 CCGGACCAACCAATATTTGTTGATA 59.642 40.000 26.05 0.00 38.90 2.15
17 18 4.159506 CCGGACCAACCAATATTTGTTGAT 59.840 41.667 26.05 14.86 38.90 2.57
18 19 3.508012 CCGGACCAACCAATATTTGTTGA 59.492 43.478 26.05 0.00 38.90 3.18
19 20 3.257127 ACCGGACCAACCAATATTTGTTG 59.743 43.478 20.30 20.30 38.90 3.33
20 21 3.257127 CACCGGACCAACCAATATTTGTT 59.743 43.478 9.46 0.00 38.90 2.83
21 22 2.823154 CACCGGACCAACCAATATTTGT 59.177 45.455 9.46 0.00 38.90 2.83
22 23 2.823154 ACACCGGACCAACCAATATTTG 59.177 45.455 9.46 0.00 38.90 2.32
23 24 2.823154 CACACCGGACCAACCAATATTT 59.177 45.455 9.46 0.00 38.90 1.40
24 25 2.040545 TCACACCGGACCAACCAATATT 59.959 45.455 9.46 0.00 38.90 1.28
25 26 1.631388 TCACACCGGACCAACCAATAT 59.369 47.619 9.46 0.00 38.90 1.28
26 27 1.057471 TCACACCGGACCAACCAATA 58.943 50.000 9.46 0.00 38.90 1.90
27 28 0.404040 ATCACACCGGACCAACCAAT 59.596 50.000 9.46 0.00 38.90 3.16
28 29 1.002659 CTATCACACCGGACCAACCAA 59.997 52.381 9.46 0.00 38.90 3.67
29 30 0.611200 CTATCACACCGGACCAACCA 59.389 55.000 9.46 0.00 38.90 3.67
30 31 0.899720 TCTATCACACCGGACCAACC 59.100 55.000 9.46 0.00 0.00 3.77
31 32 2.798499 CGATCTATCACACCGGACCAAC 60.798 54.545 9.46 0.00 0.00 3.77
32 33 1.407618 CGATCTATCACACCGGACCAA 59.592 52.381 9.46 0.00 0.00 3.67
33 34 1.029681 CGATCTATCACACCGGACCA 58.970 55.000 9.46 0.00 0.00 4.02
34 35 0.314302 CCGATCTATCACACCGGACC 59.686 60.000 9.46 0.00 42.49 4.46
35 36 1.030457 ACCGATCTATCACACCGGAC 58.970 55.000 9.46 0.00 42.49 4.79
36 37 1.029681 CACCGATCTATCACACCGGA 58.970 55.000 9.46 0.00 42.49 5.14
37 38 0.032130 CCACCGATCTATCACACCGG 59.968 60.000 0.00 0.00 45.09 5.28
38 39 0.744874 ACCACCGATCTATCACACCG 59.255 55.000 0.00 0.00 0.00 4.94
39 40 1.202533 CCACCACCGATCTATCACACC 60.203 57.143 0.00 0.00 0.00 4.16
40 41 1.202533 CCCACCACCGATCTATCACAC 60.203 57.143 0.00 0.00 0.00 3.82
41 42 1.119684 CCCACCACCGATCTATCACA 58.880 55.000 0.00 0.00 0.00 3.58
42 43 0.249911 GCCCACCACCGATCTATCAC 60.250 60.000 0.00 0.00 0.00 3.06
43 44 1.407656 GGCCCACCACCGATCTATCA 61.408 60.000 0.00 0.00 35.26 2.15
44 45 1.122019 AGGCCCACCACCGATCTATC 61.122 60.000 0.00 0.00 39.06 2.08
45 46 1.074471 AGGCCCACCACCGATCTAT 60.074 57.895 0.00 0.00 39.06 1.98
46 47 1.760875 GAGGCCCACCACCGATCTA 60.761 63.158 0.00 0.00 39.06 1.98
47 48 3.083997 GAGGCCCACCACCGATCT 61.084 66.667 0.00 0.00 39.06 2.75
48 49 4.176752 GGAGGCCCACCACCGATC 62.177 72.222 11.18 0.00 36.92 3.69
52 53 3.338250 TGATGGAGGCCCACCACC 61.338 66.667 19.52 12.15 46.98 4.61
54 55 1.852157 AAGTGATGGAGGCCCACCA 60.852 57.895 19.44 19.44 46.98 4.17
55 56 1.379044 CAAGTGATGGAGGCCCACC 60.379 63.158 0.00 3.98 46.98 4.61
56 57 4.326255 CAAGTGATGGAGGCCCAC 57.674 61.111 0.00 0.00 46.98 4.61
65 66 2.414994 AGACATGGAGCCAAGTGATG 57.585 50.000 1.64 0.00 0.00 3.07
66 67 4.785346 AATAGACATGGAGCCAAGTGAT 57.215 40.909 1.64 0.00 0.00 3.06
67 68 4.574674 AAATAGACATGGAGCCAAGTGA 57.425 40.909 1.64 0.00 0.00 3.41
68 69 5.220931 GCTAAAATAGACATGGAGCCAAGTG 60.221 44.000 1.64 0.00 0.00 3.16
69 70 4.884164 GCTAAAATAGACATGGAGCCAAGT 59.116 41.667 0.00 0.00 0.00 3.16
70 71 5.128919 AGCTAAAATAGACATGGAGCCAAG 58.871 41.667 0.00 0.00 0.00 3.61
71 72 5.116084 AGCTAAAATAGACATGGAGCCAA 57.884 39.130 0.00 0.00 0.00 4.52
72 73 4.444876 GGAGCTAAAATAGACATGGAGCCA 60.445 45.833 0.00 0.00 0.00 4.75
73 74 4.068599 GGAGCTAAAATAGACATGGAGCC 58.931 47.826 0.00 0.00 0.00 4.70
74 75 4.967036 AGGAGCTAAAATAGACATGGAGC 58.033 43.478 0.00 0.00 0.00 4.70
75 76 6.352516 ACAAGGAGCTAAAATAGACATGGAG 58.647 40.000 0.00 0.00 0.00 3.86
76 77 6.313519 ACAAGGAGCTAAAATAGACATGGA 57.686 37.500 0.00 0.00 0.00 3.41
77 78 7.396540 AAACAAGGAGCTAAAATAGACATGG 57.603 36.000 0.00 0.00 0.00 3.66
78 79 7.475840 GGAAACAAGGAGCTAAAATAGACATG 58.524 38.462 0.00 0.00 0.00 3.21
79 80 6.316390 CGGAAACAAGGAGCTAAAATAGACAT 59.684 38.462 0.00 0.00 0.00 3.06
80 81 5.642063 CGGAAACAAGGAGCTAAAATAGACA 59.358 40.000 0.00 0.00 0.00 3.41
81 82 5.642491 ACGGAAACAAGGAGCTAAAATAGAC 59.358 40.000 0.00 0.00 0.00 2.59
82 83 5.801380 ACGGAAACAAGGAGCTAAAATAGA 58.199 37.500 0.00 0.00 0.00 1.98
83 84 5.064834 GGACGGAAACAAGGAGCTAAAATAG 59.935 44.000 0.00 0.00 0.00 1.73
84 85 4.939439 GGACGGAAACAAGGAGCTAAAATA 59.061 41.667 0.00 0.00 0.00 1.40
85 86 3.756963 GGACGGAAACAAGGAGCTAAAAT 59.243 43.478 0.00 0.00 0.00 1.82
86 87 3.143728 GGACGGAAACAAGGAGCTAAAA 58.856 45.455 0.00 0.00 0.00 1.52
87 88 2.105134 TGGACGGAAACAAGGAGCTAAA 59.895 45.455 0.00 0.00 0.00 1.85
88 89 1.695242 TGGACGGAAACAAGGAGCTAA 59.305 47.619 0.00 0.00 0.00 3.09
89 90 1.344065 TGGACGGAAACAAGGAGCTA 58.656 50.000 0.00 0.00 0.00 3.32
90 91 0.693049 ATGGACGGAAACAAGGAGCT 59.307 50.000 0.00 0.00 0.00 4.09
91 92 0.804989 CATGGACGGAAACAAGGAGC 59.195 55.000 0.00 0.00 0.00 4.70
92 93 1.453155 CCATGGACGGAAACAAGGAG 58.547 55.000 5.56 0.00 0.00 3.69
93 94 0.037590 CCCATGGACGGAAACAAGGA 59.962 55.000 15.22 0.00 0.00 3.36
94 95 0.965363 CCCCATGGACGGAAACAAGG 60.965 60.000 15.22 0.00 0.00 3.61
95 96 0.965363 CCCCCATGGACGGAAACAAG 60.965 60.000 15.22 0.00 35.39 3.16
96 97 1.075836 CCCCCATGGACGGAAACAA 59.924 57.895 15.22 0.00 35.39 2.83
97 98 1.848431 TCCCCCATGGACGGAAACA 60.848 57.895 15.22 0.00 38.61 2.83
98 99 3.083386 TCCCCCATGGACGGAAAC 58.917 61.111 15.22 0.00 38.61 2.78
115 116 6.068010 TGTTAGTGGTCATCCAGAAACAAAT 58.932 36.000 10.09 0.00 45.24 2.32
124 125 3.196901 AGCGTATTGTTAGTGGTCATCCA 59.803 43.478 0.00 0.00 42.05 3.41
156 157 5.601662 ACGGTATCAGTTATGTCTGAATGG 58.398 41.667 5.92 0.93 45.65 3.16
157 158 7.148738 GCATACGGTATCAGTTATGTCTGAATG 60.149 40.741 0.00 5.67 45.65 2.67
159 160 6.183360 TGCATACGGTATCAGTTATGTCTGAA 60.183 38.462 0.00 0.00 45.65 3.02
164 165 6.096673 TCATGCATACGGTATCAGTTATGT 57.903 37.500 0.00 0.00 0.00 2.29
167 168 5.245075 TGGATCATGCATACGGTATCAGTTA 59.755 40.000 0.00 0.00 0.00 2.24
169 170 3.578282 TGGATCATGCATACGGTATCAGT 59.422 43.478 0.00 0.00 0.00 3.41
170 171 4.192429 TGGATCATGCATACGGTATCAG 57.808 45.455 0.00 0.00 0.00 2.90
171 172 4.615588 TTGGATCATGCATACGGTATCA 57.384 40.909 0.00 0.79 0.00 2.15
172 173 5.178061 TCATTGGATCATGCATACGGTATC 58.822 41.667 0.00 0.00 0.00 2.24
173 174 5.164620 TCATTGGATCATGCATACGGTAT 57.835 39.130 0.00 0.00 0.00 2.73
174 175 4.615588 TCATTGGATCATGCATACGGTA 57.384 40.909 0.00 0.00 0.00 4.02
215 216 3.541713 GGAGGAGCGTAGGGCCAG 61.542 72.222 6.18 0.00 45.17 4.85
240 249 1.307084 ACTAGGAACAGGGGAGGCC 60.307 63.158 0.00 0.00 0.00 5.19
242 251 2.952116 CTAGACTAGGAACAGGGGAGG 58.048 57.143 1.11 0.00 0.00 4.30
243 252 2.091555 AGCTAGACTAGGAACAGGGGAG 60.092 54.545 11.48 0.00 0.00 4.30
244 253 1.930914 AGCTAGACTAGGAACAGGGGA 59.069 52.381 11.48 0.00 0.00 4.81
245 254 2.463047 AGCTAGACTAGGAACAGGGG 57.537 55.000 11.48 0.00 0.00 4.79
253 262 7.113658 TCCAGAAACAAATAGCTAGACTAGG 57.886 40.000 11.48 0.00 33.29 3.02
286 295 5.538118 ACATCGAAGTGTATCAGTGTTCAA 58.462 37.500 0.00 0.00 0.00 2.69
287 296 5.134202 ACATCGAAGTGTATCAGTGTTCA 57.866 39.130 0.00 0.00 0.00 3.18
288 297 6.467723 AAACATCGAAGTGTATCAGTGTTC 57.532 37.500 0.00 0.00 30.73 3.18
290 299 5.179368 CCAAAACATCGAAGTGTATCAGTGT 59.821 40.000 0.00 0.00 0.00 3.55
304 327 3.389221 CCAAAAAGGTCCCAAAACATCG 58.611 45.455 0.00 0.00 0.00 3.84
385 421 3.557595 GGCTTGAACTGAATGGAGTATCG 59.442 47.826 0.00 0.00 34.37 2.92
389 425 1.272147 GGGGCTTGAACTGAATGGAGT 60.272 52.381 0.00 0.00 0.00 3.85
405 441 1.223211 GAGAGAAAGCAGAGGGGGC 59.777 63.158 0.00 0.00 0.00 5.80
406 442 1.760029 GTAGAGAGAAAGCAGAGGGGG 59.240 57.143 0.00 0.00 0.00 5.40
421 457 9.660180 AAGAAGAAAACAAATAGCTAGGTAGAG 57.340 33.333 7.83 2.65 0.00 2.43
423 459 9.660180 AGAAGAAGAAAACAAATAGCTAGGTAG 57.340 33.333 7.83 0.00 0.00 3.18
443 479 6.018262 CGGATAAATAAATCCACGCAGAAGAA 60.018 38.462 3.94 0.00 44.98 2.52
453 489 5.063204 CCAGAGCACGGATAAATAAATCCA 58.937 41.667 3.94 0.00 44.98 3.41
484 520 2.037641 TGATGATGTAGCGAGGGAATGG 59.962 50.000 0.00 0.00 0.00 3.16
500 536 1.137086 GCTAAGAAGCCGGAGTGATGA 59.863 52.381 5.05 0.00 43.40 2.92
620 781 1.065126 ACCAAGAGATAGGGCTGCAAC 60.065 52.381 0.50 0.00 0.00 4.17
621 782 1.289160 ACCAAGAGATAGGGCTGCAA 58.711 50.000 0.50 0.00 0.00 4.08
624 785 3.054802 AGTCAAACCAAGAGATAGGGCTG 60.055 47.826 0.00 0.00 0.00 4.85
625 786 3.185455 AGTCAAACCAAGAGATAGGGCT 58.815 45.455 0.00 0.00 0.00 5.19
645 813 0.179056 ACCACATAATCGGGCGGAAG 60.179 55.000 0.00 0.00 0.00 3.46
657 825 2.040545 ACCCAATTCGGTCAACCACATA 59.959 45.455 0.00 0.00 35.14 2.29
714 882 6.309712 ACACACATGTCTGAATTCTGAAAG 57.690 37.500 15.70 11.11 31.55 2.62
744 914 3.055530 ACCCTCAGCAGAATCTGTACAAG 60.056 47.826 12.29 4.90 35.63 3.16
756 926 3.381272 TGAAAAGTGAAAACCCTCAGCAG 59.619 43.478 0.00 0.00 0.00 4.24
770 940 0.385390 AAAGCGGGCACTGAAAAGTG 59.615 50.000 1.45 1.45 42.32 3.16
771 941 1.607148 GTAAAGCGGGCACTGAAAAGT 59.393 47.619 0.00 0.00 36.31 2.66
772 942 1.068541 GGTAAAGCGGGCACTGAAAAG 60.069 52.381 0.00 0.00 36.31 2.27
773 943 0.955905 GGTAAAGCGGGCACTGAAAA 59.044 50.000 0.00 0.00 36.31 2.29
774 944 1.231958 CGGTAAAGCGGGCACTGAAA 61.232 55.000 0.00 0.00 36.31 2.69
819 989 9.303116 GAAGATAGAGATAGTCATAGGGTGAAA 57.697 37.037 0.00 0.00 38.90 2.69
842 1012 7.928908 TTTTTCGGAAAACATTCTCATGAAG 57.071 32.000 15.06 0.00 34.11 3.02
843 1013 8.359642 AGATTTTTCGGAAAACATTCTCATGAA 58.640 29.630 15.06 0.00 37.56 2.57
854 1024 6.908820 ACGAACAGTAAGATTTTTCGGAAAAC 59.091 34.615 15.06 5.67 42.58 2.43
866 1036 4.680110 CAGTGAAACGACGAACAGTAAGAT 59.320 41.667 0.00 0.00 45.86 2.40
867 1037 4.039703 CAGTGAAACGACGAACAGTAAGA 58.960 43.478 0.00 0.00 45.86 2.10
868 1038 3.181774 CCAGTGAAACGACGAACAGTAAG 59.818 47.826 0.00 0.00 45.86 2.34
870 1040 2.358582 TCCAGTGAAACGACGAACAGTA 59.641 45.455 0.00 0.00 45.86 2.74
872 1042 1.521423 GTCCAGTGAAACGACGAACAG 59.479 52.381 0.00 0.00 45.86 3.16
873 1043 1.563111 GTCCAGTGAAACGACGAACA 58.437 50.000 0.00 0.00 45.86 3.18
874 1044 0.857287 GGTCCAGTGAAACGACGAAC 59.143 55.000 0.00 0.00 45.86 3.95
875 1045 0.460722 TGGTCCAGTGAAACGACGAA 59.539 50.000 0.00 0.00 45.86 3.85
877 1047 0.031585 TCTGGTCCAGTGAAACGACG 59.968 55.000 18.65 0.00 45.86 5.12
878 1048 2.069273 CATCTGGTCCAGTGAAACGAC 58.931 52.381 18.65 0.00 45.86 4.34
882 1052 5.304686 ACTTAACATCTGGTCCAGTGAAA 57.695 39.130 18.65 13.27 32.61 2.69
918 1088 6.390721 TCTGCACAGACTTTAGACAAGATAC 58.609 40.000 0.00 0.00 31.41 2.24
919 1089 6.590234 TCTGCACAGACTTTAGACAAGATA 57.410 37.500 0.00 0.00 31.41 1.98
920 1090 5.474578 TCTGCACAGACTTTAGACAAGAT 57.525 39.130 0.00 0.00 31.41 2.40
921 1091 4.937201 TCTGCACAGACTTTAGACAAGA 57.063 40.909 0.00 0.00 31.41 3.02
931 1101 1.696336 AGACCACAATCTGCACAGACT 59.304 47.619 1.71 0.00 40.75 3.24
932 1102 1.802960 CAGACCACAATCTGCACAGAC 59.197 52.381 1.71 0.00 39.77 3.51
967 1137 0.671781 CAGGACTCGCCCACAGAAAG 60.672 60.000 0.00 0.00 37.37 2.62
1080 1250 1.067283 ACCTCACTCTCGATGTTGCAG 60.067 52.381 0.00 0.00 0.00 4.41
1155 1325 4.081752 AGCCTAATGTGTCTGACTCTGAAG 60.082 45.833 9.51 4.62 0.00 3.02
1191 1361 3.448301 CCAACAATGTACCGGAGTAGGTA 59.552 47.826 9.46 0.00 43.89 3.08
1326 1496 3.527775 CTCGCCCTCATAGCTGGCC 62.528 68.421 6.44 0.00 42.29 5.36
1356 1526 5.483685 ACGTGCCTTCACCATATATGTAT 57.516 39.130 11.73 0.00 40.04 2.29
1533 1703 1.712401 TATTGCCGGTGTACGTGTTC 58.288 50.000 1.90 0.00 42.24 3.18
1599 1769 0.457166 TGCCTTCGTACGAATCACCG 60.457 55.000 29.25 17.46 33.28 4.94
1641 1811 5.892119 ACTCCATGTATAGATACCATACCCG 59.108 44.000 0.00 0.00 32.33 5.28
2373 2574 8.560374 ACTGTTACTTTTCAGCAGAGAAATAAC 58.440 33.333 6.74 6.74 37.35 1.89
2384 2585 4.816925 AGTCTTCCACTGTTACTTTTCAGC 59.183 41.667 0.00 0.00 35.37 4.26
2401 2602 0.995728 GCTAGCACAGCGAAGTCTTC 59.004 55.000 10.63 2.18 41.37 2.87
2425 2626 3.816523 GGACTAGAGATCTGGTAAGGACG 59.183 52.174 0.00 0.00 37.82 4.79
2500 2705 8.464770 TGCTCTGTTATCAATTTAAAATGCAC 57.535 30.769 0.00 0.00 0.00 4.57
2541 2746 6.359804 ACAGAACATATACATGTGAATGCCT 58.640 36.000 9.11 9.55 44.83 4.75
2862 3069 8.598075 ACGACGTGATTTATAAGTCCAAATAAC 58.402 33.333 0.00 0.00 0.00 1.89
2864 3071 7.975058 TCACGACGTGATTTATAAGTCCAAATA 59.025 33.333 26.04 0.00 37.67 1.40
2875 3082 8.380644 CAGAAATAACTTCACGACGTGATTTAT 58.619 33.333 29.60 26.98 42.40 1.40
2881 3088 3.428870 AGCAGAAATAACTTCACGACGTG 59.571 43.478 21.88 21.88 36.40 4.49
2882 3089 3.650139 AGCAGAAATAACTTCACGACGT 58.350 40.909 0.00 0.00 36.40 4.34
2884 3091 5.786401 ATGAGCAGAAATAACTTCACGAC 57.214 39.130 0.00 0.00 36.40 4.34
2886 3093 9.559958 AAAATAATGAGCAGAAATAACTTCACG 57.440 29.630 0.00 0.00 36.40 4.35
3153 3372 9.755804 TCACTGAACAAGCTTATATAATGAGAG 57.244 33.333 0.00 0.00 0.00 3.20
3189 3463 7.542025 TCACACTAGCACTGCATGATATATAG 58.458 38.462 3.30 0.00 0.00 1.31
3201 3475 5.618056 ACATTCAAATCACACTAGCACTG 57.382 39.130 0.00 0.00 0.00 3.66
3205 3479 7.272084 GTCATCAAACATTCAAATCACACTAGC 59.728 37.037 0.00 0.00 0.00 3.42
3213 3487 9.073368 CAGAATCAGTCATCAAACATTCAAATC 57.927 33.333 0.00 0.00 0.00 2.17
3359 3635 5.503927 AGAGGTGTGCATTAGTTGATGATT 58.496 37.500 0.00 0.00 0.00 2.57
3379 3655 7.090173 TGTGAACAAGAAAAACCTCAAAAGAG 58.910 34.615 0.00 0.00 0.00 2.85
3383 3659 6.816140 GGAATGTGAACAAGAAAAACCTCAAA 59.184 34.615 0.00 0.00 0.00 2.69
3394 3672 8.328758 ACTCCATAAATAGGAATGTGAACAAGA 58.671 33.333 0.00 0.00 34.08 3.02
3446 3724 3.249917 ACAACAAAACGGAACTGCAAAG 58.750 40.909 0.00 0.00 0.00 2.77
3564 3842 4.963318 ATCCTTCAGAGTTGTGTTCTCA 57.037 40.909 0.00 0.00 34.73 3.27
3600 3878 6.010219 CCAAGAAGGTTCCAGATAAAAGGAA 58.990 40.000 0.00 0.00 41.41 3.36
3621 3899 2.139323 TAAGTAGAGCCTCTCGCCAA 57.861 50.000 0.00 0.00 38.78 4.52
3784 4062 7.907045 GTGATGACATATTTCAGCAAGTAACAG 59.093 37.037 11.16 0.00 43.24 3.16
3931 4214 9.113838 TGATGCAAAATTACTTTTAGGCAAAAA 57.886 25.926 7.18 0.00 39.61 1.94
3932 4215 8.668510 TGATGCAAAATTACTTTTAGGCAAAA 57.331 26.923 7.18 0.00 39.61 2.44
3955 4238 4.933505 TGCACATTTCTTGGTCAATTGA 57.066 36.364 3.38 3.38 0.00 2.57
4338 4624 3.499918 CGCAAAGAAGATCACTGGAACTT 59.500 43.478 0.00 0.00 38.67 2.66
4445 4765 3.365832 GGCACAAAACATGCTATGATCG 58.634 45.455 0.00 0.00 42.93 3.69
4563 4883 5.416083 GTCTGTTGGGTTATTTTTATGGGC 58.584 41.667 0.00 0.00 0.00 5.36
4592 4913 0.111001 CAACGGGTACAAAGTTCGCG 60.111 55.000 0.00 0.00 42.61 5.87
4953 5281 2.117156 CCCAAATCCAGCAGCCGAG 61.117 63.158 0.00 0.00 0.00 4.63
5018 5346 7.176865 GCCATATCTGTTACAGGAGTAGTGATA 59.823 40.741 12.79 1.26 31.51 2.15
5026 5354 4.586421 TCAGAGCCATATCTGTTACAGGAG 59.414 45.833 12.79 0.52 45.70 3.69
5031 5359 5.023533 TGGTTCAGAGCCATATCTGTTAC 57.976 43.478 0.90 4.15 45.70 2.50
5035 5363 3.624861 GTGTTGGTTCAGAGCCATATCTG 59.375 47.826 6.86 0.00 46.70 2.90
5038 5366 3.244875 TGTGTGTTGGTTCAGAGCCATAT 60.245 43.478 6.86 0.00 35.71 1.78
5039 5367 2.105649 TGTGTGTTGGTTCAGAGCCATA 59.894 45.455 6.86 0.00 35.71 2.74
5051 5379 0.180171 TCCCACTCTGTGTGTGTTGG 59.820 55.000 8.81 3.47 44.81 3.77
5055 5383 0.107456 AAGCTCCCACTCTGTGTGTG 59.893 55.000 8.81 0.00 44.81 3.82
5056 5384 0.839946 AAAGCTCCCACTCTGTGTGT 59.160 50.000 8.81 0.00 44.81 3.72
5057 5385 1.605710 CAAAAGCTCCCACTCTGTGTG 59.394 52.381 2.97 2.97 45.80 3.82
5058 5386 1.477558 CCAAAAGCTCCCACTCTGTGT 60.478 52.381 0.00 0.00 0.00 3.72
5063 5428 1.202818 AGTCACCAAAAGCTCCCACTC 60.203 52.381 0.00 0.00 0.00 3.51
5099 5464 1.146774 TGGATCTGAACCCTGCCAAAA 59.853 47.619 1.16 0.00 0.00 2.44
5111 5476 1.997311 CACCCCCAGCTGGATCTGA 60.997 63.158 34.91 0.00 36.19 3.27
5168 5533 1.605232 TCGTAGAACGACTTGCTGTCA 59.395 47.619 0.00 0.00 46.73 3.58
5294 5659 3.209812 TCGACCGCGGAGATGGAG 61.210 66.667 35.90 13.93 38.28 3.86
5416 5798 0.536687 CGGAAGATCATGCCATGCCT 60.537 55.000 0.00 0.00 0.00 4.75
5418 5800 1.285023 GCGGAAGATCATGCCATGC 59.715 57.895 0.00 0.00 0.00 4.06
5505 5895 5.609423 TGGTTTGTGCTTATGCTTGAAAAT 58.391 33.333 1.96 0.00 40.48 1.82
5612 6019 4.209080 CACATATATTCGCGCAGAAAGTCA 59.791 41.667 16.29 5.51 42.91 3.41
5654 6061 0.040058 TTCCAGATGCCCAGCACATT 59.960 50.000 0.00 0.00 43.04 2.71
5786 6193 5.107875 GCAATCGTGTTGGAAATTCAGTTTC 60.108 40.000 0.00 0.00 44.43 2.78
5846 6253 0.251341 GGAGTCCAAACCCTGTGCAT 60.251 55.000 3.60 0.00 0.00 3.96
5847 6254 1.150536 GGAGTCCAAACCCTGTGCA 59.849 57.895 3.60 0.00 0.00 4.57
5848 6255 0.890996 CTGGAGTCCAAACCCTGTGC 60.891 60.000 14.17 0.00 30.80 4.57
5849 6256 0.764890 TCTGGAGTCCAAACCCTGTG 59.235 55.000 14.17 0.00 30.80 3.66
5850 6257 0.765510 GTCTGGAGTCCAAACCCTGT 59.234 55.000 14.17 0.00 30.80 4.00
5921 6328 7.427214 TGTTATTTAGTTTTGGGTGCTTACAC 58.573 34.615 0.00 0.00 46.66 2.90
5947 6354 1.135286 GTGCTACAAATCTGCTTGCCC 60.135 52.381 0.00 0.00 0.00 5.36
5973 6389 2.047061 TCATATAGGGGTGTGGAGCAC 58.953 52.381 0.00 0.00 46.97 4.40
5974 6390 2.438021 GTTCATATAGGGGTGTGGAGCA 59.562 50.000 0.00 0.00 0.00 4.26
5975 6391 2.438021 TGTTCATATAGGGGTGTGGAGC 59.562 50.000 0.00 0.00 0.00 4.70
5976 6392 4.982241 ATGTTCATATAGGGGTGTGGAG 57.018 45.455 0.00 0.00 0.00 3.86
5977 6393 6.833346 TTAATGTTCATATAGGGGTGTGGA 57.167 37.500 0.00 0.00 0.00 4.02
5978 6394 8.477419 AATTTAATGTTCATATAGGGGTGTGG 57.523 34.615 0.00 0.00 0.00 4.17
6009 6425 1.541379 GGGTGTGGAGCGGTATTTTT 58.459 50.000 0.00 0.00 0.00 1.94
6010 6426 0.323087 GGGGTGTGGAGCGGTATTTT 60.323 55.000 0.00 0.00 0.00 1.82
6011 6427 1.205460 AGGGGTGTGGAGCGGTATTT 61.205 55.000 0.00 0.00 0.00 1.40
6012 6428 0.325860 TAGGGGTGTGGAGCGGTATT 60.326 55.000 0.00 0.00 0.00 1.89
6013 6429 0.105142 ATAGGGGTGTGGAGCGGTAT 60.105 55.000 0.00 0.00 0.00 2.73
6014 6430 0.557238 TATAGGGGTGTGGAGCGGTA 59.443 55.000 0.00 0.00 0.00 4.02
6015 6431 1.047034 GTATAGGGGTGTGGAGCGGT 61.047 60.000 0.00 0.00 0.00 5.68
6016 6432 1.746517 GTATAGGGGTGTGGAGCGG 59.253 63.158 0.00 0.00 0.00 5.52
6017 6433 1.105167 TCGTATAGGGGTGTGGAGCG 61.105 60.000 0.00 0.00 0.00 5.03
6134 6553 5.754890 GCCACCAATATGTTTCATGGATTTC 59.245 40.000 0.00 0.00 36.75 2.17
6138 6557 3.706183 TGCCACCAATATGTTTCATGGA 58.294 40.909 0.00 0.00 36.75 3.41
6142 6563 5.798125 TTTCTTGCCACCAATATGTTTCA 57.202 34.783 0.00 0.00 0.00 2.69
6177 6598 8.356657 TCCAAACAGTTTTGTTCTATACATTGG 58.643 33.333 0.00 0.00 46.54 3.16
6232 6653 4.518278 ACCAGGAAATGTATACATGGCA 57.482 40.909 18.94 0.00 38.76 4.92
6276 6697 3.444388 ACGTGGGTTCTCAATCTACTCTC 59.556 47.826 0.00 0.00 0.00 3.20
6277 6698 3.432378 ACGTGGGTTCTCAATCTACTCT 58.568 45.455 0.00 0.00 0.00 3.24
6281 6702 4.610605 TGAAACGTGGGTTCTCAATCTA 57.389 40.909 0.00 0.00 34.62 1.98


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

AutoCloner maintained by Alex Coulton.