Multiple sequence alignment - TraesCS6B01G063300

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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 TraesCS6B01G063300 chr6B 100.000 3844 0 0 713 4556 41991358 41995201 0.000000e+00 7099.0
1 TraesCS6B01G063300 chr6B 100.000 396 0 0 1 396 41990646 41991041 0.000000e+00 732.0
2 TraesCS6B01G063300 chr6D 93.536 3249 178 13 713 3946 25781100 25784331 0.000000e+00 4807.0
3 TraesCS6B01G063300 chr6D 82.186 247 44 0 1 247 25780224 25780470 3.570000e-51 213.0
4 TraesCS6B01G063300 chr6D 90.683 161 10 4 4401 4556 25786161 25786321 4.620000e-50 209.0
5 TraesCS6B01G063300 chr6D 93.023 86 6 0 4471 4556 25788430 25788515 4.780000e-25 126.0
6 TraesCS6B01G063300 chr6D 92.000 50 4 0 10 59 25779557 25779606 2.270000e-08 71.3
7 TraesCS6B01G063300 chr6A 93.141 3222 166 22 734 3932 23887398 23890587 0.000000e+00 4674.0
8 TraesCS6B01G063300 chr1D 86.985 1552 132 41 1645 3150 347396265 347397792 0.000000e+00 1683.0
9 TraesCS6B01G063300 chr1D 86.747 581 69 8 714 1287 347395351 347395930 1.380000e-179 640.0
10 TraesCS6B01G063300 chr1B 86.537 1545 142 29 1645 3146 468503631 468505152 0.000000e+00 1640.0
11 TraesCS6B01G063300 chr1B 87.091 581 67 6 714 1287 468502676 468503255 0.000000e+00 651.0
12 TraesCS6B01G063300 chr1A 87.817 1379 140 11 1641 3000 448009552 448010921 0.000000e+00 1591.0
13 TraesCS6B01G063300 chr1A 85.714 581 75 4 714 1287 448007994 448008573 1.400000e-169 606.0
14 TraesCS6B01G063300 chr7B 85.557 1544 151 31 1646 3146 126777738 126779252 0.000000e+00 1550.0
15 TraesCS6B01G063300 chrUn 85.168 1544 163 31 1646 3146 16578971 16580491 0.000000e+00 1522.0
16 TraesCS6B01G063300 chr3A 85.266 414 58 2 2014 2425 477589314 477588902 1.520000e-114 424.0
17 TraesCS6B01G063300 chr3A 80.425 424 57 16 2582 2998 477586465 477586061 2.660000e-77 300.0
18 TraesCS6B01G063300 chr3B 86.875 320 40 2 2106 2425 463111948 463111631 1.560000e-94 357.0
19 TraesCS6B01G063300 chr3B 80.189 424 58 16 2582 2998 463111511 463111107 1.240000e-75 294.0
20 TraesCS6B01G063300 chr3B 85.279 197 20 5 1087 1276 463113305 463113111 1.290000e-45 195.0


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 TraesCS6B01G063300 chr6B 41990646 41995201 4555 False 3915.50 7099 100.000000 1 4556 2 chr6B.!!$F1 4555
1 TraesCS6B01G063300 chr6D 25779557 25788515 8958 False 1085.26 4807 90.285600 1 4556 5 chr6D.!!$F1 4555
2 TraesCS6B01G063300 chr6A 23887398 23890587 3189 False 4674.00 4674 93.141000 734 3932 1 chr6A.!!$F1 3198
3 TraesCS6B01G063300 chr1D 347395351 347397792 2441 False 1161.50 1683 86.866000 714 3150 2 chr1D.!!$F1 2436
4 TraesCS6B01G063300 chr1B 468502676 468505152 2476 False 1145.50 1640 86.814000 714 3146 2 chr1B.!!$F1 2432
5 TraesCS6B01G063300 chr1A 448007994 448010921 2927 False 1098.50 1591 86.765500 714 3000 2 chr1A.!!$F1 2286
6 TraesCS6B01G063300 chr7B 126777738 126779252 1514 False 1550.00 1550 85.557000 1646 3146 1 chr7B.!!$F1 1500
7 TraesCS6B01G063300 chrUn 16578971 16580491 1520 False 1522.00 1522 85.168000 1646 3146 1 chrUn.!!$F1 1500
8 TraesCS6B01G063300 chr3A 477586061 477589314 3253 True 362.00 424 82.845500 2014 2998 2 chr3A.!!$R1 984
9 TraesCS6B01G063300 chr3B 463111107 463113305 2198 True 282.00 357 84.114333 1087 2998 3 chr3B.!!$R1 1911

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
206 883 0.110486 AAACGACCATGCCAGGAGTT 59.890 50.0 0.00 2.24 35.69 3.01 F
1338 2904 0.034616 GGAACTCTGAGCTGTGCAGT 59.965 55.0 4.19 0.00 34.98 4.40 F
2592 7542 0.039165 CCTGCAAAAGGTTCGGAAGC 60.039 55.0 11.81 11.81 41.74 3.86 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1502 3880 0.546122 TCAGCGCCCTAATCAACCAT 59.454 50.0 2.29 0.0 0.00 3.55 R
2879 7840 0.184933 CCTGGACCCCAACTGTTTGA 59.815 55.0 0.00 0.0 34.24 2.69 R
4240 9455 0.035056 CCCTCCTTCGGCATCAAAGT 60.035 55.0 0.00 0.0 0.00 2.66 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
80 660 0.608035 GGACTGGAATTGGGCGACAA 60.608 55.000 0.00 0.00 44.54 3.18
86 666 0.171231 GAATTGGGCGACAAAGGAGC 59.829 55.000 0.00 0.00 43.46 4.70
123 703 1.444119 GAAGCTGGAAACGGTGCACA 61.444 55.000 20.43 0.00 39.64 4.57
126 803 1.724582 GCTGGAAACGGTGCACAACT 61.725 55.000 20.43 0.00 39.64 3.16
127 804 1.588674 CTGGAAACGGTGCACAACTA 58.411 50.000 20.43 1.88 0.00 2.24
129 806 1.134340 TGGAAACGGTGCACAACTACT 60.134 47.619 20.43 0.00 0.00 2.57
136 813 1.497991 GTGCACAACTACTTGCGAGA 58.502 50.000 13.17 0.00 41.96 4.04
144 821 4.142160 ACAACTACTTGCGAGATGCTATGA 60.142 41.667 8.31 0.00 46.63 2.15
147 824 1.482182 ACTTGCGAGATGCTATGACCA 59.518 47.619 8.31 0.00 46.63 4.02
151 828 1.196354 GCGAGATGCTATGACCATTGC 59.804 52.381 8.99 8.99 41.73 3.56
153 830 1.802960 GAGATGCTATGACCATTGCCG 59.197 52.381 12.42 0.00 38.48 5.69
185 862 4.180946 CGGTCGACGGAGGAGCTG 62.181 72.222 17.47 0.00 39.42 4.24
195 872 1.301716 GAGGAGCTGCAAACGACCA 60.302 57.895 8.35 0.00 0.00 4.02
196 873 0.674895 GAGGAGCTGCAAACGACCAT 60.675 55.000 8.35 0.00 0.00 3.55
200 877 2.918345 GCTGCAAACGACCATGCCA 61.918 57.895 0.00 0.00 41.87 4.92
204 881 1.926511 GCAAACGACCATGCCAGGAG 61.927 60.000 0.00 0.00 36.56 3.69
205 882 0.606401 CAAACGACCATGCCAGGAGT 60.606 55.000 0.00 0.00 0.00 3.85
206 883 0.110486 AAACGACCATGCCAGGAGTT 59.890 50.000 0.00 2.24 35.69 3.01
215 892 3.624777 CATGCCAGGAGTTAGAAATGGT 58.375 45.455 0.00 0.00 33.42 3.55
219 896 4.263905 TGCCAGGAGTTAGAAATGGTGAAT 60.264 41.667 0.00 0.00 33.42 2.57
220 897 4.706962 GCCAGGAGTTAGAAATGGTGAATT 59.293 41.667 0.00 0.00 33.42 2.17
226 903 4.638865 AGTTAGAAATGGTGAATTACGGCC 59.361 41.667 0.00 0.00 0.00 6.13
228 905 3.016736 AGAAATGGTGAATTACGGCCTG 58.983 45.455 0.00 0.00 0.00 4.85
231 908 1.377987 GGTGAATTACGGCCTGCCA 60.378 57.895 9.17 0.00 35.37 4.92
236 913 1.103398 AATTACGGCCTGCCAGATGC 61.103 55.000 9.17 0.00 41.77 3.91
290 1379 1.210967 CCAGCGGTACCCTAATTTCCA 59.789 52.381 6.25 0.00 0.00 3.53
291 1380 2.285977 CAGCGGTACCCTAATTTCCAC 58.714 52.381 6.25 0.00 0.00 4.02
297 1386 3.181468 GGTACCCTAATTTCCACCGAGAG 60.181 52.174 0.00 0.00 0.00 3.20
298 1387 2.829023 ACCCTAATTTCCACCGAGAGA 58.171 47.619 0.00 0.00 0.00 3.10
299 1388 2.500504 ACCCTAATTTCCACCGAGAGAC 59.499 50.000 0.00 0.00 0.00 3.36
300 1389 2.481449 CCCTAATTTCCACCGAGAGACG 60.481 54.545 0.00 0.00 42.18 4.18
310 1399 3.980136 CGAGAGACGGAACAGACTC 57.020 57.895 0.00 0.00 38.46 3.36
312 1401 0.812549 GAGAGACGGAACAGACTCCC 59.187 60.000 0.00 0.00 34.35 4.30
313 1402 0.612453 AGAGACGGAACAGACTCCCC 60.612 60.000 0.00 0.00 34.35 4.81
314 1403 1.935327 GAGACGGAACAGACTCCCCG 61.935 65.000 0.00 0.00 46.65 5.73
323 1412 2.762875 GACTCCCCGTCCCCGATT 60.763 66.667 0.00 0.00 36.62 3.34
326 1415 4.445710 TCCCCGTCCCCGATTCGA 62.446 66.667 7.83 0.00 35.63 3.71
366 1458 2.614057 ACTCAAGAAACCAAACAGCTCG 59.386 45.455 0.00 0.00 0.00 5.03
825 1917 3.465403 CAGCTGGGGGTCCTCTCG 61.465 72.222 5.57 0.00 0.00 4.04
1014 2106 2.202987 GGGATGCAGCTCCTCGTG 60.203 66.667 0.22 0.00 35.50 4.35
1324 2890 5.068198 CGAAATGGATGAATGATTGGGAACT 59.932 40.000 0.00 0.00 0.00 3.01
1338 2904 0.034616 GGAACTCTGAGCTGTGCAGT 59.965 55.000 4.19 0.00 34.98 4.40
1339 2905 1.542108 GGAACTCTGAGCTGTGCAGTT 60.542 52.381 4.19 0.00 34.98 3.16
1340 2906 2.289072 GGAACTCTGAGCTGTGCAGTTA 60.289 50.000 4.19 0.00 34.98 2.24
1341 2907 2.447244 ACTCTGAGCTGTGCAGTTAC 57.553 50.000 4.19 0.00 34.98 2.50
1429 2995 5.946486 AGAGGATGGAGATGGATTTAAACC 58.054 41.667 0.00 0.00 0.00 3.27
1469 3042 6.584563 GCAATTGCGTTTGTAGAATTCCTTAA 59.415 34.615 15.87 0.00 0.00 1.85
1502 3880 8.344446 ACAGAATGAATGAATGAATGACTCAA 57.656 30.769 0.00 0.00 39.69 3.02
1698 4091 8.918202 TTATACCTTAGCATGGTTTCCATAAG 57.082 34.615 1.12 0.00 43.15 1.73
1924 4317 3.689347 TGCAGCCACTCTTGTTCATAAT 58.311 40.909 0.00 0.00 0.00 1.28
1927 4320 3.693085 CAGCCACTCTTGTTCATAATGCT 59.307 43.478 0.00 0.00 0.00 3.79
2050 4473 8.371571 TGACATATGACCTTATCTGCAGATAT 57.628 34.615 31.73 20.13 36.94 1.63
2110 4658 0.890542 TGCACCTTCCTGTCACATGC 60.891 55.000 0.00 0.00 0.00 4.06
2152 4700 7.981102 ATTTCTTAGCGAGTTAAAAGGAGTT 57.019 32.000 0.00 0.00 0.00 3.01
2155 4703 8.530269 TTCTTAGCGAGTTAAAAGGAGTTAAG 57.470 34.615 0.00 0.00 0.00 1.85
2212 4760 6.921857 GGGAATTCATTGCTGTATTTGATGAG 59.078 38.462 7.93 0.00 0.00 2.90
2437 4985 5.085275 AGGATGAGGTCTTGATCTCCATA 57.915 43.478 8.26 0.00 0.00 2.74
2592 7542 0.039165 CCTGCAAAAGGTTCGGAAGC 60.039 55.000 11.81 11.81 41.74 3.86
2604 7554 1.120530 TCGGAAGCTGGGAAGTATCC 58.879 55.000 0.00 0.00 45.77 2.59
2801 7762 2.158957 TCTGTTGTGTCTTCAGGTGGAC 60.159 50.000 0.00 0.00 0.00 4.02
2879 7840 2.758736 TTGCTGTGTTTTTGCCTGTT 57.241 40.000 0.00 0.00 0.00 3.16
2931 7892 0.036732 TCACTCCCATGTGGTTGCTC 59.963 55.000 0.00 0.00 38.40 4.26
2978 7939 2.917701 TGACTGCAAATTGGTATGCG 57.082 45.000 0.00 0.00 45.47 4.73
3007 7968 6.365520 TGAACCTACAGCTCTATCATAGTCA 58.634 40.000 0.00 0.00 0.00 3.41
3058 8022 3.570125 GCTCTAATGGTTTCATAAGGCCC 59.430 47.826 0.00 0.00 32.44 5.80
3109 8074 6.018669 GCAGTTGTACAGATAATAAGTCTGCC 60.019 42.308 0.00 0.00 45.42 4.85
3146 8111 4.464597 TGTTTGCCTTTTAGACCAGTGTTT 59.535 37.500 0.00 0.00 0.00 2.83
3222 8187 0.314935 CACCTGCGTTTCATTGCCTT 59.685 50.000 0.00 0.00 0.00 4.35
3228 8193 4.236935 CTGCGTTTCATTGCCTTTACAAT 58.763 39.130 0.00 0.00 40.90 2.71
3301 8266 7.913674 AGAAATGTGTTATCTTTCCTCTCAC 57.086 36.000 0.00 0.00 30.84 3.51
3326 8291 4.571919 TGTTAGCAAGCGTACCTATGTTT 58.428 39.130 0.00 0.00 0.00 2.83
3339 8304 7.654568 CGTACCTATGTTTCTATGATGTGGTA 58.345 38.462 0.00 0.00 0.00 3.25
3390 8356 4.083802 GGAGTTTGTCACACTATCTTGCAC 60.084 45.833 0.00 0.00 0.00 4.57
3404 8370 0.743688 TTGCACATTTTGACAGCCGT 59.256 45.000 0.00 0.00 0.00 5.68
3405 8371 0.030504 TGCACATTTTGACAGCCGTG 59.969 50.000 0.00 0.00 0.00 4.94
3406 8372 0.030638 GCACATTTTGACAGCCGTGT 59.969 50.000 0.00 0.00 40.71 4.49
3414 8380 2.244946 GACAGCCGTGTCCCTTTTC 58.755 57.895 0.00 0.00 46.58 2.29
3415 8381 0.250338 GACAGCCGTGTCCCTTTTCT 60.250 55.000 0.00 0.00 46.58 2.52
3419 8385 2.882137 CAGCCGTGTCCCTTTTCTTTTA 59.118 45.455 0.00 0.00 0.00 1.52
3420 8386 3.316868 CAGCCGTGTCCCTTTTCTTTTAA 59.683 43.478 0.00 0.00 0.00 1.52
3444 8410 3.889815 TCCTGCCAGGTATGATTTTGAG 58.110 45.455 11.27 0.00 36.53 3.02
3561 8527 2.303311 GGTGGAGTGGGAATAGGATAGC 59.697 54.545 0.00 0.00 0.00 2.97
3766 8732 4.756642 GCCTTTTGATTTTTCTTTCCCCTG 59.243 41.667 0.00 0.00 0.00 4.45
3783 8749 3.326297 CCCCTGTCCTCCTAAGATTGATC 59.674 52.174 0.00 0.00 0.00 2.92
3814 8795 5.163513 AGCTGATTTTCATTTTACTTGCGG 58.836 37.500 0.00 0.00 0.00 5.69
3946 8927 6.690194 ATTGAGTTGACATGAATTAGCCTC 57.310 37.500 0.00 0.00 0.00 4.70
3949 8930 4.265073 AGTTGACATGAATTAGCCTCACC 58.735 43.478 0.00 0.00 0.00 4.02
3951 8932 4.508551 TGACATGAATTAGCCTCACCAT 57.491 40.909 0.00 0.00 0.00 3.55
3956 9145 8.043113 TGACATGAATTAGCCTCACCATATATC 58.957 37.037 0.00 0.00 0.00 1.63
3984 9173 2.785540 TCAGTGCTGGCATATGTGAA 57.214 45.000 4.29 0.00 0.00 3.18
3985 9174 3.070476 TCAGTGCTGGCATATGTGAAA 57.930 42.857 4.29 0.00 0.00 2.69
3989 9178 5.297527 TCAGTGCTGGCATATGTGAAAATAG 59.702 40.000 4.29 0.00 0.00 1.73
3990 9179 4.581824 AGTGCTGGCATATGTGAAAATAGG 59.418 41.667 4.29 0.00 0.00 2.57
3995 9184 6.239120 GCTGGCATATGTGAAAATAGGAACAT 60.239 38.462 4.29 0.00 37.11 2.71
3996 9185 7.041635 TGGCATATGTGAAAATAGGAACATG 57.958 36.000 4.29 0.00 35.07 3.21
3997 9186 6.606796 TGGCATATGTGAAAATAGGAACATGT 59.393 34.615 4.29 0.00 35.07 3.21
3999 9188 7.981225 GGCATATGTGAAAATAGGAACATGTTT 59.019 33.333 13.36 0.00 35.07 2.83
4019 9208 7.946655 TGTTTATAGATTTCATACAGCTCGG 57.053 36.000 0.00 0.00 0.00 4.63
4025 9214 5.491982 AGATTTCATACAGCTCGGAAGTTT 58.508 37.500 0.00 0.00 0.00 2.66
4031 9220 3.409026 ACAGCTCGGAAGTTTGAATCT 57.591 42.857 0.00 0.00 0.00 2.40
4032 9221 3.070018 ACAGCTCGGAAGTTTGAATCTG 58.930 45.455 0.00 0.00 0.00 2.90
4033 9222 2.079925 AGCTCGGAAGTTTGAATCTGC 58.920 47.619 0.00 0.00 0.00 4.26
4035 9224 2.426522 CTCGGAAGTTTGAATCTGCCA 58.573 47.619 1.41 0.00 30.21 4.92
4039 9228 4.280677 TCGGAAGTTTGAATCTGCCAAAAT 59.719 37.500 1.41 0.00 35.57 1.82
4042 9231 6.644592 CGGAAGTTTGAATCTGCCAAAATTTA 59.355 34.615 1.41 0.00 40.43 1.40
4043 9232 7.331687 CGGAAGTTTGAATCTGCCAAAATTTAT 59.668 33.333 1.41 0.00 40.43 1.40
4044 9233 9.651913 GGAAGTTTGAATCTGCCAAAATTTATA 57.348 29.630 0.00 0.00 40.43 0.98
4051 9240 8.970020 TGAATCTGCCAAAATTTATATGTCAGT 58.030 29.630 0.00 0.00 0.00 3.41
4052 9241 9.807649 GAATCTGCCAAAATTTATATGTCAGTT 57.192 29.630 0.00 0.00 0.00 3.16
4053 9242 9.590451 AATCTGCCAAAATTTATATGTCAGTTG 57.410 29.630 0.00 0.00 0.00 3.16
4054 9243 7.546358 TCTGCCAAAATTTATATGTCAGTTGG 58.454 34.615 0.00 0.00 37.83 3.77
4058 9247 8.133754 CCAAAATTTATATGTCAGTTGGCATG 57.866 34.615 9.36 0.00 41.05 4.06
4059 9248 7.980662 CCAAAATTTATATGTCAGTTGGCATGA 59.019 33.333 9.36 0.00 41.05 3.07
4060 9249 9.368674 CAAAATTTATATGTCAGTTGGCATGAA 57.631 29.630 9.36 1.42 41.05 2.57
4061 9250 9.590451 AAAATTTATATGTCAGTTGGCATGAAG 57.410 29.630 9.36 0.00 41.05 3.02
4063 9252 2.885135 ATGTCAGTTGGCATGAAGGA 57.115 45.000 0.00 0.00 39.19 3.36
4064 9253 2.885135 TGTCAGTTGGCATGAAGGAT 57.115 45.000 0.00 0.00 0.00 3.24
4067 9256 3.896888 TGTCAGTTGGCATGAAGGATTTT 59.103 39.130 0.00 0.00 0.00 1.82
4068 9257 4.240096 GTCAGTTGGCATGAAGGATTTTG 58.760 43.478 0.00 0.00 0.00 2.44
4069 9258 3.896888 TCAGTTGGCATGAAGGATTTTGT 59.103 39.130 0.00 0.00 0.00 2.83
4070 9259 5.048083 GTCAGTTGGCATGAAGGATTTTGTA 60.048 40.000 0.00 0.00 0.00 2.41
4071 9260 5.183713 TCAGTTGGCATGAAGGATTTTGTAG 59.816 40.000 0.00 0.00 0.00 2.74
4072 9261 5.183713 CAGTTGGCATGAAGGATTTTGTAGA 59.816 40.000 0.00 0.00 0.00 2.59
4074 9263 3.696051 TGGCATGAAGGATTTTGTAGAGC 59.304 43.478 0.00 0.00 0.00 4.09
4076 9265 4.400567 GGCATGAAGGATTTTGTAGAGCTT 59.599 41.667 0.00 0.00 0.00 3.74
4077 9266 5.338365 GCATGAAGGATTTTGTAGAGCTTG 58.662 41.667 0.00 0.00 0.00 4.01
4078 9267 5.124457 GCATGAAGGATTTTGTAGAGCTTGA 59.876 40.000 0.00 0.00 0.00 3.02
4079 9268 6.349611 GCATGAAGGATTTTGTAGAGCTTGAA 60.350 38.462 0.00 0.00 0.00 2.69
4081 9270 7.581213 TGAAGGATTTTGTAGAGCTTGAAAA 57.419 32.000 0.00 0.00 0.00 2.29
4082 9271 7.425606 TGAAGGATTTTGTAGAGCTTGAAAAC 58.574 34.615 0.00 0.00 0.00 2.43
4083 9272 6.959639 AGGATTTTGTAGAGCTTGAAAACA 57.040 33.333 0.00 0.00 0.00 2.83
4084 9273 7.530426 AGGATTTTGTAGAGCTTGAAAACAT 57.470 32.000 0.00 0.00 0.00 2.71
4085 9274 7.373493 AGGATTTTGTAGAGCTTGAAAACATG 58.627 34.615 0.00 0.00 0.00 3.21
4113 9305 5.065914 TCCATTCTCCATGCTAACATAAGC 58.934 41.667 0.00 0.00 43.08 3.09
4162 9366 8.298854 TGTTTCATACCACATTCTTTTGAGATG 58.701 33.333 0.00 0.00 0.00 2.90
4170 9374 6.404403 CCACATTCTTTTGAGATGGATCAGTG 60.404 42.308 0.00 0.00 31.85 3.66
4184 9388 8.443176 AGATGGATCAGTGAAAATATACACCAT 58.557 33.333 0.00 0.00 37.69 3.55
4203 9407 8.463930 ACACCATTGATAAAACTCTTGAAAGA 57.536 30.769 0.00 0.00 0.00 2.52
4205 9409 9.565213 CACCATTGATAAAACTCTTGAAAGATC 57.435 33.333 0.00 0.00 33.93 2.75
4206 9410 9.300681 ACCATTGATAAAACTCTTGAAAGATCA 57.699 29.630 0.00 0.00 33.93 2.92
4207 9411 9.565213 CCATTGATAAAACTCTTGAAAGATCAC 57.435 33.333 0.00 0.00 34.61 3.06
4210 9414 8.244494 TGATAAAACTCTTGAAAGATCACTCG 57.756 34.615 0.00 0.00 34.61 4.18
4226 9441 8.115490 AGATCACTCGAATCCAAAAGAAAATT 57.885 30.769 0.00 0.00 0.00 1.82
4234 9449 5.767277 ATCCAAAAGAAAATTGCTGGGAT 57.233 34.783 0.00 0.00 0.00 3.85
4235 9450 5.151297 TCCAAAAGAAAATTGCTGGGATC 57.849 39.130 0.00 0.00 0.00 3.36
4236 9451 4.840115 TCCAAAAGAAAATTGCTGGGATCT 59.160 37.500 0.00 0.00 0.00 2.75
4239 9454 5.397142 AAAGAAAATTGCTGGGATCTGTC 57.603 39.130 0.00 0.00 0.00 3.51
4240 9455 4.038271 AGAAAATTGCTGGGATCTGTCA 57.962 40.909 0.00 0.00 0.00 3.58
4244 9459 2.957402 TTGCTGGGATCTGTCACTTT 57.043 45.000 0.00 0.00 0.00 2.66
4250 9465 2.019984 GGGATCTGTCACTTTGATGCC 58.980 52.381 0.00 0.00 40.46 4.40
4294 9509 1.211457 CAGATAGAGCAAGTTGGGGCT 59.789 52.381 4.75 0.00 44.48 5.19
4296 9511 2.310052 AGATAGAGCAAGTTGGGGCTTT 59.690 45.455 4.75 0.00 41.22 3.51
4297 9512 3.523564 AGATAGAGCAAGTTGGGGCTTTA 59.476 43.478 4.75 0.00 41.22 1.85
4298 9513 2.907458 AGAGCAAGTTGGGGCTTTAT 57.093 45.000 4.75 0.00 41.22 1.40
4299 9514 2.450476 AGAGCAAGTTGGGGCTTTATG 58.550 47.619 4.75 0.00 41.22 1.90
4300 9515 1.478105 GAGCAAGTTGGGGCTTTATGG 59.522 52.381 4.75 0.00 41.22 2.74
4301 9516 0.108186 GCAAGTTGGGGCTTTATGGC 60.108 55.000 4.75 0.00 40.96 4.40
4302 9517 0.173255 CAAGTTGGGGCTTTATGGCG 59.827 55.000 0.00 0.00 42.84 5.69
4303 9518 0.251608 AAGTTGGGGCTTTATGGCGT 60.252 50.000 0.00 0.00 42.84 5.68
4304 9519 0.679960 AGTTGGGGCTTTATGGCGTC 60.680 55.000 0.00 0.00 42.84 5.19
4306 9521 0.679640 TTGGGGCTTTATGGCGTCTG 60.680 55.000 0.00 0.00 42.84 3.51
4307 9522 2.481471 GGGGCTTTATGGCGTCTGC 61.481 63.158 0.00 0.00 42.84 4.26
4308 9523 1.452108 GGGCTTTATGGCGTCTGCT 60.452 57.895 0.00 0.00 42.84 4.24
4309 9524 1.718757 GGGCTTTATGGCGTCTGCTG 61.719 60.000 0.00 0.00 42.84 4.41
4310 9525 1.718757 GGCTTTATGGCGTCTGCTGG 61.719 60.000 0.00 0.00 42.25 4.85
4312 9527 2.040213 CTTTATGGCGTCTGCTGGCG 62.040 60.000 13.70 13.70 42.25 5.69
4332 9547 3.236816 CGCAGCAAAGATTGTTAACAGG 58.763 45.455 8.56 0.00 0.00 4.00
4333 9548 3.578688 GCAGCAAAGATTGTTAACAGGG 58.421 45.455 8.56 0.00 0.00 4.45
4336 9551 2.353704 GCAAAGATTGTTAACAGGGGGC 60.354 50.000 8.56 5.94 0.00 5.80
4337 9552 3.165071 CAAAGATTGTTAACAGGGGGCT 58.835 45.455 8.56 0.81 0.00 5.19
4338 9553 2.514458 AGATTGTTAACAGGGGGCTG 57.486 50.000 8.56 0.00 0.00 4.85
4339 9554 0.817654 GATTGTTAACAGGGGGCTGC 59.182 55.000 8.56 0.00 0.00 5.25
4340 9555 0.409484 ATTGTTAACAGGGGGCTGCT 59.591 50.000 8.56 0.00 0.00 4.24
4341 9556 0.539438 TTGTTAACAGGGGGCTGCTG 60.539 55.000 8.56 0.00 0.00 4.41
4343 9558 3.918253 TTAACAGGGGGCTGCTGCG 62.918 63.158 9.65 0.00 40.82 5.18
4350 9565 2.256461 GGGCTGCTGCGAACAAAG 59.744 61.111 9.65 0.00 40.82 2.77
4351 9566 2.260869 GGGCTGCTGCGAACAAAGA 61.261 57.895 9.65 0.00 40.82 2.52
4354 9569 1.672881 GGCTGCTGCGAACAAAGATAT 59.327 47.619 9.65 0.00 40.82 1.63
4355 9570 2.098117 GGCTGCTGCGAACAAAGATATT 59.902 45.455 9.65 0.00 40.82 1.28
4356 9571 3.357897 GCTGCTGCGAACAAAGATATTC 58.642 45.455 0.00 0.00 0.00 1.75
4357 9572 3.181507 GCTGCTGCGAACAAAGATATTCA 60.182 43.478 0.00 0.00 0.00 2.57
4358 9573 4.672542 GCTGCTGCGAACAAAGATATTCAA 60.673 41.667 0.00 0.00 0.00 2.69
4359 9574 5.369685 TGCTGCGAACAAAGATATTCAAA 57.630 34.783 0.00 0.00 0.00 2.69
4360 9575 5.393124 TGCTGCGAACAAAGATATTCAAAG 58.607 37.500 0.00 0.00 0.00 2.77
4361 9576 4.795278 GCTGCGAACAAAGATATTCAAAGG 59.205 41.667 0.00 0.00 0.00 3.11
4363 9578 4.217334 TGCGAACAAAGATATTCAAAGGCA 59.783 37.500 0.00 0.00 0.00 4.75
4366 9581 6.311200 GCGAACAAAGATATTCAAAGGCAATT 59.689 34.615 0.00 0.00 0.00 2.32
4367 9582 7.463251 GCGAACAAAGATATTCAAAGGCAATTC 60.463 37.037 0.00 0.00 0.00 2.17
4370 9585 5.581126 AAGATATTCAAAGGCAATTCGCA 57.419 34.783 0.00 0.00 45.17 5.10
4371 9586 4.925068 AGATATTCAAAGGCAATTCGCAC 58.075 39.130 0.00 0.00 45.17 5.34
4373 9588 2.879002 TTCAAAGGCAATTCGCACAA 57.121 40.000 0.00 0.00 45.17 3.33
4374 9589 2.132740 TCAAAGGCAATTCGCACAAC 57.867 45.000 0.00 0.00 45.17 3.32
4375 9590 1.406898 TCAAAGGCAATTCGCACAACA 59.593 42.857 0.00 0.00 45.17 3.33
4376 9591 2.035704 TCAAAGGCAATTCGCACAACAT 59.964 40.909 0.00 0.00 45.17 2.71
4377 9592 2.801679 CAAAGGCAATTCGCACAACATT 59.198 40.909 0.00 0.00 45.17 2.71
4379 9594 3.932545 AGGCAATTCGCACAACATTTA 57.067 38.095 0.00 0.00 45.17 1.40
4381 9596 2.345341 GGCAATTCGCACAACATTTAGC 59.655 45.455 2.98 0.00 45.17 3.09
4382 9597 2.985809 GCAATTCGCACAACATTTAGCA 59.014 40.909 0.00 0.00 41.79 3.49
4383 9598 3.181541 GCAATTCGCACAACATTTAGCAC 60.182 43.478 0.00 0.00 41.79 4.40
4384 9599 3.913548 ATTCGCACAACATTTAGCACA 57.086 38.095 0.00 0.00 0.00 4.57
4385 9600 2.679355 TCGCACAACATTTAGCACAC 57.321 45.000 0.00 0.00 0.00 3.82
4387 9602 3.394719 TCGCACAACATTTAGCACACTA 58.605 40.909 0.00 0.00 0.00 2.74
4406 9621 8.385111 GCACACTAAAATTCATTCATTCATTGG 58.615 33.333 0.00 0.00 0.00 3.16
4410 10786 8.095792 ACTAAAATTCATTCATTCATTGGCACA 58.904 29.630 0.00 0.00 0.00 4.57
4419 10795 1.179152 TCATTGGCACATGGCTCTTG 58.821 50.000 7.00 2.42 44.01 3.02
4451 10830 6.662755 TCTTCAGTTTATAGGATTGCCACAT 58.337 36.000 0.00 0.00 36.29 3.21
4459 10838 2.381911 AGGATTGCCACATAAGCCTTG 58.618 47.619 0.00 0.00 40.82 3.61
4467 10846 2.035449 CCACATAAGCCTTGCATGGATG 59.965 50.000 22.21 17.44 0.00 3.51
4486 10865 6.166279 TGGATGAGAAAGATGTAGACAACAC 58.834 40.000 0.00 0.00 42.09 3.32
4488 10867 6.091441 GGATGAGAAAGATGTAGACAACACAC 59.909 42.308 0.00 0.00 42.09 3.82
4490 10869 5.985530 TGAGAAAGATGTAGACAACACACAG 59.014 40.000 0.00 0.00 42.09 3.66
4508 10887 7.781056 ACACACAGAAATGTTACAAAAGGAAT 58.219 30.769 0.00 0.00 0.00 3.01
4521 10900 4.141251 ACAAAAGGAATAGACCCACACACT 60.141 41.667 0.00 0.00 0.00 3.55
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 1.337817 CGTTTCCAGCTCTCGACGTG 61.338 60.000 0.00 0.00 0.00 4.49
1 2 1.081376 CGTTTCCAGCTCTCGACGT 60.081 57.895 0.00 0.00 0.00 4.34
3 4 1.066114 CGTCGTTTCCAGCTCTCGAC 61.066 60.000 12.45 12.45 44.49 4.20
4 5 1.209383 CGTCGTTTCCAGCTCTCGA 59.791 57.895 0.00 0.00 0.00 4.04
5 6 2.437343 GCGTCGTTTCCAGCTCTCG 61.437 63.158 0.00 0.00 0.00 4.04
6 7 0.737715 ATGCGTCGTTTCCAGCTCTC 60.738 55.000 0.00 0.00 0.00 3.20
7 8 1.016130 CATGCGTCGTTTCCAGCTCT 61.016 55.000 0.00 0.00 0.00 4.09
8 9 1.421485 CATGCGTCGTTTCCAGCTC 59.579 57.895 0.00 0.00 0.00 4.09
9 10 2.034879 CCATGCGTCGTTTCCAGCT 61.035 57.895 0.00 0.00 0.00 4.24
10 11 2.480555 CCATGCGTCGTTTCCAGC 59.519 61.111 0.00 0.00 0.00 4.85
11 12 2.480555 GCCATGCGTCGTTTCCAG 59.519 61.111 0.00 0.00 0.00 3.86
42 43 3.334751 CGTCGCCAACAGTCGCAA 61.335 61.111 0.00 0.00 0.00 4.85
60 640 1.749258 GTCGCCCAATTCCAGTCCC 60.749 63.158 0.00 0.00 0.00 4.46
62 642 1.200020 CTTTGTCGCCCAATTCCAGTC 59.800 52.381 0.00 0.00 31.81 3.51
101 681 2.032071 ACCGTTTCCAGCTTCCGG 59.968 61.111 0.00 0.00 44.06 5.14
105 685 1.034838 TTGTGCACCGTTTCCAGCTT 61.035 50.000 15.69 0.00 0.00 3.74
123 703 4.363999 GTCATAGCATCTCGCAAGTAGTT 58.636 43.478 0.00 0.00 46.13 2.24
126 803 2.693074 TGGTCATAGCATCTCGCAAGTA 59.307 45.455 0.00 0.00 46.13 2.24
127 804 1.482182 TGGTCATAGCATCTCGCAAGT 59.518 47.619 0.00 0.00 46.13 3.16
129 806 2.874086 CAATGGTCATAGCATCTCGCAA 59.126 45.455 0.00 0.00 46.13 4.85
136 813 2.156917 CATCGGCAATGGTCATAGCAT 58.843 47.619 0.00 0.00 38.04 3.79
144 821 1.028330 CAGCTCACATCGGCAATGGT 61.028 55.000 3.68 0.00 39.90 3.55
147 824 0.035152 TTCCAGCTCACATCGGCAAT 60.035 50.000 0.00 0.00 0.00 3.56
151 828 1.811266 CGGTTCCAGCTCACATCGG 60.811 63.158 0.00 0.00 0.00 4.18
153 830 0.741221 GACCGGTTCCAGCTCACATC 60.741 60.000 9.42 0.00 0.00 3.06
182 859 2.126346 GGCATGGTCGTTTGCAGC 60.126 61.111 0.00 0.00 40.66 5.25
185 862 1.926511 CTCCTGGCATGGTCGTTTGC 61.927 60.000 0.00 0.00 38.14 3.68
195 872 3.266772 TCACCATTTCTAACTCCTGGCAT 59.733 43.478 0.00 0.00 0.00 4.40
196 873 2.642311 TCACCATTTCTAACTCCTGGCA 59.358 45.455 0.00 0.00 0.00 4.92
200 877 6.113411 CCGTAATTCACCATTTCTAACTCCT 58.887 40.000 0.00 0.00 0.00 3.69
204 881 4.638865 AGGCCGTAATTCACCATTTCTAAC 59.361 41.667 0.00 0.00 0.00 2.34
205 882 4.638421 CAGGCCGTAATTCACCATTTCTAA 59.362 41.667 0.00 0.00 0.00 2.10
206 883 4.196193 CAGGCCGTAATTCACCATTTCTA 58.804 43.478 0.00 0.00 0.00 2.10
215 892 0.546122 ATCTGGCAGGCCGTAATTCA 59.454 50.000 15.73 0.00 39.42 2.57
219 896 2.124736 GCATCTGGCAGGCCGTAA 60.125 61.111 15.73 0.00 43.97 3.18
228 905 2.680913 AACGTTCGCTGCATCTGGC 61.681 57.895 0.00 0.00 45.13 4.85
231 908 2.680913 GCCAACGTTCGCTGCATCT 61.681 57.895 10.84 0.00 0.00 2.90
236 913 3.423154 GGAGGCCAACGTTCGCTG 61.423 66.667 17.37 0.00 0.00 5.18
237 914 4.699522 GGGAGGCCAACGTTCGCT 62.700 66.667 17.37 3.86 0.00 4.93
276 1365 3.703052 TCTCTCGGTGGAAATTAGGGTAC 59.297 47.826 0.00 0.00 0.00 3.34
297 1386 2.572284 CGGGGAGTCTGTTCCGTC 59.428 66.667 0.00 0.00 38.17 4.79
299 1388 2.572284 GACGGGGAGTCTGTTCCG 59.428 66.667 11.19 11.19 46.13 4.30
314 1403 1.601412 GGTACGAATCGAATCGGGGAC 60.601 57.143 25.30 18.61 46.82 4.46
323 1412 7.013559 TGAGTATTTAAGATGGGTACGAATCGA 59.986 37.037 10.55 0.00 0.00 3.59
326 1415 8.701895 TCTTGAGTATTTAAGATGGGTACGAAT 58.298 33.333 0.00 0.00 0.00 3.34
1324 2890 3.574396 AGTAAGTAACTGCACAGCTCAGA 59.426 43.478 7.84 0.00 36.93 3.27
1338 2904 7.159372 CCAGAACTGCTAAAGGAAGTAAGTAA 58.841 38.462 0.00 0.00 31.23 2.24
1339 2905 6.295688 CCCAGAACTGCTAAAGGAAGTAAGTA 60.296 42.308 0.00 0.00 31.23 2.24
1340 2906 5.513267 CCCAGAACTGCTAAAGGAAGTAAGT 60.513 44.000 0.00 0.00 31.23 2.24
1341 2907 4.938226 CCCAGAACTGCTAAAGGAAGTAAG 59.062 45.833 0.00 0.00 31.23 2.34
1461 3034 8.893563 TTCATTCTGTACCCAAATTAAGGAAT 57.106 30.769 0.80 0.00 0.00 3.01
1463 3036 8.112822 TCATTCATTCTGTACCCAAATTAAGGA 58.887 33.333 0.80 0.00 0.00 3.36
1464 3037 8.292444 TCATTCATTCTGTACCCAAATTAAGG 57.708 34.615 0.00 0.00 0.00 2.69
1469 3042 7.959658 TCATTCATTCATTCTGTACCCAAAT 57.040 32.000 0.00 0.00 0.00 2.32
1502 3880 0.546122 TCAGCGCCCTAATCAACCAT 59.454 50.000 2.29 0.00 0.00 3.55
1698 4091 7.222224 CCTTGCATAATCAGAAGATTGAAAAGC 59.778 37.037 1.21 0.00 44.03 3.51
1744 4137 1.210155 GTGGCGCAGTGTTTCCATC 59.790 57.895 10.83 0.00 0.00 3.51
1924 4317 3.173965 GTGAAGCCTATCCCCTATAGCA 58.826 50.000 0.00 0.00 36.92 3.49
1927 4320 4.160329 CACAGTGAAGCCTATCCCCTATA 58.840 47.826 0.00 0.00 0.00 1.31
1986 4401 4.742438 TTCCGAAACAGAACATGCTAAC 57.258 40.909 0.00 0.00 0.00 2.34
2050 4473 3.767673 ACATAACTCGTTCCTGCTCCTTA 59.232 43.478 0.00 0.00 0.00 2.69
2057 4480 3.926616 AGGTTGACATAACTCGTTCCTG 58.073 45.455 0.00 0.00 0.00 3.86
2110 4658 6.452494 AGAAATTTCTCTGAGGCATCAATG 57.548 37.500 15.11 0.00 34.23 2.82
2152 4700 6.272324 TCTTTCTTTTCATCTCTGGGTCCTTA 59.728 38.462 0.00 0.00 0.00 2.69
2155 4703 4.911390 TCTTTCTTTTCATCTCTGGGTCC 58.089 43.478 0.00 0.00 0.00 4.46
2212 4760 7.417612 TCTTCTTTTCTAACATGTGAGCAAAC 58.582 34.615 5.19 0.00 0.00 2.93
2231 4779 6.704056 TTCAGGTCTTTTCCCTATCTTCTT 57.296 37.500 0.00 0.00 0.00 2.52
2335 4883 6.095300 CACCTACATTGTGATGGCTTTTGATA 59.905 38.462 0.00 0.00 37.60 2.15
2604 7554 4.408182 AGAATGACTCCGGGACATTTAG 57.592 45.455 16.79 2.97 34.94 1.85
2879 7840 0.184933 CCTGGACCCCAACTGTTTGA 59.815 55.000 0.00 0.00 34.24 2.69
2931 7892 3.199946 TCCTCACTGGTAATTGCCCTTAG 59.800 47.826 10.34 3.57 37.07 2.18
2978 7939 2.409948 AGAGCTGTAGGTTCAATGCC 57.590 50.000 0.00 0.00 0.00 4.40
3007 7968 3.624777 CATCATAGAGTTGCAAAGGGGT 58.375 45.455 0.00 0.00 0.00 4.95
3033 7995 4.884164 GCCTTATGAAACCATTAGAGCACT 59.116 41.667 0.00 0.00 0.00 4.40
3052 8016 0.323725 CCATGTAGTGCAAGGGCCTT 60.324 55.000 14.48 14.48 40.13 4.35
3054 8018 2.418083 GCCATGTAGTGCAAGGGCC 61.418 63.158 13.95 0.00 42.37 5.80
3058 8022 1.372582 ATGTCGCCATGTAGTGCAAG 58.627 50.000 0.00 0.00 0.00 4.01
3081 8046 9.102757 CAGACTTATTATCTGTACAACTGCAAT 57.897 33.333 0.00 0.00 39.04 3.56
3109 8074 7.406799 AAAGGCAAACAGAACAATATTTTCG 57.593 32.000 0.00 0.00 0.00 3.46
3146 8111 6.409704 AGCATTCACAAACTAATCTAGCAGA 58.590 36.000 0.00 0.00 0.00 4.26
3202 8167 0.823356 AGGCAATGAAACGCAGGTGT 60.823 50.000 0.00 0.00 0.00 4.16
3222 8187 9.762381 AAATCCTATTACCAAGACCAATTGTAA 57.238 29.630 4.43 0.00 0.00 2.41
3276 8241 8.816894 AGTGAGAGGAAAGATAACACATTTCTA 58.183 33.333 0.00 0.00 34.19 2.10
3301 8266 4.630069 ACATAGGTACGCTTGCTAACAAAG 59.370 41.667 0.00 0.00 34.74 2.77
3376 8341 5.761003 TGTCAAAATGTGCAAGATAGTGTG 58.239 37.500 0.00 0.00 0.00 3.82
3377 8342 5.563475 GCTGTCAAAATGTGCAAGATAGTGT 60.563 40.000 0.00 0.00 0.00 3.55
3378 8343 4.855388 GCTGTCAAAATGTGCAAGATAGTG 59.145 41.667 0.00 0.00 0.00 2.74
3379 8344 4.082571 GGCTGTCAAAATGTGCAAGATAGT 60.083 41.667 0.00 0.00 0.00 2.12
3404 8370 6.463755 GGCAGGATTTTAAAAGAAAAGGGACA 60.464 38.462 6.79 0.00 0.00 4.02
3405 8371 5.932303 GGCAGGATTTTAAAAGAAAAGGGAC 59.068 40.000 6.79 0.00 0.00 4.46
3406 8372 5.604650 TGGCAGGATTTTAAAAGAAAAGGGA 59.395 36.000 6.79 0.00 0.00 4.20
3407 8373 5.863965 TGGCAGGATTTTAAAAGAAAAGGG 58.136 37.500 6.79 0.00 0.00 3.95
3414 8380 6.773976 TCATACCTGGCAGGATTTTAAAAG 57.226 37.500 38.99 16.65 37.67 2.27
3415 8381 7.732222 AATCATACCTGGCAGGATTTTAAAA 57.268 32.000 38.99 15.53 37.67 1.52
3419 8385 5.721000 TCAAAATCATACCTGGCAGGATTTT 59.279 36.000 38.99 31.17 44.50 1.82
3420 8386 5.271598 TCAAAATCATACCTGGCAGGATTT 58.728 37.500 38.99 27.92 37.67 2.17
3561 8527 0.892755 ATTGCACCACCAGAGCATTG 59.107 50.000 0.00 0.00 38.19 2.82
3632 8598 4.165779 CTGCAAATTTAGCACTAAACCCG 58.834 43.478 5.03 0.00 37.80 5.28
3734 8700 7.895975 AGAAAAATCAAAAGGCATAGAAAGC 57.104 32.000 0.00 0.00 0.00 3.51
3739 8705 6.595326 GGGGAAAGAAAAATCAAAAGGCATAG 59.405 38.462 0.00 0.00 0.00 2.23
3783 8749 9.635520 AGTAAAATGAAAATCAGCTCAAAGATG 57.364 29.630 0.00 0.00 31.83 2.90
3873 8854 9.911788 ACAGTAATAAATGATGAGACCAATTCT 57.088 29.630 0.00 0.00 37.23 2.40
3925 8906 4.937620 GTGAGGCTAATTCATGTCAACTCA 59.062 41.667 0.00 0.00 0.00 3.41
3989 9178 9.884465 GCTGTATGAAATCTATAAACATGTTCC 57.116 33.333 12.39 0.00 0.00 3.62
3995 9184 7.722363 TCCGAGCTGTATGAAATCTATAAACA 58.278 34.615 0.00 0.00 0.00 2.83
3996 9185 8.589335 TTCCGAGCTGTATGAAATCTATAAAC 57.411 34.615 0.00 0.00 0.00 2.01
3997 9186 8.421784 ACTTCCGAGCTGTATGAAATCTATAAA 58.578 33.333 0.00 0.00 0.00 1.40
3999 9188 7.526142 ACTTCCGAGCTGTATGAAATCTATA 57.474 36.000 0.00 0.00 0.00 1.31
4000 9189 6.412362 ACTTCCGAGCTGTATGAAATCTAT 57.588 37.500 0.00 0.00 0.00 1.98
4001 9190 5.854010 ACTTCCGAGCTGTATGAAATCTA 57.146 39.130 0.00 0.00 0.00 1.98
4002 9191 4.744795 ACTTCCGAGCTGTATGAAATCT 57.255 40.909 0.00 0.00 0.00 2.40
4003 9192 5.351465 TCAAACTTCCGAGCTGTATGAAATC 59.649 40.000 0.00 0.00 0.00 2.17
4004 9193 5.245531 TCAAACTTCCGAGCTGTATGAAAT 58.754 37.500 0.00 0.00 0.00 2.17
4005 9194 4.637276 TCAAACTTCCGAGCTGTATGAAA 58.363 39.130 0.00 0.00 0.00 2.69
4006 9195 4.265904 TCAAACTTCCGAGCTGTATGAA 57.734 40.909 0.00 0.00 0.00 2.57
4007 9196 3.953712 TCAAACTTCCGAGCTGTATGA 57.046 42.857 0.00 0.00 0.00 2.15
4008 9197 4.872691 AGATTCAAACTTCCGAGCTGTATG 59.127 41.667 0.00 0.00 0.00 2.39
4009 9198 4.872691 CAGATTCAAACTTCCGAGCTGTAT 59.127 41.667 0.00 0.00 0.00 2.29
4010 9199 4.245660 CAGATTCAAACTTCCGAGCTGTA 58.754 43.478 0.00 0.00 0.00 2.74
4011 9200 3.070018 CAGATTCAAACTTCCGAGCTGT 58.930 45.455 0.00 0.00 0.00 4.40
4012 9201 2.159599 GCAGATTCAAACTTCCGAGCTG 60.160 50.000 0.00 0.00 0.00 4.24
4013 9202 2.079925 GCAGATTCAAACTTCCGAGCT 58.920 47.619 0.00 0.00 0.00 4.09
4014 9203 1.131315 GGCAGATTCAAACTTCCGAGC 59.869 52.381 0.00 0.00 0.00 5.03
4017 9206 3.641437 TTTGGCAGATTCAAACTTCCG 57.359 42.857 0.00 0.00 0.00 4.30
4033 9222 7.980662 TCATGCCAACTGACATATAAATTTTGG 59.019 33.333 0.00 0.00 36.20 3.28
4035 9224 9.590451 CTTCATGCCAACTGACATATAAATTTT 57.410 29.630 0.00 0.00 0.00 1.82
4039 9228 6.422333 TCCTTCATGCCAACTGACATATAAA 58.578 36.000 0.00 0.00 0.00 1.40
4042 9231 4.508551 TCCTTCATGCCAACTGACATAT 57.491 40.909 0.00 0.00 0.00 1.78
4043 9232 3.998913 TCCTTCATGCCAACTGACATA 57.001 42.857 0.00 0.00 0.00 2.29
4044 9233 2.885135 TCCTTCATGCCAACTGACAT 57.115 45.000 0.00 0.00 0.00 3.06
4045 9234 2.885135 ATCCTTCATGCCAACTGACA 57.115 45.000 0.00 0.00 0.00 3.58
4046 9235 4.240096 CAAAATCCTTCATGCCAACTGAC 58.760 43.478 0.00 0.00 0.00 3.51
4048 9237 4.261578 ACAAAATCCTTCATGCCAACTG 57.738 40.909 0.00 0.00 0.00 3.16
4049 9238 5.324409 TCTACAAAATCCTTCATGCCAACT 58.676 37.500 0.00 0.00 0.00 3.16
4051 9240 4.158394 GCTCTACAAAATCCTTCATGCCAA 59.842 41.667 0.00 0.00 0.00 4.52
4052 9241 3.696051 GCTCTACAAAATCCTTCATGCCA 59.304 43.478 0.00 0.00 0.00 4.92
4053 9242 3.950395 AGCTCTACAAAATCCTTCATGCC 59.050 43.478 0.00 0.00 0.00 4.40
4054 9243 5.124457 TCAAGCTCTACAAAATCCTTCATGC 59.876 40.000 0.00 0.00 0.00 4.06
4055 9244 6.748333 TCAAGCTCTACAAAATCCTTCATG 57.252 37.500 0.00 0.00 0.00 3.07
4057 9246 7.068103 TGTTTTCAAGCTCTACAAAATCCTTCA 59.932 33.333 0.00 0.00 0.00 3.02
4058 9247 7.425606 TGTTTTCAAGCTCTACAAAATCCTTC 58.574 34.615 0.00 0.00 0.00 3.46
4059 9248 7.346751 TGTTTTCAAGCTCTACAAAATCCTT 57.653 32.000 0.00 0.00 0.00 3.36
4060 9249 6.959639 TGTTTTCAAGCTCTACAAAATCCT 57.040 33.333 0.00 0.00 0.00 3.24
4061 9250 7.147976 ACATGTTTTCAAGCTCTACAAAATCC 58.852 34.615 0.00 0.00 0.00 3.01
4067 9256 8.264347 TGGATATACATGTTTTCAAGCTCTACA 58.736 33.333 2.30 0.00 0.00 2.74
4068 9257 8.662781 TGGATATACATGTTTTCAAGCTCTAC 57.337 34.615 2.30 0.00 0.00 2.59
4069 9258 9.851686 AATGGATATACATGTTTTCAAGCTCTA 57.148 29.630 2.30 0.00 0.00 2.43
4070 9259 8.757982 AATGGATATACATGTTTTCAAGCTCT 57.242 30.769 2.30 0.00 0.00 4.09
4071 9260 8.844244 AGAATGGATATACATGTTTTCAAGCTC 58.156 33.333 2.30 0.00 0.00 4.09
4072 9261 8.757982 AGAATGGATATACATGTTTTCAAGCT 57.242 30.769 2.30 0.00 0.00 3.74
4074 9263 9.123902 TGGAGAATGGATATACATGTTTTCAAG 57.876 33.333 2.30 0.00 0.00 3.02
4076 9265 9.070179 CATGGAGAATGGATATACATGTTTTCA 57.930 33.333 2.30 0.00 32.10 2.69
4077 9266 8.025445 GCATGGAGAATGGATATACATGTTTTC 58.975 37.037 2.30 0.00 37.23 2.29
4078 9267 7.727186 AGCATGGAGAATGGATATACATGTTTT 59.273 33.333 2.30 0.00 37.23 2.43
4079 9268 7.236529 AGCATGGAGAATGGATATACATGTTT 58.763 34.615 2.30 0.00 37.23 2.83
4081 9270 6.384342 AGCATGGAGAATGGATATACATGT 57.616 37.500 0.00 2.69 37.23 3.21
4082 9271 7.825761 TGTTAGCATGGAGAATGGATATACATG 59.174 37.037 0.00 0.00 36.71 3.21
4083 9272 7.921304 TGTTAGCATGGAGAATGGATATACAT 58.079 34.615 0.00 0.00 36.71 2.29
4084 9273 7.315066 TGTTAGCATGGAGAATGGATATACA 57.685 36.000 0.00 0.00 36.71 2.29
4085 9274 9.890629 TTATGTTAGCATGGAGAATGGATATAC 57.109 33.333 1.80 0.00 36.71 1.47
4089 9278 5.709164 GCTTATGTTAGCATGGAGAATGGAT 59.291 40.000 1.80 0.00 40.89 3.41
4140 9332 6.720309 TCCATCTCAAAAGAATGTGGTATGA 58.280 36.000 0.00 0.00 32.94 2.15
4162 9366 8.450578 TCAATGGTGTATATTTTCACTGATCC 57.549 34.615 0.00 0.00 35.26 3.36
4184 9388 8.712363 CGAGTGATCTTTCAAGAGTTTTATCAA 58.288 33.333 0.00 0.00 38.66 2.57
4203 9407 6.587608 GCAATTTTCTTTTGGATTCGAGTGAT 59.412 34.615 0.00 0.00 0.00 3.06
4205 9409 5.922544 AGCAATTTTCTTTTGGATTCGAGTG 59.077 36.000 0.00 0.00 0.00 3.51
4206 9410 5.922544 CAGCAATTTTCTTTTGGATTCGAGT 59.077 36.000 0.00 0.00 0.00 4.18
4207 9411 5.346822 CCAGCAATTTTCTTTTGGATTCGAG 59.653 40.000 0.00 0.00 0.00 4.04
4209 9413 4.389687 CCCAGCAATTTTCTTTTGGATTCG 59.610 41.667 0.00 0.00 0.00 3.34
4210 9414 5.550290 TCCCAGCAATTTTCTTTTGGATTC 58.450 37.500 0.00 0.00 0.00 2.52
4226 9441 1.699083 TCAAAGTGACAGATCCCAGCA 59.301 47.619 0.00 0.00 0.00 4.41
4234 9449 2.416747 CTTCGGCATCAAAGTGACAGA 58.583 47.619 0.00 0.00 0.00 3.41
4235 9450 1.466167 CCTTCGGCATCAAAGTGACAG 59.534 52.381 0.00 0.00 0.00 3.51
4236 9451 1.071542 TCCTTCGGCATCAAAGTGACA 59.928 47.619 0.00 0.00 0.00 3.58
4239 9454 1.089920 CCTCCTTCGGCATCAAAGTG 58.910 55.000 0.00 0.00 0.00 3.16
4240 9455 0.035056 CCCTCCTTCGGCATCAAAGT 60.035 55.000 0.00 0.00 0.00 2.66
4250 9465 1.078848 CCTTCACAGCCCTCCTTCG 60.079 63.158 0.00 0.00 0.00 3.79
4261 9476 2.234661 CTCTATCTGTGGCACCTTCACA 59.765 50.000 16.26 0.00 42.11 3.58
4262 9477 2.898705 CTCTATCTGTGGCACCTTCAC 58.101 52.381 16.26 0.00 35.82 3.18
4263 9478 1.208052 GCTCTATCTGTGGCACCTTCA 59.792 52.381 16.26 0.00 0.00 3.02
4277 9492 2.907458 AAAGCCCCAACTTGCTCTAT 57.093 45.000 0.00 0.00 36.66 1.98
4294 9509 2.106074 CGCCAGCAGACGCCATAAA 61.106 57.895 0.00 0.00 39.83 1.40
4307 9522 0.038892 AACAATCTTTGCTGCGCCAG 60.039 50.000 4.18 3.40 34.12 4.85
4308 9523 1.242989 TAACAATCTTTGCTGCGCCA 58.757 45.000 4.18 0.00 0.00 5.69
4309 9524 1.985684 GTTAACAATCTTTGCTGCGCC 59.014 47.619 4.18 0.00 0.00 6.53
4310 9525 2.658325 CTGTTAACAATCTTTGCTGCGC 59.342 45.455 10.03 0.00 0.00 6.09
4312 9527 3.578688 CCCTGTTAACAATCTTTGCTGC 58.421 45.455 10.03 0.00 0.00 5.25
4315 9530 2.353704 GCCCCCTGTTAACAATCTTTGC 60.354 50.000 10.03 4.50 0.00 3.68
4316 9531 3.056607 CAGCCCCCTGTTAACAATCTTTG 60.057 47.826 10.03 1.15 34.31 2.77
4317 9532 3.165071 CAGCCCCCTGTTAACAATCTTT 58.835 45.455 10.03 0.00 34.31 2.52
4319 9534 1.616994 GCAGCCCCCTGTTAACAATCT 60.617 52.381 10.03 0.01 41.26 2.40
4320 9535 0.817654 GCAGCCCCCTGTTAACAATC 59.182 55.000 10.03 0.00 41.26 2.67
4321 9536 0.409484 AGCAGCCCCCTGTTAACAAT 59.591 50.000 10.03 0.00 41.26 2.71
4322 9537 0.539438 CAGCAGCCCCCTGTTAACAA 60.539 55.000 10.03 0.00 41.26 2.83
4324 9539 2.343426 GCAGCAGCCCCCTGTTAAC 61.343 63.158 0.00 0.00 41.26 2.01
4325 9540 2.035626 GCAGCAGCCCCCTGTTAA 59.964 61.111 0.00 0.00 41.26 2.01
4326 9541 4.408821 CGCAGCAGCCCCCTGTTA 62.409 66.667 0.00 0.00 41.26 2.41
4332 9547 3.273080 CTTTGTTCGCAGCAGCCCC 62.273 63.158 0.00 0.00 37.52 5.80
4333 9548 1.589716 ATCTTTGTTCGCAGCAGCCC 61.590 55.000 0.00 0.00 37.52 5.19
4336 9551 4.604843 TGAATATCTTTGTTCGCAGCAG 57.395 40.909 0.00 0.00 0.00 4.24
4337 9552 5.369685 TTTGAATATCTTTGTTCGCAGCA 57.630 34.783 0.00 0.00 0.00 4.41
4338 9553 4.795278 CCTTTGAATATCTTTGTTCGCAGC 59.205 41.667 0.00 0.00 0.00 5.25
4339 9554 4.795278 GCCTTTGAATATCTTTGTTCGCAG 59.205 41.667 0.00 0.00 0.00 5.18
4340 9555 4.217334 TGCCTTTGAATATCTTTGTTCGCA 59.783 37.500 0.00 0.00 0.00 5.10
4341 9556 4.732784 TGCCTTTGAATATCTTTGTTCGC 58.267 39.130 0.00 0.00 0.00 4.70
4343 9558 7.463251 GCGAATTGCCTTTGAATATCTTTGTTC 60.463 37.037 0.00 0.00 37.76 3.18
4344 9559 6.311200 GCGAATTGCCTTTGAATATCTTTGTT 59.689 34.615 0.00 0.00 37.76 2.83
4345 9560 5.807011 GCGAATTGCCTTTGAATATCTTTGT 59.193 36.000 0.00 0.00 37.76 2.83
4347 9562 5.807011 GTGCGAATTGCCTTTGAATATCTTT 59.193 36.000 0.00 0.00 45.60 2.52
4350 9565 4.671377 TGTGCGAATTGCCTTTGAATATC 58.329 39.130 0.00 0.00 45.60 1.63
4351 9566 4.717233 TGTGCGAATTGCCTTTGAATAT 57.283 36.364 0.00 0.00 45.60 1.28
4354 9569 2.159184 TGTTGTGCGAATTGCCTTTGAA 60.159 40.909 0.00 0.00 45.60 2.69
4355 9570 1.406898 TGTTGTGCGAATTGCCTTTGA 59.593 42.857 0.00 0.00 45.60 2.69
4356 9571 1.850377 TGTTGTGCGAATTGCCTTTG 58.150 45.000 0.00 0.00 45.60 2.77
4357 9572 2.818130 ATGTTGTGCGAATTGCCTTT 57.182 40.000 0.00 0.00 45.60 3.11
4358 9573 2.818130 AATGTTGTGCGAATTGCCTT 57.182 40.000 0.00 0.00 45.60 4.35
4359 9574 2.818130 AAATGTTGTGCGAATTGCCT 57.182 40.000 0.00 0.00 45.60 4.75
4360 9575 2.345341 GCTAAATGTTGTGCGAATTGCC 59.655 45.455 0.00 0.00 45.60 4.52
4361 9576 2.985809 TGCTAAATGTTGTGCGAATTGC 59.014 40.909 0.00 0.00 46.70 3.56
4363 9578 3.980775 GTGTGCTAAATGTTGTGCGAATT 59.019 39.130 0.00 0.00 0.00 2.17
4366 9581 2.217750 AGTGTGCTAAATGTTGTGCGA 58.782 42.857 0.00 0.00 0.00 5.10
4367 9582 2.686558 AGTGTGCTAAATGTTGTGCG 57.313 45.000 0.00 0.00 0.00 5.34
4370 9585 9.762933 AATGAATTTTAGTGTGCTAAATGTTGT 57.237 25.926 1.35 0.00 44.02 3.32
4379 9594 9.146984 CAATGAATGAATGAATTTTAGTGTGCT 57.853 29.630 0.00 0.00 0.00 4.40
4381 9596 8.385111 GCCAATGAATGAATGAATTTTAGTGTG 58.615 33.333 0.00 0.00 0.00 3.82
4382 9597 8.095792 TGCCAATGAATGAATGAATTTTAGTGT 58.904 29.630 0.00 0.00 0.00 3.55
4383 9598 8.385111 GTGCCAATGAATGAATGAATTTTAGTG 58.615 33.333 0.00 0.00 0.00 2.74
4384 9599 8.095792 TGTGCCAATGAATGAATGAATTTTAGT 58.904 29.630 0.00 0.00 0.00 2.24
4385 9600 8.481974 TGTGCCAATGAATGAATGAATTTTAG 57.518 30.769 0.00 0.00 0.00 1.85
4387 9602 7.148154 CCATGTGCCAATGAATGAATGAATTTT 60.148 33.333 0.00 0.00 0.00 1.82
4390 9605 5.364778 CCATGTGCCAATGAATGAATGAAT 58.635 37.500 0.00 0.00 0.00 2.57
4391 9606 4.760878 CCATGTGCCAATGAATGAATGAA 58.239 39.130 0.00 0.00 0.00 2.57
4392 9607 3.431068 GCCATGTGCCAATGAATGAATGA 60.431 43.478 0.00 0.00 0.00 2.57
4395 9610 2.166870 GAGCCATGTGCCAATGAATGAA 59.833 45.455 2.95 0.00 42.71 2.57
4396 9611 1.752498 GAGCCATGTGCCAATGAATGA 59.248 47.619 2.95 0.00 42.71 2.57
4397 9612 1.754803 AGAGCCATGTGCCAATGAATG 59.245 47.619 2.95 0.00 42.71 2.67
4398 9613 2.154567 AGAGCCATGTGCCAATGAAT 57.845 45.000 2.95 0.00 42.71 2.57
4400 9615 1.179152 CAAGAGCCATGTGCCAATGA 58.821 50.000 2.95 0.00 42.71 2.57
4401 9616 1.135199 GTCAAGAGCCATGTGCCAATG 60.135 52.381 2.95 1.11 42.71 2.82
4403 9618 0.111061 AGTCAAGAGCCATGTGCCAA 59.889 50.000 2.95 0.00 42.71 4.52
4404 9619 0.111061 AAGTCAAGAGCCATGTGCCA 59.889 50.000 2.95 0.00 42.71 4.92
4406 9621 0.445436 CGAAGTCAAGAGCCATGTGC 59.555 55.000 0.00 0.00 41.71 4.57
4410 10786 3.196469 TGAAGATCGAAGTCAAGAGCCAT 59.804 43.478 0.00 0.00 0.00 4.40
4419 10795 8.973378 CAATCCTATAAACTGAAGATCGAAGTC 58.027 37.037 0.00 0.00 0.00 3.01
4451 10830 3.650281 TTCTCATCCATGCAAGGCTTA 57.350 42.857 2.20 0.00 0.00 3.09
4459 10838 5.363101 TGTCTACATCTTTCTCATCCATGC 58.637 41.667 0.00 0.00 0.00 4.06
4467 10846 6.216569 TCTGTGTGTTGTCTACATCTTTCTC 58.783 40.000 0.00 0.00 39.39 2.87
4486 10865 9.612620 GTCTATTCCTTTTGTAACATTTCTGTG 57.387 33.333 0.00 0.00 35.22 3.66
4488 10867 8.244113 GGGTCTATTCCTTTTGTAACATTTCTG 58.756 37.037 0.00 0.00 0.00 3.02
4490 10869 8.027189 GTGGGTCTATTCCTTTTGTAACATTTC 58.973 37.037 0.00 0.00 0.00 2.17
4521 10900 4.067192 CGCTGGGATCATGATATTCACAA 58.933 43.478 8.54 0.00 0.00 3.33


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

AutoCloner maintained by Alex Coulton.