Multiple sequence alignment - TraesCS1D01G398500

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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 TraesCS1D01G398500 chr1D 100.000 5372 0 0 1583 6954 465531817 465537188 0.000000e+00 9921.0
1 TraesCS1D01G398500 chr1D 100.000 1266 0 0 1 1266 465530235 465531500 0.000000e+00 2338.0
2 TraesCS1D01G398500 chr1A 92.869 2903 127 31 1583 4435 557948343 557951215 0.000000e+00 4141.0
3 TraesCS1D01G398500 chr1A 91.634 2522 144 27 4472 6954 557951218 557953711 0.000000e+00 3426.0
4 TraesCS1D01G398500 chr1A 93.764 433 12 8 846 1266 557947852 557948281 2.740000e-178 636.0
5 TraesCS1D01G398500 chr1A 83.480 454 34 26 9 458 557946770 557947186 1.090000e-102 385.0
6 TraesCS1D01G398500 chr1A 89.338 272 17 8 543 813 557947499 557947759 1.450000e-86 331.0
7 TraesCS1D01G398500 chr1B 91.874 2941 143 33 1583 4435 642471067 642473999 0.000000e+00 4019.0
8 TraesCS1D01G398500 chr1B 92.617 2113 99 16 4472 6579 642474002 642476062 0.000000e+00 2985.0
9 TraesCS1D01G398500 chr1B 86.712 444 23 18 846 1266 642470578 642471008 1.770000e-125 460.0
10 TraesCS1D01G398500 chr1B 90.106 283 11 4 6684 6954 642476063 642476340 1.110000e-92 351.0
11 TraesCS1D01G398500 chr7D 76.476 1186 231 35 4473 5641 564972023 564973177 9.980000e-168 601.0
12 TraesCS1D01G398500 chr7D 85.027 187 26 2 1081 1266 564967962 564968147 9.210000e-44 189.0
13 TraesCS1D01G398500 chr7B 76.491 1157 213 41 4504 5641 614872819 614873935 6.050000e-160 575.0
14 TraesCS1D01G398500 chr7B 74.893 932 183 36 4708 5625 614914038 614914932 1.830000e-100 377.0
15 TraesCS1D01G398500 chr7B 82.273 220 36 3 1048 1264 614868665 614868884 3.310000e-43 187.0
16 TraesCS1D01G398500 chr7A 76.114 1189 228 40 4473 5641 650626777 650627929 7.830000e-159 571.0
17 TraesCS1D01G398500 chr7A 76.875 480 89 16 5173 5641 650720287 650720755 1.160000e-62 252.0
18 TraesCS1D01G398500 chr7A 86.022 186 26 0 1081 1266 650622701 650622886 4.250000e-47 200.0
19 TraesCS1D01G398500 chr7A 76.879 173 34 6 5202 5371 650891371 650891540 7.430000e-15 93.5
20 TraesCS1D01G398500 chr7A 76.879 173 34 6 5202 5371 650904548 650904717 7.430000e-15 93.5
21 TraesCS1D01G398500 chr3A 78.316 392 52 20 353 723 149714798 149714419 9.080000e-54 222.0
22 TraesCS1D01G398500 chr3D 80.970 268 34 14 458 723 134957556 134957304 5.500000e-46 196.0
23 TraesCS1D01G398500 chr3B 100.000 31 0 0 72 102 423074430 423074400 2.710000e-04 58.4


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS1D01G398500 chr1D 465530235 465537188 6953 False 6129.50 9921 100.00000 1 6954 2 chr1D.!!$F1 6953
1 TraesCS1D01G398500 chr1A 557946770 557953711 6941 False 1783.80 4141 90.21700 9 6954 5 chr1A.!!$F1 6945
2 TraesCS1D01G398500 chr1B 642470578 642476340 5762 False 1953.75 4019 90.32725 846 6954 4 chr1B.!!$F1 6108
3 TraesCS1D01G398500 chr7D 564967962 564973177 5215 False 395.00 601 80.75150 1081 5641 2 chr7D.!!$F1 4560
4 TraesCS1D01G398500 chr7B 614868665 614873935 5270 False 381.00 575 79.38200 1048 5641 2 chr7B.!!$F2 4593
5 TraesCS1D01G398500 chr7B 614914038 614914932 894 False 377.00 377 74.89300 4708 5625 1 chr7B.!!$F1 917
6 TraesCS1D01G398500 chr7A 650622701 650627929 5228 False 385.50 571 81.06800 1081 5641 2 chr7A.!!$F4 4560

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
284 286 0.171231 GAGCGGAAACTTGGCAATCC 59.829 55.000 0.0 4.15 0.00 3.01 F
822 1052 0.179032 TCCGAAAGCTTGCCACTTGA 60.179 50.000 0.0 0.00 0.00 3.02 F
823 1053 0.883833 CCGAAAGCTTGCCACTTGAT 59.116 50.000 0.0 0.00 0.00 2.57 F
824 1054 1.401931 CCGAAAGCTTGCCACTTGATG 60.402 52.381 0.0 0.00 0.00 3.07 F
2343 3188 0.586319 ATGGTGCAAGAAACGTGTCG 59.414 50.000 0.0 0.00 0.00 4.35 F
2886 4145 0.765510 ACCAGTGGAAAGAGGTGACC 59.234 55.000 18.4 0.00 32.04 4.02 F
3441 4700 0.102120 CAAGGCTGCACCGTTCAAAA 59.898 50.000 0.5 0.00 46.52 2.44 F
4672 5993 0.249868 TCACTTCAGGGCAGAACACG 60.250 55.000 0.0 0.00 0.00 4.49 F
5635 6960 0.618458 AGAAAGATAACCAGGCCGCA 59.382 50.000 0.0 0.00 0.00 5.69 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1633 1979 0.320073 TGCATTTTGCTGCCTGAAGC 60.320 50.000 0.00 0.0 45.31 3.86 R
2320 3165 1.529438 CACGTTTCTTGCACCATACGT 59.471 47.619 9.60 9.6 42.22 3.57 R
2343 3188 1.763968 GGATTCCCCAAAGTAGGTGC 58.236 55.000 0.00 0.0 34.14 5.01 R
2634 3893 2.161855 TCCAATGCTGCAACCAAGTAG 58.838 47.619 6.36 0.0 0.00 2.57 R
3223 4482 0.317020 GTGTGCTGGCGAAGAACAAC 60.317 55.000 0.55 0.0 46.63 3.32 R
3771 5030 0.807496 GCAGAGGCTGACCATTGTTC 59.193 55.000 0.00 0.0 39.06 3.18 R
5174 6498 0.815734 CTCTGGAATGCCTGCAAAGG 59.184 55.000 0.00 0.0 33.46 3.11 R
5648 6973 0.034616 GCTCAAGACACTGGCTGAGT 59.965 55.000 11.01 0.0 34.02 3.41 R
6647 7995 0.842635 ACAGGAAGGCCATCTCCATC 59.157 55.000 17.96 0.0 36.29 3.51 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
175 177 2.654863 CGGTCCTCTATTGGGCATTTT 58.345 47.619 0.00 0.00 32.35 1.82
176 178 3.023832 CGGTCCTCTATTGGGCATTTTT 58.976 45.455 0.00 0.00 32.35 1.94
177 179 3.181487 CGGTCCTCTATTGGGCATTTTTG 60.181 47.826 0.00 0.00 32.35 2.44
194 196 6.648725 GCATTTTTGCACACCCTTATTCTTTA 59.351 34.615 0.00 0.00 34.41 1.85
225 227 5.578727 GGAGTTATATTCAGCTTCTATGCCG 59.421 44.000 0.00 0.00 0.00 5.69
244 246 1.353091 GGAGGCGGAGGGAAAGATAT 58.647 55.000 0.00 0.00 0.00 1.63
248 250 2.158608 AGGCGGAGGGAAAGATATTTGG 60.159 50.000 0.00 0.00 0.00 3.28
250 252 2.618709 GCGGAGGGAAAGATATTTGGTG 59.381 50.000 0.00 0.00 0.00 4.17
251 253 2.618709 CGGAGGGAAAGATATTTGGTGC 59.381 50.000 0.00 0.00 0.00 5.01
252 254 3.631250 GGAGGGAAAGATATTTGGTGCA 58.369 45.455 0.00 0.00 0.00 4.57
253 255 3.633986 GGAGGGAAAGATATTTGGTGCAG 59.366 47.826 0.00 0.00 0.00 4.41
254 256 4.526970 GAGGGAAAGATATTTGGTGCAGA 58.473 43.478 0.00 0.00 0.00 4.26
255 257 4.273318 AGGGAAAGATATTTGGTGCAGAC 58.727 43.478 0.00 0.00 0.00 3.51
257 259 3.065371 GGAAAGATATTTGGTGCAGACCG 59.935 47.826 0.00 0.00 46.62 4.79
258 260 1.668419 AGATATTTGGTGCAGACCGC 58.332 50.000 0.00 0.00 46.62 5.68
259 261 0.663153 GATATTTGGTGCAGACCGCC 59.337 55.000 0.00 0.00 46.62 6.13
260 262 0.751643 ATATTTGGTGCAGACCGCCC 60.752 55.000 0.00 0.00 46.62 6.13
261 263 1.847798 TATTTGGTGCAGACCGCCCT 61.848 55.000 0.00 0.00 46.62 5.19
262 264 3.993609 TATTTGGTGCAGACCGCCCTG 62.994 57.143 0.00 0.00 46.62 4.45
267 269 4.803426 GCAGACCGCCCTGTCGAG 62.803 72.222 0.00 0.00 40.26 4.04
268 270 4.803426 CAGACCGCCCTGTCGAGC 62.803 72.222 0.00 0.00 40.26 5.03
274 276 3.119096 GCCCTGTCGAGCGGAAAC 61.119 66.667 1.56 0.00 0.00 2.78
275 277 2.657237 CCCTGTCGAGCGGAAACT 59.343 61.111 1.56 0.00 0.00 2.66
276 278 1.004918 CCCTGTCGAGCGGAAACTT 60.005 57.895 1.56 0.00 0.00 2.66
277 279 1.291877 CCCTGTCGAGCGGAAACTTG 61.292 60.000 1.56 0.00 0.00 3.16
278 280 1.291877 CCTGTCGAGCGGAAACTTGG 61.292 60.000 0.00 0.00 0.00 3.61
279 281 1.901650 CTGTCGAGCGGAAACTTGGC 61.902 60.000 0.00 0.00 0.00 4.52
280 282 1.959226 GTCGAGCGGAAACTTGGCA 60.959 57.895 0.00 0.00 0.00 4.92
281 283 1.227704 TCGAGCGGAAACTTGGCAA 60.228 52.632 0.00 0.00 0.00 4.52
282 284 0.605319 TCGAGCGGAAACTTGGCAAT 60.605 50.000 0.00 0.00 0.00 3.56
283 285 0.179189 CGAGCGGAAACTTGGCAATC 60.179 55.000 0.00 0.00 0.00 2.67
284 286 0.171231 GAGCGGAAACTTGGCAATCC 59.829 55.000 0.00 4.15 0.00 3.01
285 287 0.251341 AGCGGAAACTTGGCAATCCT 60.251 50.000 14.59 0.00 0.00 3.24
286 288 0.171231 GCGGAAACTTGGCAATCCTC 59.829 55.000 14.59 4.96 0.00 3.71
287 289 1.826385 CGGAAACTTGGCAATCCTCT 58.174 50.000 14.59 0.00 0.00 3.69
288 290 2.939640 GCGGAAACTTGGCAATCCTCTA 60.940 50.000 14.59 0.00 0.00 2.43
289 291 3.343617 CGGAAACTTGGCAATCCTCTAA 58.656 45.455 14.59 0.00 0.00 2.10
290 292 3.375299 CGGAAACTTGGCAATCCTCTAAG 59.625 47.826 14.59 0.00 0.00 2.18
374 377 9.083080 GTTAAGTATTTTGTGCAAAAGTTGAGT 57.917 29.630 14.24 1.49 42.72 3.41
378 381 2.957491 TGTGCAAAAGTTGAGTTGGG 57.043 45.000 0.00 0.00 0.00 4.12
388 391 8.282592 GCAAAAGTTGAGTTGGGAAAATAATTC 58.717 33.333 0.00 0.00 0.00 2.17
449 452 5.947228 TCATGTGCACTAGAAGAAAAAGG 57.053 39.130 19.41 0.00 0.00 3.11
478 508 2.161609 CACCTAAAATGTGTCGGCTTCC 59.838 50.000 0.00 0.00 0.00 3.46
485 515 5.552870 AAATGTGTCGGCTTCCTATAGAT 57.447 39.130 0.00 0.00 0.00 1.98
551 586 3.037549 ACAAATTTGAAGGCCCACAAGA 58.962 40.909 24.64 0.00 0.00 3.02
552 587 3.181466 ACAAATTTGAAGGCCCACAAGAC 60.181 43.478 24.64 0.00 0.00 3.01
553 588 2.380064 ATTTGAAGGCCCACAAGACA 57.620 45.000 0.00 0.00 0.00 3.41
555 590 2.380064 TTGAAGGCCCACAAGACATT 57.620 45.000 0.00 0.00 0.00 2.71
557 592 3.071874 TGAAGGCCCACAAGACATTAG 57.928 47.619 0.00 0.00 0.00 1.73
558 593 2.642311 TGAAGGCCCACAAGACATTAGA 59.358 45.455 0.00 0.00 0.00 2.10
559 594 2.789409 AGGCCCACAAGACATTAGAC 57.211 50.000 0.00 0.00 0.00 2.59
560 595 1.066143 AGGCCCACAAGACATTAGACG 60.066 52.381 0.00 0.00 0.00 4.18
562 597 1.943968 GCCCACAAGACATTAGACGCA 60.944 52.381 0.00 0.00 0.00 5.24
569 798 6.074302 CCACAAGACATTAGACGCACATATAC 60.074 42.308 0.00 0.00 0.00 1.47
593 823 5.927954 TGCCTTTCTTTTTCATTGATTGC 57.072 34.783 0.00 0.00 0.00 3.56
602 832 9.761504 TTCTTTTTCATTGATTGCACAGATTTA 57.238 25.926 0.00 0.00 0.00 1.40
650 880 5.152623 TGTTCCACATTTCAAAACAACCA 57.847 34.783 0.00 0.00 0.00 3.67
658 888 7.095691 CCACATTTCAAAACAACCACATCATAC 60.096 37.037 0.00 0.00 0.00 2.39
659 889 7.437565 CACATTTCAAAACAACCACATCATACA 59.562 33.333 0.00 0.00 0.00 2.29
660 890 7.652909 ACATTTCAAAACAACCACATCATACAG 59.347 33.333 0.00 0.00 0.00 2.74
661 891 6.707440 TTCAAAACAACCACATCATACAGT 57.293 33.333 0.00 0.00 0.00 3.55
662 892 7.809546 TTCAAAACAACCACATCATACAGTA 57.190 32.000 0.00 0.00 0.00 2.74
663 893 7.809546 TCAAAACAACCACATCATACAGTAA 57.190 32.000 0.00 0.00 0.00 2.24
664 894 8.402798 TCAAAACAACCACATCATACAGTAAT 57.597 30.769 0.00 0.00 0.00 1.89
665 895 9.508642 TCAAAACAACCACATCATACAGTAATA 57.491 29.630 0.00 0.00 0.00 0.98
679 909 8.635328 TCATACAGTAATAAAGATCGGTAAGCA 58.365 33.333 0.00 0.00 0.00 3.91
683 913 6.144724 CAGTAATAAAGATCGGTAAGCAGAGC 59.855 42.308 0.00 0.00 0.00 4.09
694 924 3.437049 GGTAAGCAGAGCAAGAATCGTTT 59.563 43.478 0.00 0.00 0.00 3.60
752 982 0.516001 GGTTCTCTCCCGCGAAAAAC 59.484 55.000 8.23 2.95 0.00 2.43
773 1003 4.466827 ACAAATAAACAAGGAGGTCGGTT 58.533 39.130 0.00 0.00 0.00 4.44
806 1036 7.603963 TTCTTTTTCCTTTTTCCTTTTTCCG 57.396 32.000 0.00 0.00 0.00 4.30
807 1037 6.937392 TCTTTTTCCTTTTTCCTTTTTCCGA 58.063 32.000 0.00 0.00 0.00 4.55
808 1038 7.387643 TCTTTTTCCTTTTTCCTTTTTCCGAA 58.612 30.769 0.00 0.00 0.00 4.30
809 1039 7.878644 TCTTTTTCCTTTTTCCTTTTTCCGAAA 59.121 29.630 0.00 0.00 0.00 3.46
810 1040 7.603963 TTTTCCTTTTTCCTTTTTCCGAAAG 57.396 32.000 0.00 0.00 30.13 2.62
811 1041 4.689071 TCCTTTTTCCTTTTTCCGAAAGC 58.311 39.130 0.00 0.00 30.13 3.51
812 1042 4.404394 TCCTTTTTCCTTTTTCCGAAAGCT 59.596 37.500 0.00 0.00 30.13 3.74
813 1043 5.105106 TCCTTTTTCCTTTTTCCGAAAGCTT 60.105 36.000 0.00 0.00 30.13 3.74
814 1044 5.006649 CCTTTTTCCTTTTTCCGAAAGCTTG 59.993 40.000 0.00 0.00 30.13 4.01
815 1045 2.793278 TCCTTTTTCCGAAAGCTTGC 57.207 45.000 0.00 0.00 0.00 4.01
816 1046 1.339929 TCCTTTTTCCGAAAGCTTGCC 59.660 47.619 0.00 0.00 0.00 4.52
817 1047 1.068434 CCTTTTTCCGAAAGCTTGCCA 59.932 47.619 0.00 0.00 0.00 4.92
818 1048 2.127251 CTTTTTCCGAAAGCTTGCCAC 58.873 47.619 0.00 0.00 0.00 5.01
819 1049 1.398692 TTTTCCGAAAGCTTGCCACT 58.601 45.000 0.00 0.00 0.00 4.00
820 1050 1.398692 TTTCCGAAAGCTTGCCACTT 58.601 45.000 0.00 0.00 0.00 3.16
821 1051 0.667993 TTCCGAAAGCTTGCCACTTG 59.332 50.000 0.00 0.00 0.00 3.16
822 1052 0.179032 TCCGAAAGCTTGCCACTTGA 60.179 50.000 0.00 0.00 0.00 3.02
823 1053 0.883833 CCGAAAGCTTGCCACTTGAT 59.116 50.000 0.00 0.00 0.00 2.57
824 1054 1.401931 CCGAAAGCTTGCCACTTGATG 60.402 52.381 0.00 0.00 0.00 3.07
835 1065 2.630158 CCACTTGATGAAGCTGGAGAG 58.370 52.381 7.44 0.00 34.65 3.20
883 1190 3.047093 GGGTTACAATTTTGTCACGTGC 58.953 45.455 11.67 6.86 42.35 5.34
930 1246 3.399181 GATGTGGAGGGCGGGACA 61.399 66.667 0.00 0.00 0.00 4.02
940 1256 2.276116 GGCGGGACAGACAGACAGA 61.276 63.158 0.00 0.00 0.00 3.41
963 1282 2.732619 GGACGGGGCCTTGGACTAG 61.733 68.421 0.84 0.00 0.00 2.57
1044 1371 2.436292 CTGCTCCTGGTGCTGCTC 60.436 66.667 20.19 0.00 0.00 4.26
1045 1372 4.383861 TGCTCCTGGTGCTGCTCG 62.384 66.667 20.19 0.00 0.00 5.03
1633 1979 6.740002 CAGTAATTTCGAGTGCAAAGATTCAG 59.260 38.462 0.00 0.00 0.00 3.02
1677 2023 5.651530 TGGTTTCGAATAGAGTGATCAGAC 58.348 41.667 0.00 0.00 0.00 3.51
1684 2031 6.096846 TCGAATAGAGTGATCAGACCAATGAA 59.903 38.462 0.00 0.00 31.76 2.57
1717 2229 7.668052 TGTAGCCCTACTGATTTGTAAATTGTT 59.332 33.333 6.96 0.00 37.00 2.83
1718 2230 6.924111 AGCCCTACTGATTTGTAAATTGTTG 58.076 36.000 0.00 0.00 0.00 3.33
1735 2304 3.420893 TGTTGATCTGCAAACCCTTAGG 58.579 45.455 0.00 0.00 38.44 2.69
1787 2488 3.503363 CAGAATGCCAGAACTAAGTTGCA 59.497 43.478 0.00 0.00 0.00 4.08
1847 2548 2.360801 TGCTTTCCACTTTTGCAGTACC 59.639 45.455 0.00 0.00 32.76 3.34
1860 2563 9.073475 ACTTTTGCAGTACCACATCTTTTATTA 57.927 29.630 0.00 0.00 31.97 0.98
1861 2564 9.559958 CTTTTGCAGTACCACATCTTTTATTAG 57.440 33.333 0.00 0.00 0.00 1.73
1864 2567 8.942338 TGCAGTACCACATCTTTTATTAGTAG 57.058 34.615 0.00 0.00 0.00 2.57
1923 2654 6.591062 TGGAAATTCATTAGACAATTGCTTGC 59.409 34.615 5.05 0.00 35.69 4.01
1931 2662 3.709987 AGACAATTGCTTGCACAGTTTC 58.290 40.909 5.05 0.00 35.69 2.78
1970 2714 5.446860 TGGGTCAGGTAACACAAATTTACA 58.553 37.500 0.00 0.00 41.41 2.41
2088 2914 6.148480 CCCTCTTGCACATCATTTATACTAGC 59.852 42.308 0.00 0.00 0.00 3.42
2191 3034 5.912892 TCGCTTGACCTTATGATGACATTA 58.087 37.500 0.00 0.00 37.87 1.90
2227 3070 9.574516 AAGAGTTTTGATAAACCATACTGTCTT 57.425 29.630 0.00 0.00 43.77 3.01
2228 3071 9.574516 AGAGTTTTGATAAACCATACTGTCTTT 57.425 29.630 0.00 0.00 43.77 2.52
2304 3149 7.307337 CCACAAATGGCAAAACTTATGAACTTC 60.307 37.037 0.00 0.00 39.82 3.01
2343 3188 0.586319 ATGGTGCAAGAAACGTGTCG 59.414 50.000 0.00 0.00 0.00 4.35
2388 3234 5.443185 TCTTCACTTTTTCTCATGCAAGG 57.557 39.130 0.00 0.00 0.00 3.61
2393 3239 3.823304 ACTTTTTCTCATGCAAGGTCTCC 59.177 43.478 0.00 0.00 0.00 3.71
2398 3244 3.679389 TCTCATGCAAGGTCTCCTTTTC 58.321 45.455 0.00 0.00 41.69 2.29
2399 3245 3.328931 TCTCATGCAAGGTCTCCTTTTCT 59.671 43.478 0.00 0.00 41.69 2.52
2403 3249 4.918810 TGCAAGGTCTCCTTTTCTTTTC 57.081 40.909 0.00 0.00 41.69 2.29
2492 3340 3.565902 AGCACTAGTTTTCCTGTTTCTGC 59.434 43.478 0.00 0.00 0.00 4.26
2528 3414 6.375455 AGTTTGCTTACCATTTGTAGATCCTG 59.625 38.462 0.00 0.00 0.00 3.86
2569 3455 7.497579 TGAGCACTTACAGATGTGAAAACTTAA 59.502 33.333 0.00 0.00 36.38 1.85
2886 4145 0.765510 ACCAGTGGAAAGAGGTGACC 59.234 55.000 18.40 0.00 32.04 4.02
2897 4156 1.269998 AGAGGTGACCGCTATATTCGC 59.730 52.381 5.94 0.00 30.33 4.70
2954 4213 2.005537 GCGACGCACTTGCAACAAG 61.006 57.895 16.42 5.80 42.21 3.16
3093 4352 2.906691 CTGACACAGGGATGAGGATC 57.093 55.000 0.00 0.00 0.00 3.36
3114 4373 3.195396 TCTTTTCTGTTGCCAACAAGCTT 59.805 39.130 11.99 0.00 41.61 3.74
3187 4446 1.133167 TCCTGGATTCCTCGGCATCTA 60.133 52.381 3.95 0.00 0.00 1.98
3273 4532 3.620488 TGATGCCAAGGATAAGTTCACC 58.380 45.455 0.00 0.00 0.00 4.02
3311 4570 1.536072 CGCTCGTAGCAGAGGCATTAA 60.536 52.381 7.47 0.00 42.58 1.40
3441 4700 0.102120 CAAGGCTGCACCGTTCAAAA 59.898 50.000 0.50 0.00 46.52 2.44
3609 4868 2.225017 CCTTAATGTGGGTGGTTCTGGT 60.225 50.000 0.00 0.00 0.00 4.00
3871 5130 4.779696 TGATAATGTGACTGGCTATTGCA 58.220 39.130 0.66 0.00 41.91 4.08
3982 5241 9.539139 CTAACTACGACGACATTATTAGTATGG 57.461 37.037 0.00 0.00 0.00 2.74
4015 5274 4.876125 TGTATGCTCGATCTCATTCTTCC 58.124 43.478 0.00 0.00 0.00 3.46
4387 5650 7.713750 TCTGTTTCTACTTAGGGATGTATTCG 58.286 38.462 0.00 0.00 0.00 3.34
4425 5692 5.136105 AGTCTGGCTTGAGTCTGAAATTTT 58.864 37.500 0.00 0.00 29.60 1.82
4426 5693 5.240403 AGTCTGGCTTGAGTCTGAAATTTTC 59.760 40.000 2.05 2.05 29.60 2.29
4427 5694 5.009010 GTCTGGCTTGAGTCTGAAATTTTCA 59.991 40.000 11.19 11.19 38.17 2.69
4428 5695 5.771666 TCTGGCTTGAGTCTGAAATTTTCAT 59.228 36.000 12.04 0.00 39.30 2.57
4432 5699 6.091437 GCTTGAGTCTGAAATTTTCATGAGG 58.909 40.000 12.04 1.59 39.30 3.86
4433 5700 5.633830 TGAGTCTGAAATTTTCATGAGGC 57.366 39.130 12.04 3.22 39.30 4.70
4436 5703 5.319453 AGTCTGAAATTTTCATGAGGCAGA 58.681 37.500 12.04 2.21 39.30 4.26
4437 5704 5.415077 AGTCTGAAATTTTCATGAGGCAGAG 59.585 40.000 12.04 0.00 39.30 3.35
4438 5705 5.182760 GTCTGAAATTTTCATGAGGCAGAGT 59.817 40.000 12.04 0.00 39.30 3.24
4439 5706 5.182570 TCTGAAATTTTCATGAGGCAGAGTG 59.817 40.000 12.04 0.00 39.30 3.51
4440 5707 4.828939 TGAAATTTTCATGAGGCAGAGTGT 59.171 37.500 7.74 0.00 34.08 3.55
4441 5708 6.003326 TGAAATTTTCATGAGGCAGAGTGTA 58.997 36.000 7.74 0.00 34.08 2.90
4442 5709 6.489700 TGAAATTTTCATGAGGCAGAGTGTAA 59.510 34.615 7.74 0.00 34.08 2.41
4443 5710 7.177216 TGAAATTTTCATGAGGCAGAGTGTAAT 59.823 33.333 7.74 0.00 34.08 1.89
4446 5713 5.675684 TTCATGAGGCAGAGTGTAATGTA 57.324 39.130 0.00 0.00 0.00 2.29
4447 5714 5.011090 TCATGAGGCAGAGTGTAATGTAC 57.989 43.478 0.00 0.00 0.00 2.90
4450 5765 5.578005 TGAGGCAGAGTGTAATGTACTAC 57.422 43.478 0.00 0.00 0.00 2.73
4451 5766 5.014202 TGAGGCAGAGTGTAATGTACTACA 58.986 41.667 0.00 0.00 0.00 2.74
4454 5769 7.340999 TGAGGCAGAGTGTAATGTACTACAATA 59.659 37.037 0.00 0.00 33.66 1.90
4467 5782 9.906660 AATGTACTACAATATTTGTGTTGTTGG 57.093 29.630 3.22 0.00 45.03 3.77
4468 5783 8.453238 TGTACTACAATATTTGTGTTGTTGGT 57.547 30.769 3.22 0.00 45.03 3.67
4469 5784 8.346300 TGTACTACAATATTTGTGTTGTTGGTG 58.654 33.333 3.22 0.00 45.03 4.17
4470 5785 7.575414 ACTACAATATTTGTGTTGTTGGTGA 57.425 32.000 3.22 0.00 45.03 4.02
4592 5911 8.347004 AGTACACTAGATCCATCACATGATAG 57.653 38.462 0.00 0.00 32.63 2.08
4596 5915 9.319060 ACACTAGATCCATCACATGATAGTATT 57.681 33.333 0.00 0.00 32.63 1.89
4672 5993 0.249868 TCACTTCAGGGCAGAACACG 60.250 55.000 0.00 0.00 0.00 4.49
4771 6092 3.393800 CTTGACGTCAATCCTCACAGTT 58.606 45.455 29.79 0.00 35.02 3.16
4919 6241 4.823790 TTAGTAGCGCTGAATACGATCA 57.176 40.909 22.90 0.00 0.00 2.92
5135 6457 6.541278 TCACTCATCCACATTTCATCTCATTC 59.459 38.462 0.00 0.00 0.00 2.67
5137 6459 6.542735 ACTCATCCACATTTCATCTCATTCTG 59.457 38.462 0.00 0.00 0.00 3.02
5141 6463 5.190330 TCCACATTTCATCTCATTCTGAGGA 59.810 40.000 4.43 0.00 44.39 3.71
5145 6467 8.467598 CACATTTCATCTCATTCTGAGGAAAAT 58.532 33.333 7.46 8.43 44.39 1.82
5635 6960 0.618458 AGAAAGATAACCAGGCCGCA 59.382 50.000 0.00 0.00 0.00 5.69
5703 7028 3.513119 TCTGACTTCAGTCCTTCAGATGG 59.487 47.826 6.15 0.00 44.15 3.51
5773 7098 3.018856 TCGCCCAAAGAGAATAGTACGA 58.981 45.455 0.00 0.00 0.00 3.43
5798 7123 6.237901 TGATCTAACTTGCTAAAGGCTTTGA 58.762 36.000 22.32 7.92 42.39 2.69
5799 7124 6.714810 TGATCTAACTTGCTAAAGGCTTTGAA 59.285 34.615 22.32 10.91 42.39 2.69
5800 7125 6.952773 TCTAACTTGCTAAAGGCTTTGAAA 57.047 33.333 22.32 11.65 42.39 2.69
5801 7126 6.970484 TCTAACTTGCTAAAGGCTTTGAAAG 58.030 36.000 22.32 20.77 42.39 2.62
5802 7127 5.598416 AACTTGCTAAAGGCTTTGAAAGT 57.402 34.783 22.32 21.32 42.39 2.66
5803 7128 4.936891 ACTTGCTAAAGGCTTTGAAAGTG 58.063 39.130 23.42 13.36 42.39 3.16
5804 7129 4.644685 ACTTGCTAAAGGCTTTGAAAGTGA 59.355 37.500 23.42 5.83 42.39 3.41
5805 7130 5.302823 ACTTGCTAAAGGCTTTGAAAGTGAT 59.697 36.000 23.42 9.03 42.39 3.06
5806 7131 5.376854 TGCTAAAGGCTTTGAAAGTGATC 57.623 39.130 22.32 0.54 42.39 2.92
5807 7132 5.072741 TGCTAAAGGCTTTGAAAGTGATCT 58.927 37.500 22.32 0.00 42.39 2.75
5808 7133 6.237901 TGCTAAAGGCTTTGAAAGTGATCTA 58.762 36.000 22.32 0.00 42.39 1.98
5809 7134 6.714810 TGCTAAAGGCTTTGAAAGTGATCTAA 59.285 34.615 22.32 0.00 42.39 2.10
5810 7135 7.024171 GCTAAAGGCTTTGAAAGTGATCTAAC 58.976 38.462 22.32 0.00 38.06 2.34
5855 7180 5.012893 AGAATCCTTTTTCATCAGGGTCAC 58.987 41.667 0.00 0.00 0.00 3.67
5864 7189 8.477419 TTTTTCATCAGGGTCACTAGAATTTT 57.523 30.769 0.00 0.00 0.00 1.82
5879 7204 8.651588 CACTAGAATTTTGTCTCTGATGTACAC 58.348 37.037 0.00 0.00 0.00 2.90
5960 7293 4.402155 TGGTTTGTTTCAGTTGCATCTCTT 59.598 37.500 0.00 0.00 0.00 2.85
5971 7304 4.093998 AGTTGCATCTCTTAACAAGCATCG 59.906 41.667 0.00 0.00 0.00 3.84
5976 7309 5.923114 GCATCTCTTAACAAGCATCGATCTA 59.077 40.000 0.00 0.00 0.00 1.98
6041 7374 7.607250 ACACAAATGGAAAGTAGACACAAAAA 58.393 30.769 0.00 0.00 0.00 1.94
6042 7375 7.544217 ACACAAATGGAAAGTAGACACAAAAAC 59.456 33.333 0.00 0.00 0.00 2.43
6126 7459 1.676635 CTGGACATGCCTGTGGTGG 60.677 63.158 0.00 0.00 35.14 4.61
6323 7657 6.092807 GGAATACCTGAGACACAACTGAAATC 59.907 42.308 0.00 0.00 0.00 2.17
6364 7703 6.985059 GTCACAGGTTTGATACTTACTATCCC 59.015 42.308 0.00 0.00 31.42 3.85
6368 7707 8.287350 ACAGGTTTGATACTTACTATCCCTAGA 58.713 37.037 0.00 0.00 31.42 2.43
6453 7792 3.372206 GCACCTAACTGCACATAACAGAG 59.628 47.826 0.00 0.00 38.55 3.35
6454 7793 4.820897 CACCTAACTGCACATAACAGAGA 58.179 43.478 0.00 0.00 38.55 3.10
6455 7794 4.867047 CACCTAACTGCACATAACAGAGAG 59.133 45.833 0.00 0.00 38.55 3.20
6465 7804 5.777802 CACATAACAGAGAGAGTGTTGAGT 58.222 41.667 0.00 0.00 38.58 3.41
6515 7854 1.995646 GAGTCGAAGCGAGGTCCCTC 61.996 65.000 3.09 3.09 36.23 4.30
6583 7922 1.146263 GGTACCGGCATCCTTCAGG 59.854 63.158 0.00 0.00 0.00 3.86
6590 7929 2.190578 CATCCTTCAGGTCGCCCC 59.809 66.667 0.00 0.00 36.34 5.80
6591 7930 3.470888 ATCCTTCAGGTCGCCCCG 61.471 66.667 0.00 0.00 38.74 5.73
6593 7932 4.452733 CCTTCAGGTCGCCCCGTC 62.453 72.222 0.00 0.00 38.74 4.79
6594 7933 3.691342 CTTCAGGTCGCCCCGTCA 61.691 66.667 0.00 0.00 38.74 4.35
6595 7934 3.934391 CTTCAGGTCGCCCCGTCAC 62.934 68.421 0.00 0.00 38.74 3.67
6596 7935 4.988716 TCAGGTCGCCCCGTCACT 62.989 66.667 0.00 0.00 38.74 3.41
6597 7936 4.742201 CAGGTCGCCCCGTCACTG 62.742 72.222 0.00 0.00 38.74 3.66
6599 7938 4.736896 GGTCGCCCCGTCACTGTC 62.737 72.222 0.00 0.00 0.00 3.51
6600 7939 3.986006 GTCGCCCCGTCACTGTCA 61.986 66.667 0.00 0.00 0.00 3.58
6602 7941 3.680786 CGCCCCGTCACTGTCAGA 61.681 66.667 6.91 0.00 0.00 3.27
6603 7942 2.982130 GCCCCGTCACTGTCAGAT 59.018 61.111 6.91 0.00 0.00 2.90
6604 7943 1.448540 GCCCCGTCACTGTCAGATG 60.449 63.158 6.91 1.57 0.00 2.90
6605 7944 1.888436 GCCCCGTCACTGTCAGATGA 61.888 60.000 6.91 4.04 0.00 2.92
6606 7945 0.108615 CCCCGTCACTGTCAGATGAC 60.109 60.000 18.23 18.23 44.97 3.06
6638 7986 2.343758 CCCGTCACTGTGAGGTGG 59.656 66.667 23.94 20.41 37.75 4.61
6642 7990 1.302033 GTCACTGTGAGGTGGCTGG 60.302 63.158 11.41 0.00 38.61 4.85
6664 8012 2.049627 GCGATGGAGATGGCCTTCCT 62.050 60.000 14.77 3.43 0.00 3.36
6668 8016 0.547471 TGGAGATGGCCTTCCTGTCA 60.547 55.000 14.77 5.99 0.00 3.58
6675 8023 1.064463 TGGCCTTCCTGTCATCCAATC 60.064 52.381 3.32 0.00 0.00 2.67
6678 8026 1.407299 CCTTCCTGTCATCCAATCGCA 60.407 52.381 0.00 0.00 0.00 5.10
6727 8075 0.748005 CATTAGTTGGGTGAGGGGCG 60.748 60.000 0.00 0.00 0.00 6.13
6769 8121 2.434702 CTCCCCTTACGTTATTGCTCCT 59.565 50.000 0.00 0.00 0.00 3.69
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
148 150 0.390860 CAATAGAGGACCGGCTCCAG 59.609 60.000 20.68 1.15 42.46 3.86
153 155 2.056906 ATGCCCAATAGAGGACCGGC 62.057 60.000 0.00 0.00 36.91 6.13
175 177 7.531857 TTGAATAAAGAATAAGGGTGTGCAA 57.468 32.000 0.00 0.00 0.00 4.08
176 178 7.309744 CCTTTGAATAAAGAATAAGGGTGTGCA 60.310 37.037 1.58 0.00 44.87 4.57
177 179 7.035612 CCTTTGAATAAAGAATAAGGGTGTGC 58.964 38.462 1.58 0.00 44.87 4.57
225 227 1.353091 ATATCTTTCCCTCCGCCTCC 58.647 55.000 0.00 0.00 0.00 4.30
250 252 4.803426 CTCGACAGGGCGGTCTGC 62.803 72.222 0.00 0.00 45.38 4.26
251 253 4.803426 GCTCGACAGGGCGGTCTG 62.803 72.222 0.00 0.00 40.40 3.51
257 259 3.119096 GTTTCCGCTCGACAGGGC 61.119 66.667 1.99 0.00 41.46 5.19
258 260 1.004918 AAGTTTCCGCTCGACAGGG 60.005 57.895 1.99 0.00 0.00 4.45
259 261 1.291877 CCAAGTTTCCGCTCGACAGG 61.292 60.000 0.00 0.00 0.00 4.00
260 262 1.901650 GCCAAGTTTCCGCTCGACAG 61.902 60.000 0.00 0.00 0.00 3.51
261 263 1.959226 GCCAAGTTTCCGCTCGACA 60.959 57.895 0.00 0.00 0.00 4.35
262 264 1.503818 TTGCCAAGTTTCCGCTCGAC 61.504 55.000 0.00 0.00 0.00 4.20
263 265 0.605319 ATTGCCAAGTTTCCGCTCGA 60.605 50.000 0.00 0.00 0.00 4.04
264 266 0.179189 GATTGCCAAGTTTCCGCTCG 60.179 55.000 0.00 0.00 0.00 5.03
265 267 0.171231 GGATTGCCAAGTTTCCGCTC 59.829 55.000 0.00 0.00 0.00 5.03
266 268 0.251341 AGGATTGCCAAGTTTCCGCT 60.251 50.000 0.00 0.00 36.29 5.52
267 269 0.171231 GAGGATTGCCAAGTTTCCGC 59.829 55.000 0.00 0.00 36.29 5.54
268 270 1.826385 AGAGGATTGCCAAGTTTCCG 58.174 50.000 0.00 0.00 36.29 4.30
269 271 4.589908 TCTTAGAGGATTGCCAAGTTTCC 58.410 43.478 0.00 0.00 36.29 3.13
270 272 7.500559 ACATATCTTAGAGGATTGCCAAGTTTC 59.499 37.037 0.00 0.00 36.29 2.78
271 273 7.349598 ACATATCTTAGAGGATTGCCAAGTTT 58.650 34.615 0.00 0.00 36.29 2.66
272 274 6.904626 ACATATCTTAGAGGATTGCCAAGTT 58.095 36.000 0.00 0.00 36.29 2.66
273 275 6.506538 ACATATCTTAGAGGATTGCCAAGT 57.493 37.500 0.00 0.00 36.29 3.16
274 276 7.675062 AGTACATATCTTAGAGGATTGCCAAG 58.325 38.462 0.00 0.00 36.29 3.61
275 277 7.618019 AGTACATATCTTAGAGGATTGCCAA 57.382 36.000 0.00 0.00 36.29 4.52
276 278 7.618019 AAGTACATATCTTAGAGGATTGCCA 57.382 36.000 0.00 0.00 36.29 4.92
277 279 9.998106 TTTAAGTACATATCTTAGAGGATTGCC 57.002 33.333 0.00 0.00 0.00 4.52
336 338 5.424121 AAATACTTAACGGATGCAGATGC 57.576 39.130 0.00 0.00 42.50 3.91
337 339 6.688385 CACAAAATACTTAACGGATGCAGATG 59.312 38.462 0.00 0.00 0.00 2.90
338 340 6.677920 GCACAAAATACTTAACGGATGCAGAT 60.678 38.462 0.00 0.00 0.00 2.90
339 341 5.391523 GCACAAAATACTTAACGGATGCAGA 60.392 40.000 0.00 0.00 0.00 4.26
340 342 4.793216 GCACAAAATACTTAACGGATGCAG 59.207 41.667 0.00 0.00 0.00 4.41
348 350 9.083080 ACTCAACTTTTGCACAAAATACTTAAC 57.917 29.630 8.86 0.00 39.29 2.01
351 353 7.064490 CCAACTCAACTTTTGCACAAAATACTT 59.936 33.333 8.86 0.00 39.29 2.24
353 355 6.238076 CCCAACTCAACTTTTGCACAAAATAC 60.238 38.462 8.86 0.00 39.29 1.89
410 413 6.982724 TGCACATGAACATGAAATTTGTTACA 59.017 30.769 19.56 0.00 41.20 2.41
428 431 5.947228 TCCTTTTTCTTCTAGTGCACATG 57.053 39.130 21.04 11.17 0.00 3.21
430 433 5.680619 TCTTCCTTTTTCTTCTAGTGCACA 58.319 37.500 21.04 4.13 0.00 4.57
431 434 6.619801 TTCTTCCTTTTTCTTCTAGTGCAC 57.380 37.500 9.40 9.40 0.00 4.57
449 452 6.314784 CCGACACATTTTAGGTGATTTCTTC 58.685 40.000 0.00 0.00 39.53 2.87
485 515 8.316640 ACATGCAAACTTGTTTTGTAAGAAAA 57.683 26.923 0.00 0.00 45.70 2.29
526 561 4.219115 TGTGGGCCTTCAAATTTGTAGAA 58.781 39.130 22.24 8.19 0.00 2.10
551 586 4.690748 GGCATGTATATGTGCGTCTAATGT 59.309 41.667 1.14 0.00 42.15 2.71
552 587 4.931601 AGGCATGTATATGTGCGTCTAATG 59.068 41.667 1.14 0.00 42.15 1.90
553 588 5.152623 AGGCATGTATATGTGCGTCTAAT 57.847 39.130 1.14 0.00 42.15 1.73
555 590 4.600692 AAGGCATGTATATGTGCGTCTA 57.399 40.909 1.14 0.00 42.15 2.59
557 592 3.809832 AGAAAGGCATGTATATGTGCGTC 59.190 43.478 1.14 5.24 42.15 5.19
558 593 3.808728 AGAAAGGCATGTATATGTGCGT 58.191 40.909 1.14 4.56 42.15 5.24
559 594 4.818534 AAGAAAGGCATGTATATGTGCG 57.181 40.909 1.14 0.00 42.15 5.34
560 595 7.035004 TGAAAAAGAAAGGCATGTATATGTGC 58.965 34.615 1.14 4.27 40.55 4.57
562 597 9.590451 CAATGAAAAAGAAAGGCATGTATATGT 57.410 29.630 1.14 0.00 36.65 2.29
569 798 6.072948 TGCAATCAATGAAAAAGAAAGGCATG 60.073 34.615 0.00 0.00 0.00 4.06
610 840 7.771361 TGTGGAACAGTCAAGTGTTTCTTTATA 59.229 33.333 9.77 0.00 45.67 0.98
612 842 5.941058 TGTGGAACAGTCAAGTGTTTCTTTA 59.059 36.000 9.77 0.00 45.67 1.85
658 888 6.144724 GCTCTGCTTACCGATCTTTATTACTG 59.855 42.308 0.00 0.00 0.00 2.74
659 889 6.183360 TGCTCTGCTTACCGATCTTTATTACT 60.183 38.462 0.00 0.00 0.00 2.24
660 890 5.983720 TGCTCTGCTTACCGATCTTTATTAC 59.016 40.000 0.00 0.00 0.00 1.89
661 891 6.156748 TGCTCTGCTTACCGATCTTTATTA 57.843 37.500 0.00 0.00 0.00 0.98
662 892 5.023533 TGCTCTGCTTACCGATCTTTATT 57.976 39.130 0.00 0.00 0.00 1.40
663 893 4.672587 TGCTCTGCTTACCGATCTTTAT 57.327 40.909 0.00 0.00 0.00 1.40
664 894 4.159693 TCTTGCTCTGCTTACCGATCTTTA 59.840 41.667 0.00 0.00 0.00 1.85
665 895 3.055819 TCTTGCTCTGCTTACCGATCTTT 60.056 43.478 0.00 0.00 0.00 2.52
671 901 1.590238 CGATTCTTGCTCTGCTTACCG 59.410 52.381 0.00 0.00 0.00 4.02
707 937 5.118990 CCTCCTTGTTATGACGAATGATGT 58.881 41.667 0.00 0.00 0.00 3.06
719 949 3.442076 AGAGAACCGACCTCCTTGTTAT 58.558 45.455 0.00 0.00 0.00 1.89
752 982 4.517453 TGAACCGACCTCCTTGTTTATTTG 59.483 41.667 0.00 0.00 0.00 2.32
773 1003 9.958180 AGGAAAAAGGAAAAAGAAAAAGAATGA 57.042 25.926 0.00 0.00 0.00 2.57
796 1026 1.339929 GGCAAGCTTTCGGAAAAAGGA 59.660 47.619 0.00 0.00 0.00 3.36
798 1028 2.127251 GTGGCAAGCTTTCGGAAAAAG 58.873 47.619 0.00 0.00 0.00 2.27
802 1032 0.667993 CAAGTGGCAAGCTTTCGGAA 59.332 50.000 0.00 0.00 0.00 4.30
805 1035 1.536766 TCATCAAGTGGCAAGCTTTCG 59.463 47.619 0.00 0.00 0.00 3.46
806 1036 3.572584 CTTCATCAAGTGGCAAGCTTTC 58.427 45.455 0.00 0.00 0.00 2.62
807 1037 2.288640 GCTTCATCAAGTGGCAAGCTTT 60.289 45.455 0.00 0.00 35.73 3.51
808 1038 1.271656 GCTTCATCAAGTGGCAAGCTT 59.728 47.619 0.00 0.00 35.73 3.74
809 1039 0.886563 GCTTCATCAAGTGGCAAGCT 59.113 50.000 0.00 0.00 35.73 3.74
810 1040 0.886563 AGCTTCATCAAGTGGCAAGC 59.113 50.000 0.00 0.00 37.72 4.01
811 1041 1.201647 CCAGCTTCATCAAGTGGCAAG 59.798 52.381 0.00 0.00 31.45 4.01
812 1042 1.202915 TCCAGCTTCATCAAGTGGCAA 60.203 47.619 0.00 0.00 33.83 4.52
813 1043 0.401356 TCCAGCTTCATCAAGTGGCA 59.599 50.000 0.00 0.00 33.83 4.92
814 1044 1.093159 CTCCAGCTTCATCAAGTGGC 58.907 55.000 0.00 0.00 33.83 5.01
815 1045 2.235650 TCTCTCCAGCTTCATCAAGTGG 59.764 50.000 0.00 0.00 34.53 4.00
816 1046 3.606595 TCTCTCCAGCTTCATCAAGTG 57.393 47.619 0.00 0.00 31.45 3.16
817 1047 3.118334 CCATCTCTCCAGCTTCATCAAGT 60.118 47.826 0.00 0.00 31.45 3.16
818 1048 3.134262 TCCATCTCTCCAGCTTCATCAAG 59.866 47.826 0.00 0.00 0.00 3.02
819 1049 3.109928 TCCATCTCTCCAGCTTCATCAA 58.890 45.455 0.00 0.00 0.00 2.57
820 1050 2.755686 TCCATCTCTCCAGCTTCATCA 58.244 47.619 0.00 0.00 0.00 3.07
821 1051 3.306919 GGATCCATCTCTCCAGCTTCATC 60.307 52.174 6.95 0.00 0.00 2.92
822 1052 2.638855 GGATCCATCTCTCCAGCTTCAT 59.361 50.000 6.95 0.00 0.00 2.57
823 1053 2.045524 GGATCCATCTCTCCAGCTTCA 58.954 52.381 6.95 0.00 0.00 3.02
824 1054 1.347378 GGGATCCATCTCTCCAGCTTC 59.653 57.143 15.23 0.00 32.90 3.86
835 1065 1.202806 TCCATTTCAGCGGGATCCATC 60.203 52.381 15.23 4.08 0.00 3.51
930 1246 0.896019 CGTCCCTGGTCTGTCTGTCT 60.896 60.000 0.00 0.00 0.00 3.41
963 1282 2.417719 CTTCAGAACTGGCACCTACAC 58.582 52.381 1.93 0.00 0.00 2.90
1623 1969 2.415625 GCTGCCTGAAGCTGAATCTTTG 60.416 50.000 0.00 0.00 42.76 2.77
1633 1979 0.320073 TGCATTTTGCTGCCTGAAGC 60.320 50.000 0.00 0.00 45.31 3.86
1717 2229 4.380843 TTTCCTAAGGGTTTGCAGATCA 57.619 40.909 0.00 0.00 0.00 2.92
1718 2230 4.082190 GGTTTTCCTAAGGGTTTGCAGATC 60.082 45.833 0.00 0.00 36.94 2.75
1757 2457 3.442977 AGTTCTGGCATTCTGAATCAAGC 59.557 43.478 0.00 1.41 36.09 4.01
1787 2488 4.161754 GCTACCAACTACTACTCCCAATGT 59.838 45.833 0.00 0.00 0.00 2.71
1860 2563 8.189460 GGATGAAGAGAACACGTAATAACTACT 58.811 37.037 0.00 0.00 0.00 2.57
1861 2564 7.165483 CGGATGAAGAGAACACGTAATAACTAC 59.835 40.741 0.00 0.00 0.00 2.73
1864 2567 5.803967 ACGGATGAAGAGAACACGTAATAAC 59.196 40.000 0.00 0.00 0.00 1.89
1923 2654 3.480470 AGGGAATGTCACTGAAACTGTG 58.520 45.455 0.00 0.00 35.20 3.66
1970 2714 2.635915 TGGTTGTCGACATTTAGGTCCT 59.364 45.455 20.80 0.00 34.24 3.85
2227 3070 9.924650 GTCTGTTTCTCTTCTAGTATTACCAAA 57.075 33.333 0.00 0.00 0.00 3.28
2228 3071 9.085645 TGTCTGTTTCTCTTCTAGTATTACCAA 57.914 33.333 0.00 0.00 0.00 3.67
2317 3162 3.998341 ACGTTTCTTGCACCATACGTAAT 59.002 39.130 12.73 0.00 40.03 1.89
2318 3163 3.184783 CACGTTTCTTGCACCATACGTAA 59.815 43.478 13.64 0.00 39.85 3.18
2319 3164 2.732500 CACGTTTCTTGCACCATACGTA 59.267 45.455 13.64 0.00 39.85 3.57
2320 3165 1.529438 CACGTTTCTTGCACCATACGT 59.471 47.619 9.60 9.60 42.22 3.57
2343 3188 1.763968 GGATTCCCCAAAGTAGGTGC 58.236 55.000 0.00 0.00 34.14 5.01
2388 3234 7.312899 TGACACAAAAGAAAAGAAAAGGAGAC 58.687 34.615 0.00 0.00 0.00 3.36
2393 3239 8.164153 CACACATGACACAAAAGAAAAGAAAAG 58.836 33.333 0.00 0.00 0.00 2.27
2398 3244 5.230726 GCTCACACATGACACAAAAGAAAAG 59.769 40.000 0.00 0.00 0.00 2.27
2399 3245 5.101628 GCTCACACATGACACAAAAGAAAA 58.898 37.500 0.00 0.00 0.00 2.29
2403 3249 3.696281 TGCTCACACATGACACAAAAG 57.304 42.857 0.00 0.00 0.00 2.27
2492 3340 6.325919 TGGTAAGCAAACTTTATTGTCTGG 57.674 37.500 0.00 0.00 37.33 3.86
2528 3414 3.501445 AGTGCTCATTCTGCTCAAAAGTC 59.499 43.478 0.00 0.00 0.00 3.01
2569 3455 5.694006 GCAGCTACATCTGATAAATCGAAGT 59.306 40.000 0.00 0.00 36.19 3.01
2634 3893 2.161855 TCCAATGCTGCAACCAAGTAG 58.838 47.619 6.36 0.00 0.00 2.57
2886 4145 4.832767 TCGTCGGCGAATATAGCG 57.167 55.556 10.97 10.39 44.92 4.26
2897 4156 0.038618 TCGCCCATAATCATCGTCGG 60.039 55.000 0.00 0.00 0.00 4.79
2950 4209 2.893489 GTGAAATCTTTGCCCTCCTTGT 59.107 45.455 0.00 0.00 0.00 3.16
2954 4213 2.238521 TGTGTGAAATCTTTGCCCTCC 58.761 47.619 0.00 0.00 0.00 4.30
3018 4277 5.281693 TCATATTTGCTCTGAACAACACG 57.718 39.130 0.00 0.00 0.00 4.49
3114 4373 1.225426 GCCACTGGCCATCATCTGA 59.775 57.895 5.51 0.00 44.06 3.27
3223 4482 0.317020 GTGTGCTGGCGAAGAACAAC 60.317 55.000 0.55 0.00 46.63 3.32
3273 4532 1.712401 CGGCATTGTTCCATTTGGTG 58.288 50.000 0.00 0.00 36.34 4.17
3311 4570 4.526970 ACCATACGAATTCAAGCCAGAAT 58.473 39.130 6.22 0.00 39.81 2.40
3378 4637 4.141892 TGCTGCCCATTATCAAGAAATTGG 60.142 41.667 0.00 0.00 0.00 3.16
3379 4638 5.013568 TGCTGCCCATTATCAAGAAATTG 57.986 39.130 0.00 0.00 0.00 2.32
3441 4700 4.808414 TGACAGCTGCAAAGTACTATCT 57.192 40.909 15.27 0.00 0.00 1.98
3609 4868 0.988832 AGTAGCCAATCAACCGGGAA 59.011 50.000 6.32 0.00 0.00 3.97
3771 5030 0.807496 GCAGAGGCTGACCATTGTTC 59.193 55.000 0.00 0.00 39.06 3.18
3871 5130 3.232213 AGCCGCGTTGAATATATCGAT 57.768 42.857 4.92 2.16 0.00 3.59
3982 5241 2.672874 TCGAGCATACATTGTCAGCAAC 59.327 45.455 13.68 7.78 37.44 4.17
4015 5274 7.562454 AATGGTTAAATACATACACCGGAAG 57.438 36.000 9.46 1.96 0.00 3.46
4368 5630 6.791371 AGGATCGAATACATCCCTAAGTAGA 58.209 40.000 0.00 0.00 40.90 2.59
4387 5650 3.556004 GCCAGACTTGGTAGCATAGGATC 60.556 52.174 0.00 0.00 46.80 3.36
4408 5675 6.091437 CCTCATGAAAATTTCAGACTCAAGC 58.909 40.000 14.10 0.00 43.98 4.01
4425 5692 4.711846 AGTACATTACACTCTGCCTCATGA 59.288 41.667 0.00 0.00 0.00 3.07
4426 5693 5.016051 AGTACATTACACTCTGCCTCATG 57.984 43.478 0.00 0.00 0.00 3.07
4427 5694 5.656859 TGTAGTACATTACACTCTGCCTCAT 59.343 40.000 0.00 0.00 0.00 2.90
4428 5695 5.014202 TGTAGTACATTACACTCTGCCTCA 58.986 41.667 0.00 0.00 0.00 3.86
4441 5708 9.906660 CCAACAACACAAATATTGTAGTACATT 57.093 29.630 3.28 3.33 43.23 2.71
4442 5709 9.073475 ACCAACAACACAAATATTGTAGTACAT 57.927 29.630 3.28 0.00 43.23 2.29
4443 5710 8.346300 CACCAACAACACAAATATTGTAGTACA 58.654 33.333 0.00 0.00 43.23 2.90
4446 5713 7.575414 TCACCAACAACACAAATATTGTAGT 57.425 32.000 0.00 0.00 43.23 2.73
4447 5714 9.474920 AAATCACCAACAACACAAATATTGTAG 57.525 29.630 0.00 0.00 43.23 2.74
4450 5765 8.610896 ACAAAATCACCAACAACACAAATATTG 58.389 29.630 0.00 0.00 0.00 1.90
4451 5766 8.729805 ACAAAATCACCAACAACACAAATATT 57.270 26.923 0.00 0.00 0.00 1.28
4454 5769 8.553459 TTTACAAAATCACCAACAACACAAAT 57.447 26.923 0.00 0.00 0.00 2.32
4592 5911 6.058183 AGCACCATGGATGAGTTAAGAATAC 58.942 40.000 21.47 0.00 0.00 1.89
4596 5915 4.574674 AAGCACCATGGATGAGTTAAGA 57.425 40.909 21.47 0.00 0.00 2.10
4771 6092 6.461092 CGGTTATTCCTGTAGATAGCTGTTGA 60.461 42.308 0.00 0.00 0.00 3.18
4919 6241 2.499685 GGCGTCGGCATACTCCTT 59.500 61.111 14.73 0.00 42.47 3.36
5174 6498 0.815734 CTCTGGAATGCCTGCAAAGG 59.184 55.000 0.00 0.00 33.46 3.11
5215 6539 1.483004 TGAAGGATGGCCGTCGATAAA 59.517 47.619 18.79 0.54 44.51 1.40
5635 6960 1.549037 GGCTGAGTATCCGAGGATCCT 60.549 57.143 16.13 16.13 36.17 3.24
5648 6973 0.034616 GCTCAAGACACTGGCTGAGT 59.965 55.000 11.01 0.00 34.02 3.41
5703 7028 1.039856 TGCTTCCTTCCCTGTTTTGC 58.960 50.000 0.00 0.00 0.00 3.68
5761 7086 8.293867 AGCAAGTTAGATCATCGTACTATTCTC 58.706 37.037 0.00 0.00 0.00 2.87
5769 7094 5.983720 GCCTTTAGCAAGTTAGATCATCGTA 59.016 40.000 0.00 0.00 42.97 3.43
5855 7180 8.763049 TGTGTACATCAGAGACAAAATTCTAG 57.237 34.615 0.00 0.00 0.00 2.43
5864 7189 5.276461 ACAAACTGTGTACATCAGAGACA 57.724 39.130 23.52 6.26 39.29 3.41
5960 7293 5.237127 CAGCCAAATAGATCGATGCTTGTTA 59.763 40.000 0.54 0.00 0.00 2.41
5976 7309 7.886629 ACACATAAATCATAGTCAGCCAAAT 57.113 32.000 0.00 0.00 0.00 2.32
6323 7657 4.396166 CCTGTGACCAAGCTTAAGTAATGG 59.604 45.833 16.79 16.79 37.19 3.16
6382 7721 6.481643 TCAAGTTAAACCTAAGGATTCCCTG 58.518 40.000 0.00 0.00 43.48 4.45
6413 7752 6.521527 AGGTGCTCCAATTCTAGGATTATT 57.478 37.500 7.70 0.00 33.99 1.40
6453 7792 3.617775 GCCCCTAAGAACTCAACACTCTC 60.618 52.174 0.00 0.00 0.00 3.20
6454 7793 2.303311 GCCCCTAAGAACTCAACACTCT 59.697 50.000 0.00 0.00 0.00 3.24
6455 7794 2.038557 TGCCCCTAAGAACTCAACACTC 59.961 50.000 0.00 0.00 0.00 3.51
6465 7804 1.284785 CTCACCCATTGCCCCTAAGAA 59.715 52.381 0.00 0.00 0.00 2.52
6583 7922 3.916392 CTGACAGTGACGGGGCGAC 62.916 68.421 0.00 0.00 0.00 5.19
6591 7930 3.175152 GACATCGTCATCTGACAGTGAC 58.825 50.000 19.74 19.74 44.99 3.67
6592 7931 2.819608 TGACATCGTCATCTGACAGTGA 59.180 45.455 14.95 3.22 44.99 3.41
6593 7932 3.221964 TGACATCGTCATCTGACAGTG 57.778 47.619 10.69 9.86 44.99 3.66
6607 7946 2.658593 CGGGGCGACGATGACATC 60.659 66.667 5.28 5.28 35.47 3.06
6610 7958 4.124351 TGACGGGGCGACGATGAC 62.124 66.667 0.00 0.00 37.61 3.06
6622 7970 2.357517 GCCACCTCACAGTGACGG 60.358 66.667 14.31 14.31 40.34 4.79
6638 7986 4.615815 ATCTCCATCGCCGCCAGC 62.616 66.667 0.00 0.00 38.52 4.85
6647 7995 0.842635 ACAGGAAGGCCATCTCCATC 59.157 55.000 17.96 0.00 36.29 3.51
6664 8012 1.138859 CCTACCTGCGATTGGATGACA 59.861 52.381 0.00 0.00 0.00 3.58
6668 8016 2.368875 CCTAACCTACCTGCGATTGGAT 59.631 50.000 0.00 0.00 0.00 3.41
6675 8023 1.153429 GCACCCTAACCTACCTGCG 60.153 63.158 0.00 0.00 0.00 5.18
6727 8075 1.207593 GCCACACATCAACACTCGC 59.792 57.895 0.00 0.00 0.00 5.03
6731 8079 1.160137 GAGGAGCCACACATCAACAC 58.840 55.000 0.00 0.00 0.00 3.32
6769 8121 2.190538 TGGATTGATCTCCAGACAGCA 58.809 47.619 0.00 0.00 40.43 4.41


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

AutoCloner maintained by Alex Coulton.