Multiple sequence alignment - TraesCS3D01G169800

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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 TraesCS3D01G169800 chr3D 100.000 5642 0 0 1645 7286 147829775 147835416 0.000000e+00 10419
1 TraesCS3D01G169800 chr3D 100.000 1221 0 0 1 1221 147828131 147829351 0.000000e+00 2255
2 TraesCS3D01G169800 chr3D 95.789 95 2 2 5171 5263 138889953 138889859 1.270000e-32 152
3 TraesCS3D01G169800 chr3D 93.269 104 4 3 5171 5271 14946973 14946870 4.550000e-32 150
4 TraesCS3D01G169800 chr3B 94.215 3561 142 37 1645 5174 214552203 214548676 0.000000e+00 5376
5 TraesCS3D01G169800 chr3B 94.823 1043 33 9 5252 6284 214548681 214547650 0.000000e+00 1607
6 TraesCS3D01G169800 chr3B 89.388 735 38 18 6327 7040 214547474 214546759 0.000000e+00 889
7 TraesCS3D01G169800 chr3B 87.798 672 55 16 1 668 214553459 214552811 0.000000e+00 761
8 TraesCS3D01G169800 chr3B 87.411 421 29 16 671 1080 214552749 214552342 5.150000e-126 462
9 TraesCS3D01G169800 chr3B 93.548 186 6 2 7100 7285 214546485 214546306 9.310000e-69 272
10 TraesCS3D01G169800 chr3B 95.536 112 4 1 1110 1220 214552345 214552234 2.090000e-40 178
11 TraesCS3D01G169800 chr3A 94.306 2371 100 20 1997 4347 165332609 165330254 0.000000e+00 3598
12 TraesCS3D01G169800 chr3A 95.147 989 34 8 5252 6227 165329664 165328677 0.000000e+00 1548
13 TraesCS3D01G169800 chr3A 94.009 918 43 10 4265 5174 165330572 165329659 0.000000e+00 1380
14 TraesCS3D01G169800 chr3A 97.194 677 9 2 1 668 165334604 165333929 0.000000e+00 1136
15 TraesCS3D01G169800 chr3A 92.607 514 30 6 6777 7286 165322553 165322044 0.000000e+00 732
16 TraesCS3D01G169800 chr3A 91.416 466 32 5 1645 2107 165333136 165332676 3.710000e-177 632
17 TraesCS3D01G169800 chr3A 92.329 365 11 10 858 1213 165333514 165333158 3.030000e-138 503
18 TraesCS3D01G169800 chr3A 86.463 458 15 17 6276 6731 165328308 165327896 6.660000e-125 459
19 TraesCS3D01G169800 chr3A 98.010 201 4 0 671 871 165333867 165333667 4.180000e-92 350
20 TraesCS3D01G169800 chr3A 86.290 124 13 3 5132 5255 215068549 215068668 1.650000e-26 132
21 TraesCS3D01G169800 chr1A 91.759 898 32 21 6030 6908 34287473 34288347 0.000000e+00 1210
22 TraesCS3D01G169800 chr1A 85.637 557 70 9 4029 4576 227261590 227261035 1.760000e-160 577
23 TraesCS3D01G169800 chr5D 89.127 561 45 14 4029 4578 256469844 256469289 0.000000e+00 684
24 TraesCS3D01G169800 chr5D 86.772 567 52 18 4029 4579 236436897 236437456 1.740000e-170 610
25 TraesCS3D01G169800 chr5D 92.053 151 11 1 47 196 72211427 72211277 2.060000e-50 211
26 TraesCS3D01G169800 chr2A 87.166 561 59 11 4028 4579 350725844 350725288 6.210000e-175 625
27 TraesCS3D01G169800 chr6A 86.511 556 59 14 4029 4576 235075996 235076543 1.350000e-166 597
28 TraesCS3D01G169800 chr6D 86.355 557 63 12 4029 4576 181693197 181692645 4.870000e-166 595
29 TraesCS3D01G169800 chr1B 83.871 558 78 10 4029 4576 249517173 249517728 8.380000e-144 521
30 TraesCS3D01G169800 chr5A 93.377 151 9 1 47 196 64756116 64755966 9.510000e-54 222
31 TraesCS3D01G169800 chr5A 92.661 109 7 1 5158 5266 635414070 635413963 9.790000e-34 156
32 TraesCS3D01G169800 chr5B 92.715 151 10 1 47 196 82241472 82241622 4.430000e-52 217
33 TraesCS3D01G169800 chr5B 95.699 93 4 0 5163 5255 520899457 520899549 4.550000e-32 150
34 TraesCS3D01G169800 chr2D 100.000 88 0 0 5168 5255 188401901 188401988 5.850000e-36 163
35 TraesCS3D01G169800 chr4B 87.500 136 17 0 73 208 73480353 73480218 2.720000e-34 158
36 TraesCS3D01G169800 chrUn 92.233 103 6 2 5162 5263 316007516 316007617 2.120000e-30 145
37 TraesCS3D01G169800 chr4A 94.681 94 3 2 5171 5263 644105971 644105879 2.120000e-30 145
38 TraesCS3D01G169800 chr7A 80.899 178 31 3 3859 4034 611003258 611003434 3.550000e-28 137
39 TraesCS3D01G169800 chr6B 91.176 102 7 2 5162 5262 534906750 534906850 3.550000e-28 137
40 TraesCS3D01G169800 chr7B 81.366 161 24 6 3863 4021 570178827 570178983 7.670000e-25 126
41 TraesCS3D01G169800 chr7D 78.075 187 30 7 3816 3992 530735836 530735651 2.780000e-19 108


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 TraesCS3D01G169800 chr3D 147828131 147835416 7285 False 6337.000000 10419 100.00000 1 7286 2 chr3D.!!$F1 7285
1 TraesCS3D01G169800 chr3B 214546306 214553459 7153 True 1363.571429 5376 91.81700 1 7285 7 chr3B.!!$R1 7284
2 TraesCS3D01G169800 chr3A 165327896 165334604 6708 True 1200.750000 3598 93.60925 1 6731 8 chr3A.!!$R2 6730
3 TraesCS3D01G169800 chr3A 165322044 165322553 509 True 732.000000 732 92.60700 6777 7286 1 chr3A.!!$R1 509
4 TraesCS3D01G169800 chr1A 34287473 34288347 874 False 1210.000000 1210 91.75900 6030 6908 1 chr1A.!!$F1 878
5 TraesCS3D01G169800 chr1A 227261035 227261590 555 True 577.000000 577 85.63700 4029 4576 1 chr1A.!!$R1 547
6 TraesCS3D01G169800 chr5D 256469289 256469844 555 True 684.000000 684 89.12700 4029 4578 1 chr5D.!!$R2 549
7 TraesCS3D01G169800 chr5D 236436897 236437456 559 False 610.000000 610 86.77200 4029 4579 1 chr5D.!!$F1 550
8 TraesCS3D01G169800 chr2A 350725288 350725844 556 True 625.000000 625 87.16600 4028 4579 1 chr2A.!!$R1 551
9 TraesCS3D01G169800 chr6A 235075996 235076543 547 False 597.000000 597 86.51100 4029 4576 1 chr6A.!!$F1 547
10 TraesCS3D01G169800 chr6D 181692645 181693197 552 True 595.000000 595 86.35500 4029 4576 1 chr6D.!!$R1 547
11 TraesCS3D01G169800 chr1B 249517173 249517728 555 False 521.000000 521 83.87100 4029 4576 1 chr1B.!!$F1 547

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
949 1194 0.179108 GGCCTCCGTTGCTAGTAGTG 60.179 60.0 0.00 0.00 0.00 2.74 F
950 1195 0.179108 GCCTCCGTTGCTAGTAGTGG 60.179 60.0 0.00 0.00 0.00 4.00 F
2125 2571 1.059913 AGAGGCAGCAACCTGTAAGT 58.940 50.0 1.69 0.00 41.32 2.24 F
2739 3199 1.544724 GCTGTCAGGTTAAATGGCCA 58.455 50.0 8.56 8.56 0.00 5.36 F
4354 5088 0.401738 ACATGTCAACACCCCCTCTG 59.598 55.0 0.00 0.00 0.00 3.35 F
5881 6630 0.249953 TACGCTTCGAAGGTGCCAAA 60.250 50.0 25.77 4.98 0.00 3.28 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1894 2153 0.175073 ATCCTTCTAACACCGCGACC 59.825 55.000 8.23 0.00 0.00 4.79 R
2531 2988 0.251634 CTCCTTCTTCCTGACCTGCC 59.748 60.000 0.00 0.00 0.00 4.85 R
3151 3613 1.001706 CCATTGATCAGCATGCCTTCG 60.002 52.381 15.66 0.36 34.76 3.79 R
4421 5157 0.393820 ATTGTTGCTGCCCACCTTTG 59.606 50.000 0.00 0.00 0.00 2.77 R
6209 6984 0.039437 TCGGCGTTGAGACTTGAGAC 60.039 55.000 6.85 0.00 0.00 3.36 R
6801 8037 0.036164 ATGCCGCTGGTACAAACTGA 59.964 50.000 0.00 0.00 38.70 3.41 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
55 56 9.321562 ACGTACATATAAACTGGTTTCCTATTG 57.678 33.333 1.77 0.00 34.23 1.90
244 245 5.183904 GGAGTTGCACCTACAGAAAATCATT 59.816 40.000 0.00 0.00 0.00 2.57
292 295 4.401022 ACTTGAGTGAAATCTGCATTGGA 58.599 39.130 0.00 0.00 0.00 3.53
293 296 4.828939 ACTTGAGTGAAATCTGCATTGGAA 59.171 37.500 0.00 0.00 0.00 3.53
668 680 3.064987 GCCGGACTAGAGCGCTTCA 62.065 63.158 13.26 0.64 0.00 3.02
669 681 1.064946 CCGGACTAGAGCGCTTCAG 59.935 63.158 13.26 14.62 0.00 3.02
684 755 0.329931 TTCAGAGAGAGAGAGGCGGT 59.670 55.000 0.00 0.00 0.00 5.68
943 1188 4.096003 GCTGGGCCTCCGTTGCTA 62.096 66.667 4.53 0.00 35.24 3.49
946 1191 1.305465 TGGGCCTCCGTTGCTAGTA 60.305 57.895 4.53 0.00 35.24 1.82
947 1192 1.327690 TGGGCCTCCGTTGCTAGTAG 61.328 60.000 4.53 0.00 35.24 2.57
948 1193 1.328430 GGGCCTCCGTTGCTAGTAGT 61.328 60.000 0.84 0.00 0.00 2.73
949 1194 0.179108 GGCCTCCGTTGCTAGTAGTG 60.179 60.000 0.00 0.00 0.00 2.74
950 1195 0.179108 GCCTCCGTTGCTAGTAGTGG 60.179 60.000 0.00 0.00 0.00 4.00
985 1237 1.135141 CAGACAAAGCGGAGAGAGAGG 60.135 57.143 0.00 0.00 0.00 3.69
1022 1276 4.379243 CTCAGTTCGGCGCCCAGT 62.379 66.667 23.46 7.97 0.00 4.00
1066 1320 3.083349 CGCAGACCCATCTCCCCA 61.083 66.667 0.00 0.00 30.42 4.96
1213 1467 4.484872 GCCCCGCCAAGAGGTACC 62.485 72.222 2.73 2.73 37.19 3.34
1667 1921 4.725556 TCCAGTCTTGTTTTCGATTTCG 57.274 40.909 0.00 0.00 41.45 3.46
1716 1974 3.804786 TGCCGTGGTTCGATTAGATTA 57.195 42.857 0.00 0.00 42.86 1.75
1777 2035 2.228103 CAGTAGCGGCGTGGATTATCTA 59.772 50.000 9.37 0.00 0.00 1.98
1802 2060 2.683859 GCGGGCGTTTCCTTGTACC 61.684 63.158 0.00 0.00 34.39 3.34
1810 2069 2.414138 CGTTTCCTTGTACCGGTGATTC 59.586 50.000 19.93 5.66 0.00 2.52
1853 2112 5.045012 AGAGGCTGATGCTATCAAATGAA 57.955 39.130 0.00 0.00 39.11 2.57
1860 2119 7.306399 GGCTGATGCTATCAAATGAAAATTTCG 60.306 37.037 0.97 0.00 39.11 3.46
1877 2136 9.559958 GAAAATTTCGATGATTGAGTATGTTGT 57.440 29.630 0.00 0.00 0.00 3.32
1894 2153 3.868661 TGTTGTTATCGATTGACCCATCG 59.131 43.478 1.71 0.00 41.24 3.84
1970 2230 3.984633 GGATCATCGAAGCAACTAGTAGC 59.015 47.826 0.00 0.00 0.00 3.58
2012 2272 5.244626 CCACAGAAAAGGAAATGATGGACTT 59.755 40.000 0.00 0.00 0.00 3.01
2057 2503 9.288576 TCAGATGTCTTGTGAACAAATAAATCT 57.711 29.630 0.00 2.17 35.15 2.40
2125 2571 1.059913 AGAGGCAGCAACCTGTAAGT 58.940 50.000 1.69 0.00 41.32 2.24
2230 2677 3.818295 ACAGGGCCCAACTATTTTGTA 57.182 42.857 27.56 0.00 0.00 2.41
2242 2689 2.941891 ATTTTGTAGTGTGCACGACG 57.058 45.000 13.13 0.00 39.36 5.12
2248 2695 2.472232 TAGTGTGCACGACGGAGCAG 62.472 60.000 16.01 0.00 40.47 4.24
2311 2764 4.585162 TGAAATTTTACCACCGGTGTCATT 59.415 37.500 31.80 18.15 36.19 2.57
2339 2793 1.732683 GGCGTGCAATTCGGGTTTG 60.733 57.895 0.00 0.00 0.00 2.93
2542 2999 2.550277 TGAAGATAGGCAGGTCAGGA 57.450 50.000 0.00 0.00 0.00 3.86
2586 3043 1.801242 TTGTGGAGGAGTGTGAGGAA 58.199 50.000 0.00 0.00 0.00 3.36
2619 3076 7.209471 TGTCAAACAAACCATATGTCCTTAC 57.791 36.000 1.24 0.00 0.00 2.34
2739 3199 1.544724 GCTGTCAGGTTAAATGGCCA 58.455 50.000 8.56 8.56 0.00 5.36
2774 3234 7.394016 TCAGTTTATCTTCAATGCTAGGTTCA 58.606 34.615 0.00 0.00 0.00 3.18
2842 3302 1.813513 ACTTGCAGAAATCACCCTCG 58.186 50.000 0.00 0.00 0.00 4.63
2852 3312 6.346096 CAGAAATCACCCTCGGTTCTTAATA 58.654 40.000 0.00 0.00 31.02 0.98
2896 3356 4.261578 ACTTTTGCAATCATTCTGTGGG 57.738 40.909 0.00 0.00 0.00 4.61
2923 3383 6.634805 TGAGCAGTTAGGTTTTGATCTAGAG 58.365 40.000 0.00 0.00 0.00 2.43
2949 3409 7.556733 TTGAACGAGGTTAGTTTTGTTATGT 57.443 32.000 0.00 0.00 31.14 2.29
2965 3425 6.164408 TGTTATGTGCGTGTAATTCTCTTG 57.836 37.500 0.00 0.00 0.00 3.02
2977 3437 9.710979 CGTGTAATTCTCTTGTTTGACTAAAAA 57.289 29.630 0.00 0.00 0.00 1.94
2995 3455 7.951591 ACTAAAAATGGACACTATTGCTTTGT 58.048 30.769 0.00 0.00 0.00 2.83
3005 3465 5.580297 ACACTATTGCTTTGTTTGTGTTTGG 59.420 36.000 0.00 0.00 34.10 3.28
3151 3613 1.844687 ATGCAGGAGAGGGCTTTTTC 58.155 50.000 0.00 0.00 0.00 2.29
3293 3755 9.612066 TCAAAATTGTTCTTTTAGATTGCCTTT 57.388 25.926 0.00 0.00 0.00 3.11
3320 3782 1.663911 ACCACCATTAGCCACCAGTA 58.336 50.000 0.00 0.00 0.00 2.74
3370 3832 4.404715 AGATTCTGCATCTGAATTTTGGGG 59.595 41.667 1.64 0.00 41.13 4.96
3457 3919 5.741011 CCTTTGGCCTCTGTACATAACTTA 58.259 41.667 3.32 0.00 0.00 2.24
3460 3922 5.353394 TGGCCTCTGTACATAACTTAAGG 57.647 43.478 3.32 0.00 0.00 2.69
3485 3947 6.795144 TGATTGCAGGATGATAAACCATTT 57.205 33.333 0.00 0.00 39.69 2.32
3492 3954 6.756542 GCAGGATGATAAACCATTTGTAAACC 59.243 38.462 0.00 0.00 39.69 3.27
3565 4027 4.284490 TGGATACCTACATGATGCTCCTTC 59.716 45.833 0.00 0.00 0.00 3.46
3644 4108 9.449719 TTCTTCCTTTCTTAATCAGTTATCACC 57.550 33.333 0.00 0.00 0.00 4.02
3893 4359 9.495754 GTGATTCACTTACAAAATCTAAGATGC 57.504 33.333 9.59 0.00 31.99 3.91
3923 4389 8.210946 TGCCTATGTAAAGCTATTCACTGTAAT 58.789 33.333 0.00 0.00 0.00 1.89
4257 4990 3.239449 TGAACTCAAGACCTTAGCTCCA 58.761 45.455 0.00 0.00 0.00 3.86
4278 5011 5.067674 TCCAATACCATGTTAAGCTTCATGC 59.932 40.000 18.30 3.35 39.74 4.06
4288 5021 1.457346 AGCTTCATGCACTAGCCAAC 58.543 50.000 11.63 0.00 45.94 3.77
4292 5025 0.605050 TCATGCACTAGCCAACGCAA 60.605 50.000 0.00 0.00 41.13 4.85
4300 5034 1.336755 CTAGCCAACGCAACCAAAGTT 59.663 47.619 0.00 0.00 37.52 2.66
4308 5042 2.937799 ACGCAACCAAAGTTCGAACTAA 59.062 40.909 29.91 0.00 38.57 2.24
4338 5072 5.787494 AGGGCTAGACAATCCACATATACAT 59.213 40.000 0.00 0.00 0.00 2.29
4339 5073 5.877012 GGGCTAGACAATCCACATATACATG 59.123 44.000 0.00 0.00 38.21 3.21
4354 5088 0.401738 ACATGTCAACACCCCCTCTG 59.598 55.000 0.00 0.00 0.00 3.35
4373 5107 3.712655 CGTGTGCGTGGAAAGTCA 58.287 55.556 0.00 0.00 0.00 3.41
4392 5126 2.343758 CACGTGGGTGGACTCAGG 59.656 66.667 7.95 0.00 40.58 3.86
4421 5157 1.400737 AGAGGCCTATACGTGGACAC 58.599 55.000 4.42 0.00 34.31 3.67
4427 5163 2.354403 GCCTATACGTGGACACAAAGGT 60.354 50.000 0.00 0.00 0.00 3.50
4506 5243 3.495001 GCTCCGATACCATGTTAAGCTTC 59.505 47.826 0.00 0.00 0.00 3.86
4539 5276 0.378962 CGCAACCAAAAGTCCGAACA 59.621 50.000 0.00 0.00 0.00 3.18
4550 5287 3.223674 AGTCCGAACAAATGGAAAGGT 57.776 42.857 0.00 0.00 35.67 3.50
4584 5322 5.122869 CCACATATCACTTCAACACTTCCAG 59.877 44.000 0.00 0.00 0.00 3.86
4615 5353 3.415212 TGGTGAAAATCTCTGCCTTGAG 58.585 45.455 0.00 0.00 35.52 3.02
4616 5354 2.751806 GGTGAAAATCTCTGCCTTGAGG 59.248 50.000 0.00 0.00 34.98 3.86
4617 5355 2.751806 GTGAAAATCTCTGCCTTGAGGG 59.248 50.000 0.00 0.00 34.98 4.30
4718 5461 7.548196 TTCTTCTGAACTGTCGTTTGTTATT 57.452 32.000 0.00 0.00 32.39 1.40
4954 5697 6.656902 AGATTGCCTAAATTCACTCATCTCA 58.343 36.000 0.00 0.00 0.00 3.27
5100 5844 5.183530 TCCATGTCCAATCAGAGAAATGT 57.816 39.130 0.00 0.00 0.00 2.71
5169 5913 4.825546 ACAATGACTGCTTCTTGACAAG 57.174 40.909 9.03 9.03 0.00 3.16
5170 5914 4.202441 ACAATGACTGCTTCTTGACAAGT 58.798 39.130 14.75 0.00 0.00 3.16
5171 5915 5.368145 ACAATGACTGCTTCTTGACAAGTA 58.632 37.500 14.75 4.74 0.00 2.24
5172 5916 5.237344 ACAATGACTGCTTCTTGACAAGTAC 59.763 40.000 14.75 6.52 0.00 2.73
5173 5917 4.672587 TGACTGCTTCTTGACAAGTACT 57.327 40.909 14.75 0.00 0.00 2.73
5174 5918 4.621991 TGACTGCTTCTTGACAAGTACTC 58.378 43.478 14.75 4.31 0.00 2.59
5175 5919 3.991121 GACTGCTTCTTGACAAGTACTCC 59.009 47.826 14.75 2.07 0.00 3.85
5176 5920 3.244249 ACTGCTTCTTGACAAGTACTCCC 60.244 47.826 14.75 0.83 0.00 4.30
5177 5921 2.972713 TGCTTCTTGACAAGTACTCCCT 59.027 45.455 14.75 0.00 0.00 4.20
5178 5922 3.006967 TGCTTCTTGACAAGTACTCCCTC 59.993 47.826 14.75 0.00 0.00 4.30
5179 5923 3.259625 GCTTCTTGACAAGTACTCCCTCT 59.740 47.826 14.75 0.00 0.00 3.69
5180 5924 4.815269 CTTCTTGACAAGTACTCCCTCTG 58.185 47.826 14.75 0.00 0.00 3.35
5181 5925 3.845860 TCTTGACAAGTACTCCCTCTGT 58.154 45.455 14.75 0.00 0.00 3.41
5182 5926 4.994282 TCTTGACAAGTACTCCCTCTGTA 58.006 43.478 14.75 0.00 0.00 2.74
5183 5927 5.391256 TCTTGACAAGTACTCCCTCTGTAA 58.609 41.667 14.75 0.00 0.00 2.41
5184 5928 5.836898 TCTTGACAAGTACTCCCTCTGTAAA 59.163 40.000 14.75 0.00 0.00 2.01
5185 5929 5.464030 TGACAAGTACTCCCTCTGTAAAC 57.536 43.478 0.00 0.00 0.00 2.01
5186 5930 5.145564 TGACAAGTACTCCCTCTGTAAACT 58.854 41.667 0.00 0.00 0.00 2.66
5187 5931 6.309357 TGACAAGTACTCCCTCTGTAAACTA 58.691 40.000 0.00 0.00 0.00 2.24
5188 5932 6.779049 TGACAAGTACTCCCTCTGTAAACTAA 59.221 38.462 0.00 0.00 0.00 2.24
5189 5933 7.453752 TGACAAGTACTCCCTCTGTAAACTAAT 59.546 37.037 0.00 0.00 0.00 1.73
5190 5934 8.890410 ACAAGTACTCCCTCTGTAAACTAATA 57.110 34.615 0.00 0.00 0.00 0.98
5191 5935 9.490083 ACAAGTACTCCCTCTGTAAACTAATAT 57.510 33.333 0.00 0.00 0.00 1.28
5197 5941 8.862085 ACTCCCTCTGTAAACTAATATAAGAGC 58.138 37.037 0.00 0.00 0.00 4.09
5198 5942 7.883217 TCCCTCTGTAAACTAATATAAGAGCG 58.117 38.462 0.00 0.00 0.00 5.03
5199 5943 7.504911 TCCCTCTGTAAACTAATATAAGAGCGT 59.495 37.037 0.00 0.00 0.00 5.07
5200 5944 8.142551 CCCTCTGTAAACTAATATAAGAGCGTT 58.857 37.037 0.00 0.00 0.00 4.84
5201 5945 9.530633 CCTCTGTAAACTAATATAAGAGCGTTT 57.469 33.333 0.00 0.00 0.00 3.60
5203 5947 9.309516 TCTGTAAACTAATATAAGAGCGTTTGG 57.690 33.333 0.00 0.00 0.00 3.28
5204 5948 9.309516 CTGTAAACTAATATAAGAGCGTTTGGA 57.690 33.333 0.00 0.00 0.00 3.53
5205 5949 9.826574 TGTAAACTAATATAAGAGCGTTTGGAT 57.173 29.630 0.00 0.00 0.00 3.41
5207 5951 8.958119 AAACTAATATAAGAGCGTTTGGATCA 57.042 30.769 0.00 0.00 32.03 2.92
5208 5952 7.948278 ACTAATATAAGAGCGTTTGGATCAC 57.052 36.000 0.00 0.00 32.03 3.06
5209 5953 7.727181 ACTAATATAAGAGCGTTTGGATCACT 58.273 34.615 0.00 0.00 32.03 3.41
5210 5954 8.857098 ACTAATATAAGAGCGTTTGGATCACTA 58.143 33.333 0.00 0.00 32.03 2.74
5211 5955 9.692749 CTAATATAAGAGCGTTTGGATCACTAA 57.307 33.333 0.00 0.00 32.03 2.24
5212 5956 8.958119 AATATAAGAGCGTTTGGATCACTAAA 57.042 30.769 0.00 0.00 32.03 1.85
5213 5957 6.663944 ATAAGAGCGTTTGGATCACTAAAC 57.336 37.500 0.00 2.49 41.72 2.01
5214 5958 4.273148 AGAGCGTTTGGATCACTAAACT 57.727 40.909 13.84 0.00 42.53 2.66
5215 5959 5.401531 AGAGCGTTTGGATCACTAAACTA 57.598 39.130 13.84 0.00 42.53 2.24
5216 5960 5.411781 AGAGCGTTTGGATCACTAAACTAG 58.588 41.667 13.84 0.00 42.53 2.57
5217 5961 5.047235 AGAGCGTTTGGATCACTAAACTAGT 60.047 40.000 13.84 0.00 42.53 2.57
5218 5962 6.152323 AGAGCGTTTGGATCACTAAACTAGTA 59.848 38.462 0.00 0.00 42.53 1.82
5219 5963 6.694447 AGCGTTTGGATCACTAAACTAGTAA 58.306 36.000 0.00 0.00 42.53 2.24
5220 5964 7.328737 AGCGTTTGGATCACTAAACTAGTAAT 58.671 34.615 0.00 0.00 42.53 1.89
5221 5965 7.491696 AGCGTTTGGATCACTAAACTAGTAATC 59.508 37.037 0.00 0.00 42.53 1.75
5222 5966 7.491696 GCGTTTGGATCACTAAACTAGTAATCT 59.508 37.037 0.00 0.00 42.53 2.40
5249 5993 9.490379 AAATGCTCTTATATTAGTTTACGGAGG 57.510 33.333 0.00 0.00 0.00 4.30
5250 5994 6.989659 TGCTCTTATATTAGTTTACGGAGGG 58.010 40.000 0.00 0.00 0.00 4.30
5251 5995 6.779049 TGCTCTTATATTAGTTTACGGAGGGA 59.221 38.462 0.00 0.00 0.00 4.20
5583 6332 3.954258 GGCCTTAAAGTAAGCATGGTGAT 59.046 43.478 0.00 0.00 34.46 3.06
5720 6469 7.328005 GTGAAGGAGAAAGAATGCAATTTCTTC 59.672 37.037 19.72 18.38 43.88 2.87
5721 6470 6.906157 AGGAGAAAGAATGCAATTTCTTCA 57.094 33.333 22.70 0.00 43.88 3.02
5726 6475 6.590292 AGAAAGAATGCAATTTCTTCATGCTG 59.410 34.615 14.14 0.00 43.42 4.41
5765 6514 0.318441 TGGACAACCTGCTCTTCTCG 59.682 55.000 0.00 0.00 37.04 4.04
5789 6538 1.591158 GACGCGTTCAGAAACAAGACA 59.409 47.619 15.53 0.00 34.93 3.41
5875 6624 1.201880 GAGGTTCTACGCTTCGAAGGT 59.798 52.381 25.77 21.83 0.00 3.50
5876 6625 1.067776 AGGTTCTACGCTTCGAAGGTG 60.068 52.381 25.77 15.20 0.00 4.00
5877 6626 0.714439 GTTCTACGCTTCGAAGGTGC 59.286 55.000 25.77 12.25 0.00 5.01
5878 6627 0.389426 TTCTACGCTTCGAAGGTGCC 60.389 55.000 25.77 8.72 0.00 5.01
5879 6628 1.080093 CTACGCTTCGAAGGTGCCA 60.080 57.895 25.77 7.28 0.00 4.92
5880 6629 0.669318 CTACGCTTCGAAGGTGCCAA 60.669 55.000 25.77 6.97 0.00 4.52
5881 6630 0.249953 TACGCTTCGAAGGTGCCAAA 60.250 50.000 25.77 4.98 0.00 3.28
5882 6631 1.207593 CGCTTCGAAGGTGCCAAAG 59.792 57.895 25.77 0.00 0.00 2.77
5883 6632 1.081175 GCTTCGAAGGTGCCAAAGC 60.081 57.895 25.77 5.73 35.99 3.51
5884 6633 1.581447 CTTCGAAGGTGCCAAAGCC 59.419 57.895 17.70 0.00 38.69 4.35
5921 6681 4.171754 GTTTGAGCTGATGCATCCTTTTC 58.828 43.478 23.67 15.35 42.74 2.29
6138 6908 9.010029 CACAAGTAGTATGTTTAGGGTGAATTT 57.990 33.333 0.00 0.00 0.00 1.82
6209 6984 1.269998 GTATAGCGTAGTCCCCAGCAG 59.730 57.143 0.00 0.00 0.00 4.24
6237 7012 1.078497 TCAACGCCGAGAATGCCAT 60.078 52.632 0.00 0.00 0.00 4.40
6258 7034 5.350365 CCATTTGATGAACTTTTGGAGCATG 59.650 40.000 0.00 0.00 0.00 4.06
6266 7042 3.416156 ACTTTTGGAGCATGGACTTCTC 58.584 45.455 0.00 0.00 0.00 2.87
6270 7057 4.908601 TTGGAGCATGGACTTCTCTTAA 57.091 40.909 0.00 0.00 0.00 1.85
6271 7375 4.908601 TGGAGCATGGACTTCTCTTAAA 57.091 40.909 0.00 0.00 0.00 1.52
6274 7378 7.141758 TGGAGCATGGACTTCTCTTAAATAT 57.858 36.000 0.00 0.00 0.00 1.28
6307 7526 7.565680 AGTCATATTTGTACCTTCTAACCAGG 58.434 38.462 0.00 0.00 37.45 4.45
6332 7562 4.557205 AGTTTTGATACTGTGGAGACGTC 58.443 43.478 7.70 7.70 0.00 4.34
6351 7581 2.345244 CTGTCGGCTTGCACCTCT 59.655 61.111 0.00 0.00 0.00 3.69
6369 7599 4.041198 ACCTCTCATCGTTTTAGTGGGAAA 59.959 41.667 0.00 0.00 0.00 3.13
6404 7634 1.341531 GTGACTCATCTGATACCCCCG 59.658 57.143 0.00 0.00 0.00 5.73
6414 7644 2.303022 CTGATACCCCCGTGCATTCTAT 59.697 50.000 0.00 0.00 0.00 1.98
6419 7649 2.104281 ACCCCCGTGCATTCTATTCTAC 59.896 50.000 0.00 0.00 0.00 2.59
6426 7656 6.380190 CCGTGCATTCTATTCTACTACTACC 58.620 44.000 0.00 0.00 0.00 3.18
6434 7664 7.704578 TCTATTCTACTACTACCATGGATGC 57.295 40.000 21.47 0.00 0.00 3.91
6435 7665 7.471041 TCTATTCTACTACTACCATGGATGCT 58.529 38.462 21.47 0.00 0.00 3.79
6436 7666 6.597832 ATTCTACTACTACCATGGATGCTC 57.402 41.667 21.47 0.00 0.00 4.26
6437 7667 5.061721 TCTACTACTACCATGGATGCTCA 57.938 43.478 21.47 0.00 0.00 4.26
6438 7668 5.645201 TCTACTACTACCATGGATGCTCAT 58.355 41.667 21.47 0.00 0.00 2.90
6439 7669 4.881019 ACTACTACCATGGATGCTCATC 57.119 45.455 21.47 1.35 37.11 2.92
6440 7670 2.827800 ACTACCATGGATGCTCATCG 57.172 50.000 21.47 0.00 38.69 3.84
6441 7671 1.270518 ACTACCATGGATGCTCATCGC 60.271 52.381 21.47 0.00 38.69 4.58
6478 7708 3.612479 CGGTGGCAGAAGAAAAATGAAGG 60.612 47.826 0.00 0.00 0.00 3.46
6550 7782 1.973515 TCAGCTGACACCTGATGAACT 59.026 47.619 13.74 0.00 34.49 3.01
6600 7832 1.531912 CTACTTACGCCGAACTGACG 58.468 55.000 0.00 0.00 0.00 4.35
6625 7857 1.069358 TCCGAACATTGTTTTTGGCCC 59.931 47.619 0.00 0.00 0.00 5.80
6657 7893 4.935495 CATGGGATCCGGTGGGCG 62.935 72.222 5.45 0.00 0.00 6.13
6801 8037 0.528924 TATCCTGCGTTGCGTGTAGT 59.471 50.000 0.00 0.00 0.00 2.73
6828 8067 1.083489 TACCAGCGGCATTTTCTTCG 58.917 50.000 1.45 0.00 0.00 3.79
6863 8106 1.334243 GCTACTACCTCTACGTGCCAG 59.666 57.143 0.00 0.00 0.00 4.85
6899 8148 4.657013 ACCCCAGCTAAGAAAAGAAAGAG 58.343 43.478 0.00 0.00 0.00 2.85
6925 8174 0.613777 GGACTCCATTTCGGTCACCT 59.386 55.000 0.00 0.00 35.57 4.00
6938 8187 2.412325 CGGTCACCTGCGACAAAATAAC 60.412 50.000 0.00 0.00 37.66 1.89
6940 8189 2.095415 GTCACCTGCGACAAAATAACCC 60.095 50.000 0.00 0.00 35.88 4.11
6987 8237 2.235402 ACGTGGATGGAAATTCGGTAGT 59.765 45.455 0.00 0.00 0.00 2.73
7006 8264 7.039923 TCGGTAGTGAGAGTGACTAGAAATTTT 60.040 37.037 0.00 0.00 0.00 1.82
7010 8268 8.918961 AGTGAGAGTGACTAGAAATTTTATCG 57.081 34.615 0.00 0.00 0.00 2.92
7167 8638 3.054434 AGGGTTCGATGATTTCCACATGA 60.054 43.478 0.00 0.00 0.00 3.07
7205 8676 1.197430 CCAGGGGAGAGCACTGAACT 61.197 60.000 0.00 0.00 34.21 3.01
7253 8726 3.217017 CGGATCTTCGGCGGAGGA 61.217 66.667 16.51 8.54 32.32 3.71
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
224 225 7.517614 TTACAATGATTTTCTGTAGGTGCAA 57.482 32.000 0.00 0.00 0.00 4.08
244 245 6.879993 TCAAAAATCTATACCGCCACTTTACA 59.120 34.615 0.00 0.00 0.00 2.41
292 295 5.367302 AGCAAATGTACAAAAACTGGCATT 58.633 33.333 0.00 0.00 36.76 3.56
293 296 4.959723 AGCAAATGTACAAAAACTGGCAT 58.040 34.783 0.00 0.00 0.00 4.40
655 667 2.093181 TCTCTCTCTGAAGCGCTCTAGT 60.093 50.000 12.06 0.00 0.00 2.57
668 680 0.682855 CCAACCGCCTCTCTCTCTCT 60.683 60.000 0.00 0.00 0.00 3.10
669 681 1.671901 CCCAACCGCCTCTCTCTCTC 61.672 65.000 0.00 0.00 0.00 3.20
684 755 1.768870 GCTATAGAGTTCCTGCCCCAA 59.231 52.381 3.21 0.00 0.00 4.12
867 939 4.840680 TCCTCCTCTGTTTCTGAGATTTCA 59.159 41.667 5.46 0.00 32.36 2.69
942 1187 1.348064 AGCTGCAACCACCACTACTA 58.652 50.000 1.02 0.00 0.00 1.82
943 1188 0.474184 AAGCTGCAACCACCACTACT 59.526 50.000 1.02 0.00 0.00 2.57
946 1191 1.893808 CGAAGCTGCAACCACCACT 60.894 57.895 1.02 0.00 0.00 4.00
947 1192 2.639286 CGAAGCTGCAACCACCAC 59.361 61.111 1.02 0.00 0.00 4.16
1022 1276 1.708551 CCCTCCCAAACCTTAACCTGA 59.291 52.381 0.00 0.00 0.00 3.86
1066 1320 1.152963 CTCCCGCGGGATGGATTTT 60.153 57.895 45.15 0.00 44.24 1.82
1654 1908 1.727880 CTACCGCCGAAATCGAAAACA 59.272 47.619 4.04 0.00 43.02 2.83
1667 1921 2.818274 CTGCCGAAACCTACCGCC 60.818 66.667 0.00 0.00 0.00 6.13
1698 1956 6.129168 CGAAATCTAATCTAATCGAACCACGG 60.129 42.308 0.00 0.00 42.82 4.94
1716 1974 2.287915 GCGCCATGTTCATACGAAATCT 59.712 45.455 0.00 0.00 31.43 2.40
1762 2020 1.792949 GCAACTAGATAATCCACGCCG 59.207 52.381 0.00 0.00 0.00 6.46
1798 2056 3.900966 AAACCCTAGAATCACCGGTAC 57.099 47.619 6.87 0.00 0.00 3.34
1802 2060 4.828829 AGTGTTAAACCCTAGAATCACCG 58.171 43.478 0.00 0.00 0.00 4.94
1810 2069 8.890718 GCCTCTAATAAAAGTGTTAAACCCTAG 58.109 37.037 0.00 0.00 0.00 3.02
1860 2119 9.803130 CAATCGATAACAACATACTCAATCATC 57.197 33.333 0.00 0.00 0.00 2.92
1894 2153 0.175073 ATCCTTCTAACACCGCGACC 59.825 55.000 8.23 0.00 0.00 4.79
1947 2207 3.085443 ACTAGTTGCTTCGATGATCCG 57.915 47.619 1.89 0.00 0.00 4.18
1970 2230 3.132289 TGTGGCTAGAGATTTTCCTACCG 59.868 47.826 0.00 0.00 0.00 4.02
2012 2272 9.017509 ACATCTGATTTTCATTTTCTCAAGCTA 57.982 29.630 0.00 0.00 0.00 3.32
2125 2571 6.936900 CCTGTGTCTAGAGATTTTCCTTTGAA 59.063 38.462 0.00 0.00 0.00 2.69
2230 2677 3.848347 CTGCTCCGTCGTGCACACT 62.848 63.158 18.64 0.00 34.86 3.55
2248 2695 9.334693 CAGATAAAGACACATTAAACAAGCTTC 57.665 33.333 0.00 0.00 0.00 3.86
2305 2758 2.282816 CCACGGGGCCAAATGACA 60.283 61.111 4.39 0.00 0.00 3.58
2339 2793 3.678056 TGGCCGTATCATTGATAGGTC 57.322 47.619 19.62 17.02 31.08 3.85
2529 2986 1.078823 TCCTTCTTCCTGACCTGCCTA 59.921 52.381 0.00 0.00 0.00 3.93
2531 2988 0.251634 CTCCTTCTTCCTGACCTGCC 59.748 60.000 0.00 0.00 0.00 4.85
2542 2999 4.630644 TGCAGAAGTCAATCTCCTTCTT 57.369 40.909 0.00 0.00 43.69 2.52
2586 3043 9.487790 CATATGGTTTGTTTGACAATTACCTTT 57.512 29.630 13.05 6.27 38.91 3.11
2813 3273 7.335924 GGGTGATTTCTGCAAGTACAGTTAATA 59.664 37.037 0.00 0.00 38.84 0.98
2842 3302 3.538634 ACTCCCGTGCTATTAAGAACC 57.461 47.619 0.00 0.00 0.00 3.62
2852 3312 1.000274 GCAATTTTCAACTCCCGTGCT 60.000 47.619 0.00 0.00 0.00 4.40
2896 3356 5.189180 AGATCAAAACCTAACTGCTCATCC 58.811 41.667 0.00 0.00 0.00 3.51
2923 3383 8.287503 ACATAACAAAACTAACCTCGTTCAATC 58.712 33.333 0.00 0.00 0.00 2.67
2949 3409 4.814234 AGTCAAACAAGAGAATTACACGCA 59.186 37.500 0.00 0.00 0.00 5.24
2965 3425 8.082242 AGCAATAGTGTCCATTTTTAGTCAAAC 58.918 33.333 0.00 0.00 0.00 2.93
2977 3437 5.068987 ACACAAACAAAGCAATAGTGTCCAT 59.931 36.000 0.00 0.00 33.94 3.41
2995 3455 5.246429 ACAGAAGGGTTAAACCAAACACAAA 59.754 36.000 13.24 0.00 41.02 2.83
3005 3465 6.918022 CACAATGAGAAACAGAAGGGTTAAAC 59.082 38.462 0.00 0.00 0.00 2.01
3062 3524 8.207545 ACCAAAACCTGAAAGCAAACATAATAA 58.792 29.630 0.00 0.00 0.00 1.40
3063 3525 7.731054 ACCAAAACCTGAAAGCAAACATAATA 58.269 30.769 0.00 0.00 0.00 0.98
3064 3526 6.591001 ACCAAAACCTGAAAGCAAACATAAT 58.409 32.000 0.00 0.00 0.00 1.28
3151 3613 1.001706 CCATTGATCAGCATGCCTTCG 60.002 52.381 15.66 0.36 34.76 3.79
3235 3697 5.283457 AGCATAGATCCTTACACTTGGTC 57.717 43.478 0.00 0.00 0.00 4.02
3293 3755 4.204012 GTGGCTAATGGTGGTAAGCATAA 58.796 43.478 0.00 0.00 43.67 1.90
3320 3782 6.595716 GCAACTTCTTATTGGATGAGTACAGT 59.404 38.462 0.00 0.00 0.00 3.55
3457 3919 5.127682 GGTTTATCATCCTGCAATCAACCTT 59.872 40.000 4.76 0.00 0.00 3.50
3460 3922 5.581126 TGGTTTATCATCCTGCAATCAAC 57.419 39.130 0.00 0.00 0.00 3.18
3565 4027 3.476552 TCAGAGGTGCAAGTTTTAGTGG 58.523 45.455 0.00 0.00 0.00 4.00
3644 4108 7.383029 ACTCAAAATCAAATGTGTTGTGCATAG 59.617 33.333 0.00 0.00 0.00 2.23
3893 4359 6.540189 AGTGAATAGCTTTACATAGGCAGTTG 59.460 38.462 0.00 0.00 0.00 3.16
4257 4990 5.653769 AGTGCATGAAGCTTAACATGGTATT 59.346 36.000 22.64 4.90 45.94 1.89
4278 5011 0.665835 TTTGGTTGCGTTGGCTAGTG 59.334 50.000 0.00 0.00 40.82 2.74
4288 5021 3.595709 TTAGTTCGAACTTTGGTTGCG 57.404 42.857 33.82 0.00 40.37 4.85
4292 5025 5.240844 CCTTTCCATTAGTTCGAACTTTGGT 59.759 40.000 35.10 20.03 39.84 3.67
4300 5034 4.028131 TCTAGCCCTTTCCATTAGTTCGA 58.972 43.478 0.00 0.00 0.00 3.71
4308 5042 2.852449 TGGATTGTCTAGCCCTTTCCAT 59.148 45.455 0.00 0.00 0.00 3.41
4338 5072 1.754380 CGTCAGAGGGGGTGTTGACA 61.754 60.000 4.61 0.00 39.83 3.58
4339 5073 1.004918 CGTCAGAGGGGGTGTTGAC 60.005 63.158 0.00 0.00 37.24 3.18
4373 5107 1.445942 CTGAGTCCACCCACGTGTT 59.554 57.895 15.65 0.00 38.41 3.32
4389 5123 3.393472 GCCTCTTGAGCCATACCTG 57.607 57.895 0.00 0.00 0.00 4.00
4421 5157 0.393820 ATTGTTGCTGCCCACCTTTG 59.606 50.000 0.00 0.00 0.00 2.77
4427 5163 5.537300 TTACTAAAAATTGTTGCTGCCCA 57.463 34.783 0.00 0.00 0.00 5.36
4506 5243 0.454957 GTTGCGTTGGCTAGTGCATG 60.455 55.000 0.00 0.00 41.91 4.06
4539 5276 5.946377 GTGGATTGTCTAGACCTTTCCATTT 59.054 40.000 27.61 5.13 36.06 2.32
4550 5287 7.660030 TGAAGTGATATGTGGATTGTCTAGA 57.340 36.000 0.00 0.00 0.00 2.43
4596 5334 2.751806 CCCTCAAGGCAGAGATTTTCAC 59.248 50.000 8.35 0.00 37.87 3.18
4615 5353 7.339466 ACAGTAGTGACAATTGATAAATTCCCC 59.661 37.037 13.59 0.00 0.00 4.81
4616 5354 8.281212 ACAGTAGTGACAATTGATAAATTCCC 57.719 34.615 13.59 0.00 0.00 3.97
4954 5697 6.479972 TCCCATTCACTCGTATTGAAGTAT 57.520 37.500 0.00 0.00 36.44 2.12
5100 5844 4.041198 CAGGACCCAGTTTAAGTACTCCAA 59.959 45.833 0.00 0.00 0.00 3.53
5148 5892 4.202441 ACTTGTCAAGAAGCAGTCATTGT 58.798 39.130 19.53 0.00 0.00 2.71
5171 5915 8.862085 GCTCTTATATTAGTTTACAGAGGGAGT 58.138 37.037 0.00 0.00 0.00 3.85
5172 5916 8.024285 CGCTCTTATATTAGTTTACAGAGGGAG 58.976 40.741 4.76 0.00 40.49 4.30
5173 5917 7.504911 ACGCTCTTATATTAGTTTACAGAGGGA 59.495 37.037 14.96 0.00 40.49 4.20
5174 5918 7.659186 ACGCTCTTATATTAGTTTACAGAGGG 58.341 38.462 8.36 8.36 42.53 4.30
5175 5919 9.530633 AAACGCTCTTATATTAGTTTACAGAGG 57.469 33.333 0.00 0.00 31.14 3.69
5177 5921 9.309516 CCAAACGCTCTTATATTAGTTTACAGA 57.690 33.333 0.00 0.00 31.63 3.41
5178 5922 9.309516 TCCAAACGCTCTTATATTAGTTTACAG 57.690 33.333 0.00 0.00 31.63 2.74
5179 5923 9.826574 ATCCAAACGCTCTTATATTAGTTTACA 57.173 29.630 0.00 0.00 31.63 2.41
5182 5926 8.827677 GTGATCCAAACGCTCTTATATTAGTTT 58.172 33.333 0.00 0.00 32.82 2.66
5183 5927 8.204836 AGTGATCCAAACGCTCTTATATTAGTT 58.795 33.333 0.00 0.00 0.00 2.24
5184 5928 7.727181 AGTGATCCAAACGCTCTTATATTAGT 58.273 34.615 0.00 0.00 0.00 2.24
5185 5929 9.692749 TTAGTGATCCAAACGCTCTTATATTAG 57.307 33.333 0.00 0.00 0.00 1.73
5187 5931 8.827677 GTTTAGTGATCCAAACGCTCTTATATT 58.172 33.333 0.00 0.00 0.00 1.28
5188 5932 8.204836 AGTTTAGTGATCCAAACGCTCTTATAT 58.795 33.333 8.27 0.00 39.18 0.86
5189 5933 7.553334 AGTTTAGTGATCCAAACGCTCTTATA 58.447 34.615 8.27 0.00 39.18 0.98
5190 5934 6.407202 AGTTTAGTGATCCAAACGCTCTTAT 58.593 36.000 8.27 0.00 39.18 1.73
5191 5935 5.790593 AGTTTAGTGATCCAAACGCTCTTA 58.209 37.500 8.27 0.00 39.18 2.10
5192 5936 4.642429 AGTTTAGTGATCCAAACGCTCTT 58.358 39.130 8.27 0.00 39.18 2.85
5193 5937 4.273148 AGTTTAGTGATCCAAACGCTCT 57.727 40.909 8.27 0.00 39.18 4.09
5194 5938 5.169295 ACTAGTTTAGTGATCCAAACGCTC 58.831 41.667 0.00 0.00 39.18 5.03
5195 5939 5.148651 ACTAGTTTAGTGATCCAAACGCT 57.851 39.130 0.00 0.00 39.18 5.07
5196 5940 6.956299 TTACTAGTTTAGTGATCCAAACGC 57.044 37.500 0.00 0.00 39.81 4.84
5197 5941 8.928270 AGATTACTAGTTTAGTGATCCAAACG 57.072 34.615 0.00 0.00 46.90 3.60
5223 5967 9.490379 CCTCCGTAAACTAATATAAGAGCATTT 57.510 33.333 0.00 0.00 0.00 2.32
5224 5968 8.095169 CCCTCCGTAAACTAATATAAGAGCATT 58.905 37.037 0.00 0.00 0.00 3.56
5225 5969 7.453752 TCCCTCCGTAAACTAATATAAGAGCAT 59.546 37.037 0.00 0.00 0.00 3.79
5226 5970 6.779049 TCCCTCCGTAAACTAATATAAGAGCA 59.221 38.462 0.00 0.00 0.00 4.26
5227 5971 7.039853 ACTCCCTCCGTAAACTAATATAAGAGC 60.040 40.741 0.00 0.00 0.00 4.09
5228 5972 8.406730 ACTCCCTCCGTAAACTAATATAAGAG 57.593 38.462 0.00 0.00 0.00 2.85
5229 5973 9.289782 GTACTCCCTCCGTAAACTAATATAAGA 57.710 37.037 0.00 0.00 0.00 2.10
5230 5974 9.294614 AGTACTCCCTCCGTAAACTAATATAAG 57.705 37.037 0.00 0.00 0.00 1.73
5231 5975 9.071276 CAGTACTCCCTCCGTAAACTAATATAA 57.929 37.037 0.00 0.00 0.00 0.98
5232 5976 8.220559 ACAGTACTCCCTCCGTAAACTAATATA 58.779 37.037 0.00 0.00 0.00 0.86
5233 5977 7.065504 ACAGTACTCCCTCCGTAAACTAATAT 58.934 38.462 0.00 0.00 0.00 1.28
5234 5978 6.426587 ACAGTACTCCCTCCGTAAACTAATA 58.573 40.000 0.00 0.00 0.00 0.98
5235 5979 5.267587 ACAGTACTCCCTCCGTAAACTAAT 58.732 41.667 0.00 0.00 0.00 1.73
5236 5980 4.666512 ACAGTACTCCCTCCGTAAACTAA 58.333 43.478 0.00 0.00 0.00 2.24
5237 5981 4.307032 ACAGTACTCCCTCCGTAAACTA 57.693 45.455 0.00 0.00 0.00 2.24
5238 5982 3.166560 ACAGTACTCCCTCCGTAAACT 57.833 47.619 0.00 0.00 0.00 2.66
5239 5983 6.488006 TGATATACAGTACTCCCTCCGTAAAC 59.512 42.308 0.00 0.00 0.00 2.01
5240 5984 6.604171 TGATATACAGTACTCCCTCCGTAAA 58.396 40.000 0.00 0.00 0.00 2.01
5241 5985 6.191657 TGATATACAGTACTCCCTCCGTAA 57.808 41.667 0.00 0.00 0.00 3.18
5242 5986 5.830799 TGATATACAGTACTCCCTCCGTA 57.169 43.478 0.00 0.00 0.00 4.02
5243 5987 4.719026 TGATATACAGTACTCCCTCCGT 57.281 45.455 0.00 0.00 0.00 4.69
5244 5988 5.254115 TGATGATATACAGTACTCCCTCCG 58.746 45.833 0.00 0.00 0.00 4.63
5245 5989 7.397476 TCATTGATGATATACAGTACTCCCTCC 59.603 40.741 0.00 0.00 0.00 4.30
5246 5990 8.354711 TCATTGATGATATACAGTACTCCCTC 57.645 38.462 0.00 0.00 0.00 4.30
5247 5991 8.727100 TTCATTGATGATATACAGTACTCCCT 57.273 34.615 0.00 0.00 36.56 4.20
5248 5992 9.593134 GATTCATTGATGATATACAGTACTCCC 57.407 37.037 0.00 0.00 36.56 4.30
5251 5995 9.631452 CGTGATTCATTGATGATATACAGTACT 57.369 33.333 0.00 0.00 36.56 2.73
5275 6019 2.869233 AGCACAAATTGAGCAAACGT 57.131 40.000 16.94 0.00 36.40 3.99
5412 6161 2.064762 CTGACTTCAGAGAGGCAAACG 58.935 52.381 0.00 0.00 46.59 3.60
5583 6332 4.805719 GCGATTCATACAGAGAACACATGA 59.194 41.667 0.00 0.00 0.00 3.07
5651 6400 3.012518 CAGGATCCTTTCAACATTCGCT 58.987 45.455 13.00 0.00 0.00 4.93
5720 6469 2.270923 ACTATGTGCACGTACAGCATG 58.729 47.619 14.85 6.91 44.79 4.06
5721 6470 2.672961 ACTATGTGCACGTACAGCAT 57.327 45.000 14.85 1.81 44.79 3.79
5726 6475 4.390603 TCCATCAAAACTATGTGCACGTAC 59.609 41.667 14.85 0.00 0.00 3.67
5765 6514 1.128015 GTTTCTGAACGCGTCGCTC 59.872 57.895 14.44 7.47 0.00 5.03
5817 6566 1.180456 TGGGTCGAGCAGTTCCGTAA 61.180 55.000 17.59 0.00 0.00 3.18
5877 6626 0.107268 AGCAAAAAGGCAGGCTTTGG 59.893 50.000 21.95 17.39 35.83 3.28
5878 6627 1.957668 AAGCAAAAAGGCAGGCTTTG 58.042 45.000 21.95 12.76 43.56 2.77
5881 6630 0.832626 ACAAAGCAAAAAGGCAGGCT 59.167 45.000 0.00 0.00 38.45 4.58
5882 6631 1.667236 AACAAAGCAAAAAGGCAGGC 58.333 45.000 0.00 0.00 35.83 4.85
5883 6632 3.269178 TCAAACAAAGCAAAAAGGCAGG 58.731 40.909 0.00 0.00 35.83 4.85
5884 6633 3.242511 GCTCAAACAAAGCAAAAAGGCAG 60.243 43.478 0.00 0.00 39.61 4.85
6031 6793 3.499338 TCAAATCACTTGGCAGGAATGT 58.501 40.909 2.65 0.00 35.56 2.71
6138 6908 4.043561 TCAGGTACCCAAAAATGAGCCTAA 59.956 41.667 8.74 0.00 0.00 2.69
6209 6984 0.039437 TCGGCGTTGAGACTTGAGAC 60.039 55.000 6.85 0.00 0.00 3.36
6237 7012 4.588106 TCCATGCTCCAAAAGTTCATCAAA 59.412 37.500 0.00 0.00 0.00 2.69
6307 7526 4.563184 CGTCTCCACAGTATCAAAACTAGC 59.437 45.833 0.00 0.00 0.00 3.42
6348 7578 6.554334 TTTTTCCCACTAAAACGATGAGAG 57.446 37.500 0.00 0.00 0.00 3.20
6369 7599 6.723052 AGATGAGTCACTTGATTCCCATTTTT 59.277 34.615 0.00 0.00 30.74 1.94
6404 7634 7.815068 CCATGGTAGTAGTAGAATAGAATGCAC 59.185 40.741 2.57 0.00 0.00 4.57
6414 7644 5.454966 TGAGCATCCATGGTAGTAGTAGAA 58.545 41.667 12.58 0.00 38.85 2.10
6419 7649 3.842820 CGATGAGCATCCATGGTAGTAG 58.157 50.000 12.58 0.00 38.85 2.57
6434 7664 2.356793 GCCCGATGAGGCGATGAG 60.357 66.667 0.00 0.00 44.57 2.90
6441 7671 2.819595 CCGTTGTGCCCGATGAGG 60.820 66.667 0.00 0.00 40.63 3.86
6550 7782 1.096967 CAACCGGCATATGCAGCTGA 61.097 55.000 28.07 2.70 44.36 4.26
6600 7832 4.385748 GCCAAAAACAATGTTCGGAATCTC 59.614 41.667 11.77 0.00 0.00 2.75
6764 8000 5.006746 CAGGATAAGTTTTGGCTGATACGTC 59.993 44.000 0.00 0.00 0.00 4.34
6801 8037 0.036164 ATGCCGCTGGTACAAACTGA 59.964 50.000 0.00 0.00 38.70 3.41
6828 8067 4.095036 GGTAGTAGCAGACAATTTGGAAGC 59.905 45.833 0.78 1.66 0.00 3.86
6899 8148 3.610911 ACCGAAATGGAGTCCAAATCTC 58.389 45.455 17.71 9.25 42.00 2.75
6925 8174 0.885196 GCTGGGGTTATTTTGTCGCA 59.115 50.000 0.00 0.00 0.00 5.10
6987 8237 7.974501 GGTCGATAAAATTTCTAGTCACTCTCA 59.025 37.037 0.00 0.00 0.00 3.27
7006 8264 2.927028 TGAGAGAATGGACGGTCGATA 58.073 47.619 6.06 0.00 0.00 2.92
7010 8268 2.223923 CCAGATGAGAGAATGGACGGTC 60.224 54.545 0.00 0.00 34.60 4.79
7167 8638 7.457535 TCCCCTGGTTGATTTCTGAAATAAAAT 59.542 33.333 15.14 0.00 0.00 1.82
7205 8676 8.148351 GGATAAACATACATAGGTAGCTGTTCA 58.852 37.037 4.27 0.00 33.66 3.18
7253 8726 5.374071 ACACTCCGATTTTTGTTACTTCCT 58.626 37.500 0.00 0.00 0.00 3.36


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

AutoCloner maintained by Alex Coulton.