Multiple sequence alignment - TraesCS1D01G103800

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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 TraesCS1D01G103800 chr1D 100.000 8611 0 0 1 8611 93131409 93122799 0.000000e+00 15902.0
1 TraesCS1D01G103800 chr1D 100.000 32 0 0 2005 2036 93129332 93129301 9.340000e-05 60.2
2 TraesCS1D01G103800 chr1D 100.000 32 0 0 2078 2109 93129405 93129374 9.340000e-05 60.2
3 TraesCS1D01G103800 chr1A 96.281 3738 99 8 3968 7668 91044861 91048595 0.000000e+00 6096.0
4 TraesCS1D01G103800 chr1A 95.733 1242 47 5 1269 2507 91041281 91042519 0.000000e+00 1995.0
5 TraesCS1D01G103800 chr1A 95.277 1228 39 8 2516 3726 91042971 91044196 0.000000e+00 1929.0
6 TraesCS1D01G103800 chr1A 86.689 879 52 23 386 1239 91040172 91041010 0.000000e+00 915.0
7 TraesCS1D01G103800 chr1A 83.087 745 82 17 7898 8609 91049496 91050229 9.430000e-179 638.0
8 TraesCS1D01G103800 chr1A 96.774 186 6 0 3793 3978 91044417 91044602 2.330000e-80 311.0
9 TraesCS1D01G103800 chr1A 88.593 263 17 7 7680 7939 91049243 91049495 3.020000e-79 307.0
10 TraesCS1D01G103800 chr1A 94.286 35 2 0 2002 2036 91042088 91042122 4.000000e-03 54.7
11 TraesCS1D01G103800 chr1B 95.362 2803 69 10 3789 6538 148475373 148472579 0.000000e+00 4399.0
12 TraesCS1D01G103800 chr1B 89.745 2116 162 33 1 2099 148479248 148477171 0.000000e+00 2654.0
13 TraesCS1D01G103800 chr1B 94.265 1639 50 20 2106 3726 148477204 148475592 0.000000e+00 2466.0
14 TraesCS1D01G103800 chr1B 96.921 1234 34 2 6619 7851 148472581 148471351 0.000000e+00 2065.0
15 TraesCS1D01G103800 chr1B 89.054 740 54 9 7894 8611 148471164 148470430 0.000000e+00 893.0
16 TraesCS1D01G103800 chr1B 100.000 32 0 0 2078 2109 148477263 148477232 9.340000e-05 60.2
17 TraesCS1D01G103800 chr4A 82.400 375 41 16 6140 6492 545604086 545604457 3.910000e-78 303.0
18 TraesCS1D01G103800 chr4B 82.471 348 30 20 6168 6492 75204423 75204084 8.510000e-70 276.0
19 TraesCS1D01G103800 chr6D 82.775 209 25 8 6267 6471 220939259 220939460 8.880000e-40 176.0
20 TraesCS1D01G103800 chr7D 98.876 89 1 0 6535 6623 22964342 22964254 8.950000e-35 159.0
21 TraesCS1D01G103800 chr7D 93.396 106 6 1 6531 6635 79628433 79628328 1.160000e-33 156.0
22 TraesCS1D01G103800 chr7D 96.809 94 1 1 6535 6626 426558984 426558891 1.160000e-33 156.0
23 TraesCS1D01G103800 chr7D 96.471 85 3 0 6536 6620 561192205 561192121 3.240000e-29 141.0
24 TraesCS1D01G103800 chr6B 81.340 209 28 8 6267 6471 396438446 396438647 8.950000e-35 159.0
25 TraesCS1D01G103800 chr5D 95.876 97 4 0 6531 6627 545227783 545227879 3.220000e-34 158.0
26 TraesCS1D01G103800 chr6A 81.373 204 26 9 6267 6466 302776808 302776613 1.160000e-33 156.0
27 TraesCS1D01G103800 chr2D 94.898 98 4 1 6535 6631 15682899 15682996 1.500000e-32 152.0
28 TraesCS1D01G103800 chr2D 91.743 109 7 2 6517 6623 574413510 574413618 5.380000e-32 150.0
29 TraesCS1D01G103800 chr2D 84.746 118 17 1 6335 6452 512098245 512098361 5.460000e-22 117.0
30 TraesCS1D01G103800 chr7A 92.381 105 7 1 6536 6640 664477292 664477189 1.940000e-31 148.0
31 TraesCS1D01G103800 chr2A 85.714 119 17 0 6334 6452 655281453 655281571 9.070000e-25 126.0
32 TraesCS1D01G103800 chrUn 87.619 105 12 1 6387 6491 48509771 48509874 4.220000e-23 121.0


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 TraesCS1D01G103800 chr1D 93122799 93131409 8610 True 5340.800000 15902 100.0000 1 8611 3 chr1D.!!$R1 8610
1 TraesCS1D01G103800 chr1A 91040172 91050229 10057 False 1530.712500 6096 92.0900 386 8609 8 chr1A.!!$F1 8223
2 TraesCS1D01G103800 chr1B 148470430 148479248 8818 True 2089.533333 4399 94.2245 1 8611 6 chr1B.!!$R1 8610

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
118 119 0.031585 ACAAGTCACGCGCAGAGTTA 59.968 50.000 18.23 0.00 39.58 2.24 F
171 172 0.109272 CGACAGTGCTACGGATGTGT 60.109 55.000 0.00 0.00 0.00 3.72 F
200 201 0.179084 ACTGGAACTGGTGACACACG 60.179 55.000 8.08 0.00 34.83 4.49 F
377 380 0.389948 CAACCGGTGACACTAGAGCC 60.390 60.000 8.52 0.00 0.00 4.70 F
1592 1858 0.750249 TTCACGCTGTTCTGACCTCA 59.250 50.000 0.00 0.00 0.00 3.86 F
2378 2657 0.327259 ACATCTCCACTGCATGCACT 59.673 50.000 18.46 4.91 0.00 4.40 F
2512 2791 0.467384 ATCTGATTCTGGGCCACGAG 59.533 55.000 0.00 0.00 0.00 4.18 F
3644 4409 1.398390 CAGAGCAACGTTCTTATGCCC 59.602 52.381 0.00 0.00 40.93 5.36 F
3727 4494 2.437651 TGGTTCATCTTGTGTCCAGACA 59.562 45.455 0.00 0.00 39.32 3.41 F
4486 5690 2.806945 ATCCTTTTGCGATGAAGGGA 57.193 45.000 4.83 5.53 42.17 4.20 F
5445 6660 4.142271 ACCTCTTGTCTATTTCTGCTCTCG 60.142 45.833 0.00 0.00 0.00 4.04 F
6716 7953 1.545136 TGTTGGTTGCACATGCTATGG 59.455 47.619 5.31 0.00 42.66 2.74 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1438 1704 0.460284 ACGCATCAACAGATCGGACC 60.460 55.000 0.00 0.00 0.00 4.46 R
1675 1941 0.863956 ACCAAATCCAGTCCCCCAAA 59.136 50.000 0.00 0.00 0.00 3.28 R
1961 2230 2.227388 GACTGCTTGATGAAACCACCAG 59.773 50.000 0.00 0.00 0.00 4.00 R
2351 2630 0.392193 CAGTGGAGATGTGGCCTGAC 60.392 60.000 3.32 0.00 0.00 3.51 R
2509 2788 0.673333 TAGTTGCATGTGTGGCCTCG 60.673 55.000 3.32 0.00 0.00 4.63 R
3763 4530 0.036010 ACTGGTTTCGCTCATGGGAG 60.036 55.000 0.00 0.00 44.33 4.30 R
3765 4532 0.606401 ACACTGGTTTCGCTCATGGG 60.606 55.000 0.00 0.00 0.00 4.00 R
4898 6113 0.182299 GATTCTCCTTCCCTGGCAGG 59.818 60.000 27.04 27.04 34.30 4.85 R
5485 6700 1.186200 AGATGGCAACGCTAGAGACA 58.814 50.000 0.00 0.00 42.51 3.41 R
6287 7524 2.489329 CCATTCAAAACATGAGCGAGGT 59.511 45.455 0.00 0.00 39.77 3.85 R
7274 8516 0.402121 GCCCAAAGAGTCTCCTTGGT 59.598 55.000 23.13 0.00 0.00 3.67 R
7915 9976 0.328258 AGCCCTAAAATCACTGGCGT 59.672 50.000 0.00 0.00 46.67 5.68 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
26 27 4.181578 ACGATGTTACTACAAGGATGTGC 58.818 43.478 0.00 0.00 40.84 4.57
27 28 4.081642 ACGATGTTACTACAAGGATGTGCT 60.082 41.667 0.00 0.00 40.84 4.40
37 38 1.302511 GGATGTGCTGGAACCGTGT 60.303 57.895 0.00 0.00 0.00 4.49
39 40 1.076332 GATGTGCTGGAACCGTGTAC 58.924 55.000 0.00 0.00 0.00 2.90
41 42 2.356553 TGCTGGAACCGTGTACGC 60.357 61.111 0.00 0.00 38.18 4.42
50 51 2.028484 CGTGTACGCTGGTGGTGT 59.972 61.111 4.67 0.00 41.91 4.16
55 56 1.138464 TGTACGCTGGTGGTGTTACAA 59.862 47.619 0.00 0.00 39.59 2.41
56 57 1.528161 GTACGCTGGTGGTGTTACAAC 59.472 52.381 0.00 0.00 39.59 3.32
58 59 1.837538 CGCTGGTGGTGTTACAACCG 61.838 60.000 0.00 0.00 43.73 4.44
60 61 0.941542 CTGGTGGTGTTACAACCGTG 59.058 55.000 0.00 0.00 43.73 4.94
76 77 0.528924 CGTGTACGTTGGGAGATGGA 59.471 55.000 0.00 0.00 34.11 3.41
88 89 1.718757 GAGATGGAACCGTGCATGCC 61.719 60.000 16.68 5.63 35.67 4.40
92 93 2.359850 GAACCGTGCATGCCAGGA 60.360 61.111 28.33 3.42 0.00 3.86
96 97 2.187685 CGTGCATGCCAGGAGCTA 59.812 61.111 16.68 0.00 44.23 3.32
102 103 1.679944 GCATGCCAGGAGCTAGAACAA 60.680 52.381 6.36 0.00 44.23 2.83
108 109 2.600731 CAGGAGCTAGAACAAGTCACG 58.399 52.381 0.00 0.00 0.00 4.35
111 112 1.009389 AGCTAGAACAAGTCACGCGC 61.009 55.000 5.73 0.00 0.00 6.86
112 113 1.282248 GCTAGAACAAGTCACGCGCA 61.282 55.000 5.73 0.00 0.00 6.09
118 119 0.031585 ACAAGTCACGCGCAGAGTTA 59.968 50.000 18.23 0.00 39.58 2.24
138 139 2.571757 TCGGTGTCGACAGGATGC 59.428 61.111 20.73 6.52 40.88 3.91
141 142 2.103042 GGTGTCGACAGGATGCTGC 61.103 63.158 20.73 4.08 42.53 5.25
158 159 4.086178 CGCCTCGTCGTCGACAGT 62.086 66.667 24.13 0.00 41.35 3.55
164 165 1.857853 CGTCGTCGACAGTGCTACG 60.858 63.158 24.13 10.63 39.71 3.51
165 166 1.511464 GTCGTCGACAGTGCTACGG 60.511 63.158 20.28 0.00 36.08 4.02
166 167 1.668793 TCGTCGACAGTGCTACGGA 60.669 57.895 17.16 0.00 36.08 4.69
167 168 1.022982 TCGTCGACAGTGCTACGGAT 61.023 55.000 17.16 0.00 36.08 4.18
168 169 0.861866 CGTCGACAGTGCTACGGATG 60.862 60.000 17.16 0.00 0.00 3.51
171 172 0.109272 CGACAGTGCTACGGATGTGT 60.109 55.000 0.00 0.00 0.00 3.72
173 174 2.414957 CGACAGTGCTACGGATGTGTAA 60.415 50.000 0.00 0.00 0.00 2.41
177 178 1.927174 GTGCTACGGATGTGTAAGCTG 59.073 52.381 0.00 0.00 0.00 4.24
182 183 1.338769 ACGGATGTGTAAGCTGGGAAC 60.339 52.381 0.00 0.00 0.00 3.62
185 186 2.359900 GATGTGTAAGCTGGGAACTGG 58.640 52.381 0.00 0.00 0.00 4.00
188 189 2.152016 GTGTAAGCTGGGAACTGGAAC 58.848 52.381 0.00 0.00 0.00 3.62
200 201 0.179084 ACTGGAACTGGTGACACACG 60.179 55.000 8.08 0.00 34.83 4.49
218 219 1.603802 ACGAAGTCACATTTGTGCCTG 59.396 47.619 5.81 0.00 45.25 4.85
258 259 0.673333 TCGGCAGTGCTACAACCATG 60.673 55.000 16.11 0.00 0.00 3.66
259 260 1.508088 GGCAGTGCTACAACCATGC 59.492 57.895 16.11 0.00 0.00 4.06
265 266 1.085893 TGCTACAACCATGCACATCG 58.914 50.000 0.00 0.00 0.00 3.84
278 279 1.305297 ACATCGAGAGCTGGGACCA 60.305 57.895 0.00 0.00 0.00 4.02
279 280 1.326213 ACATCGAGAGCTGGGACCAG 61.326 60.000 13.99 13.99 46.15 4.00
298 299 1.374631 TGACGTGTGGAGCTGCATC 60.375 57.895 12.38 5.31 0.00 3.91
314 315 1.742831 GCATCGGTGCCTACAAAATGA 59.257 47.619 10.29 0.00 45.76 2.57
317 318 1.742831 TCGGTGCCTACAAAATGATGC 59.257 47.619 0.00 0.00 0.00 3.91
319 320 1.742831 GGTGCCTACAAAATGATGCGA 59.257 47.619 0.00 0.00 0.00 5.10
331 332 2.505494 ATGCGACCCATCATGCGA 59.495 55.556 0.00 0.00 0.00 5.10
336 337 1.826024 GACCCATCATGCGAGGAGT 59.174 57.895 2.20 0.00 0.00 3.85
346 347 1.218316 GCGAGGAGTTGGAATCGGT 59.782 57.895 0.00 0.00 35.76 4.69
351 352 3.522553 GAGGAGTTGGAATCGGTAACAG 58.477 50.000 0.00 0.00 0.00 3.16
370 373 2.719354 GGTTGCAACCGGTGACAC 59.281 61.111 31.73 7.64 39.66 3.67
372 375 0.533308 GGTTGCAACCGGTGACACTA 60.533 55.000 31.73 0.00 39.66 2.74
377 380 0.389948 CAACCGGTGACACTAGAGCC 60.390 60.000 8.52 0.00 0.00 4.70
384 387 1.226435 GACACTAGAGCCGCGACAG 60.226 63.158 8.23 0.00 0.00 3.51
385 388 2.580867 CACTAGAGCCGCGACAGC 60.581 66.667 8.23 1.62 40.74 4.40
388 391 2.126071 TAGAGCCGCGACAGCAAC 60.126 61.111 8.23 1.17 45.49 4.17
439 442 2.375766 GCGCTGTTGAGACGGTGAG 61.376 63.158 0.00 0.00 43.79 3.51
540 544 1.615392 GAAGCAGGAAAATGGTGCTGT 59.385 47.619 0.00 0.00 46.86 4.40
556 560 1.069090 TGTTGAGACAGGGTGCGAC 59.931 57.895 0.00 0.00 0.00 5.19
559 563 1.399744 TTGAGACAGGGTGCGACAGT 61.400 55.000 0.00 0.00 0.00 3.55
566 570 2.046892 GGTGCGACAGTCATGGCT 60.047 61.111 0.00 0.00 29.20 4.75
586 590 1.629861 TGTCAATGGAGGAGCATGTCA 59.370 47.619 0.00 0.00 0.00 3.58
592 596 3.382803 GAGGAGCATGTCAGCGGCT 62.383 63.158 0.00 0.00 41.35 5.52
645 659 2.807967 CACACAAGATTTTCTCGCTCCA 59.192 45.455 0.00 0.00 0.00 3.86
657 671 1.448540 CGCTCCATGGGTGACACTC 60.449 63.158 13.02 1.01 0.00 3.51
706 720 2.802667 CTTTGATCACGCGGCTCCG 61.803 63.158 12.47 3.56 43.09 4.63
739 754 4.665833 TTTGATATTCTGACCGGTCGAT 57.334 40.909 28.70 22.68 0.00 3.59
790 805 3.003378 CGTTCATGCTGTAGACGATAGGA 59.997 47.826 0.00 0.00 43.77 2.94
794 809 2.239400 TGCTGTAGACGATAGGATGGG 58.761 52.381 0.00 0.00 43.77 4.00
795 810 2.240279 GCTGTAGACGATAGGATGGGT 58.760 52.381 0.00 0.00 43.77 4.51
796 811 3.181437 TGCTGTAGACGATAGGATGGGTA 60.181 47.826 0.00 0.00 43.77 3.69
797 812 3.190953 GCTGTAGACGATAGGATGGGTAC 59.809 52.174 0.00 0.00 43.77 3.34
798 813 3.405831 TGTAGACGATAGGATGGGTACG 58.594 50.000 0.00 0.00 43.77 3.67
1217 1244 2.674754 GTGGGATCCGGCCAAGAA 59.325 61.111 5.45 0.00 0.00 2.52
1230 1257 1.318576 CCAAGAACTGGTTGGTGGAC 58.681 55.000 6.28 0.00 40.78 4.02
1234 1261 2.333701 GAACTGGTTGGTGGACGGGT 62.334 60.000 0.00 0.00 0.00 5.28
1236 1263 2.768769 TGGTTGGTGGACGGGTGA 60.769 61.111 0.00 0.00 0.00 4.02
1355 1621 3.288484 TCGTGCTCGATCTGCCTT 58.712 55.556 6.80 0.00 41.35 4.35
1390 1656 3.842923 CAGCGCGGAGAGGTCCAT 61.843 66.667 8.83 0.00 44.18 3.41
1544 1810 7.939039 TGAAGGAGCTTCGGAATGATATTTATT 59.061 33.333 0.00 0.00 42.78 1.40
1554 1820 9.581289 TCGGAATGATATTTATTTGTGGGTATT 57.419 29.630 0.00 0.00 0.00 1.89
1588 1854 3.482598 CGATCATTTCACGCTGTTCTGAC 60.483 47.826 0.00 0.00 0.00 3.51
1592 1858 0.750249 TTCACGCTGTTCTGACCTCA 59.250 50.000 0.00 0.00 0.00 3.86
1633 1899 2.044555 GCGGTAGGTTTTGGGAGCC 61.045 63.158 0.00 0.00 0.00 4.70
1675 1941 2.171448 AGGCTCGATAGGAAATTGCAGT 59.829 45.455 0.00 0.00 0.00 4.40
1678 1944 4.346129 GCTCGATAGGAAATTGCAGTTTG 58.654 43.478 12.36 0.00 0.00 2.93
1683 1949 1.132881 AGGAAATTGCAGTTTGGGGGA 60.133 47.619 12.36 0.00 0.00 4.81
1710 1976 7.106890 TGGATTTGGTAATTGTGTCTCGATTA 58.893 34.615 0.00 0.00 32.85 1.75
1850 2116 7.708752 TCATTAAATTTTGTTGGAAGTGTGGAC 59.291 33.333 0.00 0.00 0.00 4.02
1950 2219 8.882415 TTAAAGACGATACTCAAAACTTCAGT 57.118 30.769 0.00 0.00 0.00 3.41
1961 2230 6.985059 ACTCAAAACTTCAGTAGTAGTGAACC 59.015 38.462 15.13 0.00 35.54 3.62
2074 2343 6.944096 AGCACACATATATCATCACTAGCAT 58.056 36.000 0.00 0.00 0.00 3.79
2251 2527 3.259625 GGCTCTTCACTTACTTCACTCCT 59.740 47.826 0.00 0.00 0.00 3.69
2351 2630 4.193826 AGCCTGACACTAACACATACAG 57.806 45.455 0.00 0.00 0.00 2.74
2378 2657 0.327259 ACATCTCCACTGCATGCACT 59.673 50.000 18.46 4.91 0.00 4.40
2388 2667 2.288666 CTGCATGCACTAATTACGGGT 58.711 47.619 18.46 0.00 0.00 5.28
2509 2788 1.211457 ACTGATCTGATTCTGGGCCAC 59.789 52.381 0.00 0.00 0.00 5.01
2512 2791 0.467384 ATCTGATTCTGGGCCACGAG 59.533 55.000 0.00 0.00 0.00 4.18
2600 3323 4.800784 TGCATCACAATGAAACATGACAG 58.199 39.130 0.00 0.00 34.61 3.51
2606 3329 5.589855 TCACAATGAAACATGACAGAACACT 59.410 36.000 0.00 0.00 0.00 3.55
2774 3497 6.120378 TCTGTTCTCGTCATGATACTGTAC 57.880 41.667 0.00 0.00 0.00 2.90
3296 4022 9.781633 TTTTAGTTATGTTCTGTTTACCTAGCA 57.218 29.630 0.00 0.00 0.00 3.49
3381 4109 9.777297 ATTTGTTTTGTAGATACTTGCCATTTT 57.223 25.926 0.00 0.00 0.00 1.82
3464 4193 2.633967 TGCTGGAAACATTTGATTGCCT 59.366 40.909 0.00 0.00 41.51 4.75
3548 4313 5.864474 CCGTAACCAGAGTTATCATGCTATC 59.136 44.000 0.00 0.00 40.50 2.08
3549 4314 6.447162 CGTAACCAGAGTTATCATGCTATCA 58.553 40.000 0.00 0.00 40.50 2.15
3550 4315 7.093354 CGTAACCAGAGTTATCATGCTATCAT 58.907 38.462 0.00 0.00 40.50 2.45
3551 4316 7.062722 CGTAACCAGAGTTATCATGCTATCATG 59.937 40.741 0.00 0.00 42.78 3.07
3568 4333 9.571816 TGCTATCATGAATTTGATACAATACCA 57.428 29.630 0.00 0.00 37.51 3.25
3572 4337 8.467963 TCATGAATTTGATACAATACCATGCT 57.532 30.769 0.00 0.00 31.68 3.79
3573 4338 9.571816 TCATGAATTTGATACAATACCATGCTA 57.428 29.630 0.00 0.00 31.68 3.49
3644 4409 1.398390 CAGAGCAACGTTCTTATGCCC 59.602 52.381 0.00 0.00 40.93 5.36
3673 4438 7.739498 TTTGACCCTGTCTTAGTTTAACATC 57.261 36.000 0.00 0.00 33.15 3.06
3726 4493 2.808543 GTGGTTCATCTTGTGTCCAGAC 59.191 50.000 0.00 0.00 35.15 3.51
3727 4494 2.437651 TGGTTCATCTTGTGTCCAGACA 59.562 45.455 0.00 0.00 39.32 3.41
3728 4495 3.072915 TGGTTCATCTTGTGTCCAGACAT 59.927 43.478 3.41 0.00 43.97 3.06
3729 4496 3.686726 GGTTCATCTTGTGTCCAGACATC 59.313 47.826 3.41 0.00 43.97 3.06
3731 4498 4.897509 TCATCTTGTGTCCAGACATCTT 57.102 40.909 3.41 0.00 43.97 2.40
3732 4499 6.166279 GTTCATCTTGTGTCCAGACATCTTA 58.834 40.000 3.41 0.00 43.97 2.10
3733 4500 5.970592 TCATCTTGTGTCCAGACATCTTAG 58.029 41.667 3.41 0.44 43.97 2.18
3737 4504 7.297936 TCTTGTGTCCAGACATCTTAGTTTA 57.702 36.000 3.41 0.00 43.97 2.01
3738 4505 7.152645 TCTTGTGTCCAGACATCTTAGTTTAC 58.847 38.462 3.41 0.00 43.97 2.01
3740 4507 6.455647 TGTGTCCAGACATCTTAGTTTACTG 58.544 40.000 3.41 0.00 43.97 2.74
3741 4508 6.041637 TGTGTCCAGACATCTTAGTTTACTGT 59.958 38.462 3.41 0.00 43.97 3.55
3743 4510 7.441458 GTGTCCAGACATCTTAGTTTACTGTTT 59.559 37.037 3.41 0.00 43.97 2.83
3744 4511 8.644216 TGTCCAGACATCTTAGTTTACTGTTTA 58.356 33.333 0.00 0.00 36.21 2.01
3745 4512 9.654663 GTCCAGACATCTTAGTTTACTGTTTAT 57.345 33.333 0.00 0.00 0.00 1.40
3766 4533 9.890352 GTTTATTCATCTTAATCATCAAGCTCC 57.110 33.333 0.00 0.00 0.00 4.70
3767 4534 8.627208 TTATTCATCTTAATCATCAAGCTCCC 57.373 34.615 0.00 0.00 0.00 4.30
3768 4535 5.635278 TCATCTTAATCATCAAGCTCCCA 57.365 39.130 0.00 0.00 0.00 4.37
3769 4536 6.196918 TCATCTTAATCATCAAGCTCCCAT 57.803 37.500 0.00 0.00 0.00 4.00
3770 4537 6.002082 TCATCTTAATCATCAAGCTCCCATG 58.998 40.000 0.00 0.00 0.00 3.66
3772 4539 5.618236 TCTTAATCATCAAGCTCCCATGAG 58.382 41.667 0.00 0.00 41.84 2.90
3895 4818 8.341173 CAGCCTATTTGTAAATCATCTGAGTTC 58.659 37.037 0.00 0.00 34.03 3.01
3972 4896 4.458295 TCCTGACGAGAAGGTAGTTACTTG 59.542 45.833 0.00 0.00 36.14 3.16
4161 5355 4.873746 CTCTCCACAGAGTTAGTTTCCA 57.126 45.455 0.00 0.00 41.40 3.53
4200 5394 9.998106 TGGACAGATAGCTTTTATATAAAGGTC 57.002 33.333 16.16 10.03 38.68 3.85
4227 5421 7.341445 ACTTTTGTCCTGTAAATTTGTAGCA 57.659 32.000 0.00 0.00 0.00 3.49
4310 5504 6.465321 GGGCCATAGCTAGTTCCTGTTATTTA 60.465 42.308 4.39 0.00 39.73 1.40
4405 5608 8.836413 TGAAAATGGTAACTTAGAACTCTGTTG 58.164 33.333 0.00 0.00 37.61 3.33
4452 5656 8.915057 AAGTGATCCGATAAAATCAGATGAAT 57.085 30.769 0.00 0.00 32.76 2.57
4486 5690 2.806945 ATCCTTTTGCGATGAAGGGA 57.193 45.000 4.83 5.53 42.17 4.20
4719 5934 4.734398 ACAGTCATTCCTGTCATCTCTC 57.266 45.455 0.00 0.00 41.84 3.20
4898 6113 6.569179 TGTTGCTAAATGTTTTACCCTCTC 57.431 37.500 0.00 0.00 0.00 3.20
5445 6660 4.142271 ACCTCTTGTCTATTTCTGCTCTCG 60.142 45.833 0.00 0.00 0.00 4.04
5485 6700 4.890158 TGTCCATACTGTGATGTTGTCT 57.110 40.909 0.00 0.00 0.00 3.41
5993 7209 5.728471 TCAGATGTCAAAGATTGAGAGGTC 58.272 41.667 0.00 0.00 41.01 3.85
6043 7259 4.818546 CCATTTAGGAACAGAGGCAGTATG 59.181 45.833 0.00 0.00 41.22 2.39
6074 7290 8.075593 TGTAACGTCATCTAAACTTAACAACC 57.924 34.615 0.00 0.00 0.00 3.77
6287 7524 6.102663 CACAATCAAACCAACAAAACCACTA 58.897 36.000 0.00 0.00 0.00 2.74
6308 7545 2.489329 ACCTCGCTCATGTTTTGAATGG 59.511 45.455 0.00 0.00 32.78 3.16
6516 7753 3.181434 ACCCTAAAAAGGATGCTGTGACA 60.181 43.478 0.00 0.00 0.00 3.58
6562 7799 5.024118 CCCTCCGTCCCATAATATAAGAGT 58.976 45.833 0.00 0.00 0.00 3.24
6569 7806 8.342634 CCGTCCCATAATATAAGAGTGTTTTTG 58.657 37.037 0.00 0.00 0.00 2.44
6685 7922 3.326588 TCCAAATCTCCTGAGGTTTTCGA 59.673 43.478 2.67 0.11 39.57 3.71
6716 7953 1.545136 TGTTGGTTGCACATGCTATGG 59.455 47.619 5.31 0.00 42.66 2.74
6730 7970 4.864704 TGCTATGGCGTAATATGAGTCA 57.135 40.909 0.00 0.00 42.25 3.41
7094 8336 3.161866 GGAGAACCCAACATTTTGCCTA 58.838 45.455 0.00 0.00 34.14 3.93
7271 8513 2.224159 AGAATCCACACCCGCACCT 61.224 57.895 0.00 0.00 0.00 4.00
7428 8670 6.270064 AGTTAAAACTTCACATTTGGAACCG 58.730 36.000 0.00 0.00 35.21 4.44
7504 8746 3.861263 GCGCGCTAAACTTCCGGG 61.861 66.667 26.67 0.00 37.87 5.73
7562 8804 4.222366 AGGGAAAACGTTTTGGTTTGGTTA 59.778 37.500 29.67 0.00 39.88 2.85
7623 8865 3.699538 GGGATATTTGAAGTTTCGCCCTT 59.300 43.478 0.00 0.00 0.00 3.95
7688 9566 0.319900 ATCGGTCTGCATATGGTCGC 60.320 55.000 4.56 0.00 0.00 5.19
7826 9704 3.315470 TGGACGATCACCGAAGAATAGAG 59.685 47.826 0.00 0.00 41.76 2.43
7829 9707 5.278561 GGACGATCACCGAAGAATAGAGAAT 60.279 44.000 0.00 0.00 41.76 2.40
7838 9716 8.818057 CACCGAAGAATAGAGAATCGTTATTTT 58.182 33.333 0.00 0.00 42.67 1.82
7869 9747 6.543465 CCATGTAGAAAGGAATGTGCTTATGA 59.457 38.462 0.00 0.00 0.00 2.15
7871 9749 6.946340 TGTAGAAAGGAATGTGCTTATGAGA 58.054 36.000 0.00 0.00 0.00 3.27
7872 9750 7.568349 TGTAGAAAGGAATGTGCTTATGAGAT 58.432 34.615 0.00 0.00 0.00 2.75
7873 9751 6.939132 AGAAAGGAATGTGCTTATGAGATG 57.061 37.500 0.00 0.00 0.00 2.90
7874 9752 6.656902 AGAAAGGAATGTGCTTATGAGATGA 58.343 36.000 0.00 0.00 0.00 2.92
7911 9972 1.781025 CGCAAGCCTTTTGTCCGTCA 61.781 55.000 0.00 0.00 0.00 4.35
7915 9976 0.537143 AGCCTTTTGTCCGTCATGCA 60.537 50.000 0.00 0.00 0.00 3.96
7933 9994 2.868253 ACGCCAGTGATTTTAGGGC 58.132 52.632 0.00 0.00 41.20 5.19
7945 10006 3.402628 TTTTAGGGCTCGATCATAGGC 57.597 47.619 9.47 9.47 38.73 3.93
8124 10212 5.656416 TGGAAAGACAATGAGACCAAAAACT 59.344 36.000 0.00 0.00 0.00 2.66
8132 10221 7.264947 ACAATGAGACCAAAAACTACCAAAAG 58.735 34.615 0.00 0.00 0.00 2.27
8258 10348 6.658831 CAAATGTCCCGTATGCAATAACTAG 58.341 40.000 0.00 0.00 0.00 2.57
8304 10394 6.725246 AGTAACAGTCAAGAAAACATTTCCG 58.275 36.000 0.00 0.00 0.00 4.30
8305 10395 3.964909 ACAGTCAAGAAAACATTTCCGC 58.035 40.909 0.00 0.00 0.00 5.54
8331 10421 6.618379 GCAACACAAAACAACTTGAAAGAAGG 60.618 38.462 0.00 0.00 0.00 3.46
8363 10456 1.069513 TCAAACCACGAGACGGTCAAT 59.930 47.619 11.27 0.00 34.99 2.57
8449 10542 2.286523 CCTCACAGGCCCTTCGTCT 61.287 63.158 0.00 0.00 0.00 4.18
8467 10560 3.257469 TCTGTGCTGGATCAGACATTC 57.743 47.619 0.00 0.00 36.04 2.67
8486 10579 4.737855 TTCTCGAGGTAGGAAAAGGATG 57.262 45.455 13.56 0.00 0.00 3.51
8487 10580 3.031736 TCTCGAGGTAGGAAAAGGATGG 58.968 50.000 13.56 0.00 0.00 3.51
8528 10623 0.942252 CATCGCCATCATCACCTGTG 59.058 55.000 0.00 0.00 0.00 3.66
8554 10650 3.512680 CTGCTAGAGAACCAAACCTACG 58.487 50.000 0.00 0.00 0.00 3.51
8593 10690 4.426704 AGAGCTAAGAAACCACTCCCTTA 58.573 43.478 0.00 0.00 0.00 2.69
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
5 6 4.268644 CAGCACATCCTTGTAGTAACATCG 59.731 45.833 0.00 0.00 34.97 3.84
10 11 4.564821 GGTTCCAGCACATCCTTGTAGTAA 60.565 45.833 0.00 0.00 33.76 2.24
11 12 3.055385 GGTTCCAGCACATCCTTGTAGTA 60.055 47.826 0.00 0.00 33.76 1.82
12 13 2.290323 GGTTCCAGCACATCCTTGTAGT 60.290 50.000 0.00 0.00 33.76 2.73
17 18 0.606401 CACGGTTCCAGCACATCCTT 60.606 55.000 0.00 0.00 0.00 3.36
19 20 0.036765 TACACGGTTCCAGCACATCC 60.037 55.000 0.00 0.00 0.00 3.51
37 38 1.540797 GGTTGTAACACCACCAGCGTA 60.541 52.381 0.00 0.00 36.73 4.42
39 40 1.837538 CGGTTGTAACACCACCAGCG 61.838 60.000 2.60 0.00 36.49 5.18
41 42 0.941542 CACGGTTGTAACACCACCAG 59.058 55.000 2.60 0.00 36.49 4.00
50 51 1.410517 TCCCAACGTACACGGTTGTAA 59.589 47.619 6.72 0.00 44.95 2.41
55 56 0.245539 CATCTCCCAACGTACACGGT 59.754 55.000 6.72 0.00 44.95 4.83
56 57 0.459585 CCATCTCCCAACGTACACGG 60.460 60.000 6.72 0.00 44.95 4.94
58 59 2.344025 GTTCCATCTCCCAACGTACAC 58.656 52.381 0.00 0.00 0.00 2.90
60 61 1.738030 CGGTTCCATCTCCCAACGTAC 60.738 57.143 0.00 0.00 0.00 3.67
76 77 2.360350 CTCCTGGCATGCACGGTT 60.360 61.111 21.36 0.00 0.00 4.44
88 89 2.600731 CGTGACTTGTTCTAGCTCCTG 58.399 52.381 0.00 0.00 0.00 3.86
92 93 1.009389 GCGCGTGACTTGTTCTAGCT 61.009 55.000 8.43 0.00 0.00 3.32
96 97 0.941463 CTCTGCGCGTGACTTGTTCT 60.941 55.000 8.43 0.00 0.00 3.01
102 103 0.243907 ATGTAACTCTGCGCGTGACT 59.756 50.000 8.43 0.00 0.00 3.41
108 109 0.736325 ACACCGATGTAACTCTGCGC 60.736 55.000 0.00 0.00 37.26 6.09
111 112 2.913777 TCGACACCGATGTAACTCTG 57.086 50.000 0.00 0.00 39.95 3.35
150 151 0.170561 ACATCCGTAGCACTGTCGAC 59.829 55.000 9.11 9.11 0.00 4.20
156 157 1.825474 AGCTTACACATCCGTAGCACT 59.175 47.619 0.00 0.00 0.00 4.40
158 159 1.134818 CCAGCTTACACATCCGTAGCA 60.135 52.381 0.00 0.00 0.00 3.49
164 165 2.359900 CAGTTCCCAGCTTACACATCC 58.640 52.381 0.00 0.00 0.00 3.51
165 166 2.027192 TCCAGTTCCCAGCTTACACATC 60.027 50.000 0.00 0.00 0.00 3.06
166 167 1.985159 TCCAGTTCCCAGCTTACACAT 59.015 47.619 0.00 0.00 0.00 3.21
167 168 1.429930 TCCAGTTCCCAGCTTACACA 58.570 50.000 0.00 0.00 0.00 3.72
168 169 2.152016 GTTCCAGTTCCCAGCTTACAC 58.848 52.381 0.00 0.00 0.00 2.90
171 172 1.351017 CCAGTTCCAGTTCCCAGCTTA 59.649 52.381 0.00 0.00 0.00 3.09
173 174 1.062488 ACCAGTTCCAGTTCCCAGCT 61.062 55.000 0.00 0.00 0.00 4.24
177 178 0.472471 TGTCACCAGTTCCAGTTCCC 59.528 55.000 0.00 0.00 0.00 3.97
182 183 0.104120 TCGTGTGTCACCAGTTCCAG 59.896 55.000 0.00 0.00 0.00 3.86
185 186 1.859080 GACTTCGTGTGTCACCAGTTC 59.141 52.381 0.00 0.00 34.80 3.01
188 189 3.659850 TGACTTCGTGTGTCACCAG 57.340 52.632 0.00 0.00 39.23 4.00
240 241 1.796151 CATGGTTGTAGCACTGCCG 59.204 57.895 0.00 0.00 0.00 5.69
258 259 1.520342 GTCCCAGCTCTCGATGTGC 60.520 63.158 0.00 0.00 35.59 4.57
259 260 1.142748 GGTCCCAGCTCTCGATGTG 59.857 63.158 0.00 0.00 0.00 3.21
262 263 3.947173 CTGGTCCCAGCTCTCGAT 58.053 61.111 0.00 0.00 37.24 3.59
278 279 2.029666 GCAGCTCCACACGTCACT 59.970 61.111 0.00 0.00 0.00 3.41
279 280 1.630244 GATGCAGCTCCACACGTCAC 61.630 60.000 0.00 0.00 0.00 3.67
298 299 1.531677 CGCATCATTTTGTAGGCACCG 60.532 52.381 0.00 0.00 0.00 4.94
314 315 1.596203 CTCGCATGATGGGTCGCAT 60.596 57.895 9.39 1.31 0.00 4.73
317 318 1.300465 CTCCTCGCATGATGGGTCG 60.300 63.158 9.39 2.53 0.00 4.79
319 320 0.107508 CAACTCCTCGCATGATGGGT 60.108 55.000 9.39 0.00 0.00 4.51
331 332 2.236395 CCTGTTACCGATTCCAACTCCT 59.764 50.000 0.00 0.00 0.00 3.69
336 337 1.364269 ACCCCTGTTACCGATTCCAA 58.636 50.000 0.00 0.00 0.00 3.53
346 347 1.228306 CCGGTTGCAACCCCTGTTA 60.228 57.895 36.75 0.00 46.53 2.41
351 352 3.292159 GTCACCGGTTGCAACCCC 61.292 66.667 36.75 18.43 46.53 4.95
368 371 2.580867 GCTGTCGCGGCTCTAGTG 60.581 66.667 13.81 0.00 32.24 2.74
369 372 2.636412 TTGCTGTCGCGGCTCTAGT 61.636 57.895 13.81 0.00 39.65 2.57
370 373 2.161486 GTTGCTGTCGCGGCTCTAG 61.161 63.158 13.81 1.32 39.65 2.43
372 375 3.996124 AGTTGCTGTCGCGGCTCT 61.996 61.111 13.81 5.38 39.65 4.09
388 391 3.767230 CACGTTGGCTCGACGCAG 61.767 66.667 13.00 4.86 44.18 5.18
392 395 4.077188 GCAGCACGTTGGCTCGAC 62.077 66.667 9.26 2.23 43.68 4.20
498 501 4.731612 ACGGCTGACAGCAGAGCG 62.732 66.667 30.48 24.05 44.75 5.03
499 502 3.117171 CACGGCTGACAGCAGAGC 61.117 66.667 30.48 12.33 44.75 4.09
500 503 2.218037 TAGCACGGCTGACAGCAGAG 62.218 60.000 30.48 24.05 44.75 3.35
501 504 2.218037 CTAGCACGGCTGACAGCAGA 62.218 60.000 30.48 10.12 44.75 4.26
503 506 1.815817 TTCTAGCACGGCTGACAGCA 61.816 55.000 27.87 6.26 44.75 4.41
525 529 2.887152 GTCTCAACAGCACCATTTTCCT 59.113 45.455 0.00 0.00 0.00 3.36
528 532 3.996150 CTGTCTCAACAGCACCATTTT 57.004 42.857 0.00 0.00 46.01 1.82
540 544 1.367471 CTGTCGCACCCTGTCTCAA 59.633 57.895 0.00 0.00 0.00 3.02
548 552 3.127533 GCCATGACTGTCGCACCC 61.128 66.667 2.98 0.00 0.00 4.61
550 554 3.171987 CAGCCATGACTGTCGCAC 58.828 61.111 0.04 0.00 32.78 5.34
556 560 2.014857 CTCCATTGACAGCCATGACTG 58.985 52.381 7.56 7.56 43.59 3.51
559 563 1.211212 CTCCTCCATTGACAGCCATGA 59.789 52.381 0.00 0.00 0.00 3.07
566 570 1.629861 TGACATGCTCCTCCATTGACA 59.370 47.619 0.00 0.00 0.00 3.58
570 574 0.463295 CGCTGACATGCTCCTCCATT 60.463 55.000 0.00 0.00 0.00 3.16
592 596 0.667487 GCTCGCGCATGGAATAGCTA 60.667 55.000 8.75 0.00 35.78 3.32
603 607 3.049674 CTTTCCAAGGCTCGCGCA 61.050 61.111 8.75 0.00 38.10 6.09
613 617 6.603201 AGAAAATCTTGTGTGTCTCTTTCCAA 59.397 34.615 0.00 0.00 0.00 3.53
621 625 3.733337 AGCGAGAAAATCTTGTGTGTCT 58.267 40.909 0.00 0.00 30.44 3.41
623 627 2.808543 GGAGCGAGAAAATCTTGTGTGT 59.191 45.455 0.00 0.00 30.44 3.72
624 628 2.807967 TGGAGCGAGAAAATCTTGTGTG 59.192 45.455 0.00 0.00 30.44 3.82
625 629 3.126001 TGGAGCGAGAAAATCTTGTGT 57.874 42.857 0.00 0.00 30.44 3.72
626 630 3.181503 CCATGGAGCGAGAAAATCTTGTG 60.182 47.826 5.56 0.00 30.44 3.33
627 631 3.012518 CCATGGAGCGAGAAAATCTTGT 58.987 45.455 5.56 0.00 30.44 3.16
628 632 2.357009 CCCATGGAGCGAGAAAATCTTG 59.643 50.000 15.22 0.00 0.00 3.02
629 633 2.025887 ACCCATGGAGCGAGAAAATCTT 60.026 45.455 15.22 0.00 0.00 2.40
630 634 1.561542 ACCCATGGAGCGAGAAAATCT 59.438 47.619 15.22 0.00 0.00 2.40
631 635 1.672881 CACCCATGGAGCGAGAAAATC 59.327 52.381 15.22 0.00 0.00 2.17
645 659 1.336887 CGTTTCTCGAGTGTCACCCAT 60.337 52.381 13.13 0.00 42.86 4.00
657 671 0.937699 TGCAACTCCGTCGTTTCTCG 60.938 55.000 0.00 0.00 41.41 4.04
678 692 2.785681 GCGTGATCAAAGTCGCATGAAG 60.786 50.000 19.84 0.00 46.40 3.02
686 700 1.696832 GGAGCCGCGTGATCAAAGTC 61.697 60.000 4.92 0.00 0.00 3.01
706 720 4.752101 CAGAATATCAAATCGGTGACCCTC 59.248 45.833 0.00 0.00 0.00 4.30
745 760 0.110104 AGGAGATGGGCAATGCTAGC 59.890 55.000 8.10 8.10 0.00 3.42
870 886 1.539496 GGTGGTTCACGCTTCACTGTA 60.539 52.381 0.00 0.00 34.83 2.74
1143 1170 3.749064 GCGAGGGCGAGACTGTCA 61.749 66.667 10.88 0.00 40.82 3.58
1175 1202 2.597805 TCGGCGATAGAGGGCTCC 60.598 66.667 4.99 0.00 39.76 4.70
1217 1244 2.770904 ACCCGTCCACCAACCAGT 60.771 61.111 0.00 0.00 0.00 4.00
1230 1257 4.135153 CGTGCTCCTCCTCACCCG 62.135 72.222 0.00 0.00 0.00 5.28
1307 1573 2.364317 TCCTCCTTCCCGCCAGAG 60.364 66.667 0.00 0.00 0.00 3.35
1308 1574 2.364317 CTCCTCCTTCCCGCCAGA 60.364 66.667 0.00 0.00 0.00 3.86
1340 1606 1.416813 CGTCAAGGCAGATCGAGCAC 61.417 60.000 2.38 0.00 0.00 4.40
1438 1704 0.460284 ACGCATCAACAGATCGGACC 60.460 55.000 0.00 0.00 0.00 4.46
1544 1810 3.306641 GCAATTCAGCCAAATACCCACAA 60.307 43.478 0.00 0.00 0.00 3.33
1554 1820 3.193056 TGAAATGATCGCAATTCAGCCAA 59.807 39.130 0.00 0.00 38.61 4.52
1588 1854 3.181485 GGATACTGGAACTTCGTCTGAGG 60.181 52.174 0.00 0.00 0.00 3.86
1592 1858 1.749634 CGGGATACTGGAACTTCGTCT 59.250 52.381 0.00 0.00 40.24 4.18
1633 1899 6.480320 AGCCTGAGTAAGATAACGCAAAATAG 59.520 38.462 0.00 0.00 0.00 1.73
1675 1941 0.863956 ACCAAATCCAGTCCCCCAAA 59.136 50.000 0.00 0.00 0.00 3.28
1678 1944 3.031013 CAATTACCAAATCCAGTCCCCC 58.969 50.000 0.00 0.00 0.00 5.40
1683 1949 4.695455 CGAGACACAATTACCAAATCCAGT 59.305 41.667 0.00 0.00 0.00 4.00
1710 1976 4.941873 CCGAAATAACAAAGAGGCTAGGTT 59.058 41.667 0.00 0.00 0.00 3.50
1850 2116 3.878103 CTCATCAAGATCAGCCTCCAAAG 59.122 47.826 0.00 0.00 0.00 2.77
1961 2230 2.227388 GACTGCTTGATGAAACCACCAG 59.773 50.000 0.00 0.00 0.00 4.00
2180 2449 6.127479 ACTCAATTGTGTGCTGTTTCCTTAAA 60.127 34.615 12.15 0.00 0.00 1.52
2181 2450 5.359576 ACTCAATTGTGTGCTGTTTCCTTAA 59.640 36.000 12.15 0.00 0.00 1.85
2188 2464 2.358898 GTGGACTCAATTGTGTGCTGTT 59.641 45.455 25.73 0.59 32.34 3.16
2251 2527 3.002791 GTGCTAGTGCTGAAACTATGCA 58.997 45.455 0.00 0.00 40.48 3.96
2351 2630 0.392193 CAGTGGAGATGTGGCCTGAC 60.392 60.000 3.32 0.00 0.00 3.51
2509 2788 0.673333 TAGTTGCATGTGTGGCCTCG 60.673 55.000 3.32 0.00 0.00 4.63
2512 2791 0.958091 TGTTAGTTGCATGTGTGGCC 59.042 50.000 0.00 0.00 0.00 5.36
2600 3323 7.307811 GGAGTTAACCATGTTGTCTAAGTGTTC 60.308 40.741 0.88 0.00 0.00 3.18
2606 3329 6.358178 TGTTGGAGTTAACCATGTTGTCTAA 58.642 36.000 0.88 0.00 39.82 2.10
2757 3480 6.247727 AGCATAGTACAGTATCATGACGAG 57.752 41.667 0.00 0.00 0.00 4.18
2970 3695 4.380761 CCGATCCAATGCAATCTGAAAACA 60.381 41.667 0.00 0.00 0.00 2.83
3431 4160 7.810766 AATGTTTCCAGCAAAAATATGTACG 57.189 32.000 0.00 0.00 0.00 3.67
3560 4325 8.978874 TCAAAGTCATAATAGCATGGTATTGT 57.021 30.769 31.03 24.76 0.00 2.71
3565 4330 8.978874 TTGTATCAAAGTCATAATAGCATGGT 57.021 30.769 1.62 1.62 0.00 3.55
3573 4338 9.283768 TCGGCAATATTGTATCAAAGTCATAAT 57.716 29.630 16.61 0.00 0.00 1.28
3574 4339 8.669946 TCGGCAATATTGTATCAAAGTCATAA 57.330 30.769 16.61 0.00 0.00 1.90
3644 4409 6.405278 AAACTAAGACAGGGTCAAAATTGG 57.595 37.500 0.00 0.00 34.60 3.16
3740 4507 9.890352 GGAGCTTGATGATTAAGATGAATAAAC 57.110 33.333 0.68 0.00 0.00 2.01
3741 4508 9.071276 GGGAGCTTGATGATTAAGATGAATAAA 57.929 33.333 0.68 0.00 0.00 1.40
3743 4510 7.748677 TGGGAGCTTGATGATTAAGATGAATA 58.251 34.615 0.68 0.00 0.00 1.75
3744 4511 6.607970 TGGGAGCTTGATGATTAAGATGAAT 58.392 36.000 0.68 0.00 0.00 2.57
3745 4512 6.005066 TGGGAGCTTGATGATTAAGATGAA 57.995 37.500 0.68 0.00 0.00 2.57
3746 4513 5.635278 TGGGAGCTTGATGATTAAGATGA 57.365 39.130 0.68 0.00 0.00 2.92
3747 4514 6.002082 TCATGGGAGCTTGATGATTAAGATG 58.998 40.000 0.68 0.00 0.00 2.90
3748 4515 6.196918 TCATGGGAGCTTGATGATTAAGAT 57.803 37.500 0.68 0.00 0.00 2.40
3749 4516 5.618236 CTCATGGGAGCTTGATGATTAAGA 58.382 41.667 0.68 0.00 33.67 2.10
3750 4517 5.943706 CTCATGGGAGCTTGATGATTAAG 57.056 43.478 0.00 0.00 33.67 1.85
3763 4530 0.036010 ACTGGTTTCGCTCATGGGAG 60.036 55.000 0.00 0.00 44.33 4.30
3765 4532 0.606401 ACACTGGTTTCGCTCATGGG 60.606 55.000 0.00 0.00 0.00 4.00
3766 4533 2.002586 CTACACTGGTTTCGCTCATGG 58.997 52.381 0.00 0.00 0.00 3.66
3767 4534 2.668457 GTCTACACTGGTTTCGCTCATG 59.332 50.000 0.00 0.00 0.00 3.07
3768 4535 2.353803 GGTCTACACTGGTTTCGCTCAT 60.354 50.000 0.00 0.00 0.00 2.90
3769 4536 1.000506 GGTCTACACTGGTTTCGCTCA 59.999 52.381 0.00 0.00 0.00 4.26
3770 4537 1.272769 AGGTCTACACTGGTTTCGCTC 59.727 52.381 0.00 0.00 0.00 5.03
3772 4539 1.270147 ACAGGTCTACACTGGTTTCGC 60.270 52.381 0.00 0.00 40.23 4.70
3773 4540 2.035449 TCACAGGTCTACACTGGTTTCG 59.965 50.000 0.00 0.00 40.23 3.46
3774 4541 3.391049 GTCACAGGTCTACACTGGTTTC 58.609 50.000 0.00 0.00 40.23 2.78
3895 4818 9.640974 CAGCAAACAAACAATCAAGAATAAAAG 57.359 29.630 0.00 0.00 0.00 2.27
3953 4877 5.766222 TGAACAAGTAACTACCTTCTCGTC 58.234 41.667 0.00 0.00 0.00 4.20
3988 5182 4.039973 AGAATGGGCATGCAGGAATAAATG 59.960 41.667 21.36 0.00 0.00 2.32
4200 5394 9.394477 GCTACAAATTTACAGGACAAAAGTAAG 57.606 33.333 0.00 0.00 0.00 2.34
4227 5421 7.982354 GTGAAATATTTGAGCTACTAGACCTGT 59.018 37.037 5.17 0.00 0.00 4.00
4452 5656 6.293735 CGCAAAAGGATAAACTGACAAAGGTA 60.294 38.462 0.00 0.00 0.00 3.08
4486 5690 4.085357 TCCAGAGTTGCACATTGTTAGT 57.915 40.909 0.00 0.00 0.00 2.24
4719 5934 3.865446 TGACTGACTGATACTGGCATTG 58.135 45.455 0.00 0.00 0.00 2.82
4898 6113 0.182299 GATTCTCCTTCCCTGGCAGG 59.818 60.000 27.04 27.04 34.30 4.85
4981 6196 8.727100 ATATATCCAGACATGTTTAGACCTCA 57.273 34.615 0.00 0.00 0.00 3.86
5238 6453 2.795231 ATGATGGAAGTCAGTGGGTG 57.205 50.000 0.00 0.00 0.00 4.61
5248 6463 2.294233 CGCCCAATGGTTATGATGGAAG 59.706 50.000 0.00 0.00 34.82 3.46
5445 6660 5.221641 TGGACATGCCCTAATAGTATGTCAC 60.222 44.000 19.02 11.44 45.73 3.67
5485 6700 1.186200 AGATGGCAACGCTAGAGACA 58.814 50.000 0.00 0.00 42.51 3.41
5993 7209 4.913924 GTGTTTTAGAAAGCATGCAGTCAG 59.086 41.667 21.98 0.00 31.84 3.51
6037 7253 7.700322 AGATGACGTTACAATAAGCATACTG 57.300 36.000 0.00 0.00 0.00 2.74
6074 7290 3.370672 GTGCTTCCAACCAACAACTTTTG 59.629 43.478 0.00 0.00 0.00 2.44
6287 7524 2.489329 CCATTCAAAACATGAGCGAGGT 59.511 45.455 0.00 0.00 39.77 3.85
6516 7753 5.165961 AGTAGGTCACAGTAAATGCACAT 57.834 39.130 0.00 0.00 0.00 3.21
6685 7922 4.522405 TGTGCAACCAACATAGCATAACTT 59.478 37.500 0.00 0.00 39.43 2.66
6716 7953 5.453648 CAGACTACCTGACTCATATTACGC 58.546 45.833 0.00 0.00 45.78 4.42
6730 7970 4.484912 AGTTTCAGACTTCCAGACTACCT 58.515 43.478 0.00 0.00 33.92 3.08
7271 8513 1.202806 CCAAAGAGTCTCCTTGGTGCA 60.203 52.381 18.71 0.00 0.00 4.57
7274 8516 0.402121 GCCCAAAGAGTCTCCTTGGT 59.598 55.000 23.13 0.00 0.00 3.67
7428 8670 5.335976 CCCATCTTTTCTTACAAGCAACTCC 60.336 44.000 0.00 0.00 0.00 3.85
7469 8711 1.269998 CGCAAACCCGGTTTAATTCCA 59.730 47.619 15.31 0.00 33.70 3.53
7504 8746 2.010497 GTTTCTCCCTCGCAGAATTCC 58.990 52.381 0.65 0.00 34.09 3.01
7562 8804 4.182693 TGTACGAGACGGAATTCACATT 57.817 40.909 7.93 0.00 0.00 2.71
7609 8851 2.096248 ACAACAAAGGGCGAAACTTCA 58.904 42.857 0.00 0.00 0.00 3.02
7623 8865 6.899393 AAAGCAGATAGGAAATCACAACAA 57.101 33.333 0.00 0.00 0.00 2.83
7688 9566 4.454504 AGTTAAGAAAGTAATGTGGCACGG 59.545 41.667 13.77 0.00 0.00 4.94
7838 9716 6.374333 GCACATTCCTTTCTACATGGTAGAAA 59.626 38.462 22.92 22.92 40.15 2.52
7850 9728 6.656902 TCATCTCATAAGCACATTCCTTTCT 58.343 36.000 0.00 0.00 0.00 2.52
7886 9764 0.385390 ACAAAAGGCTTGCGGAGTTG 59.615 50.000 0.00 2.83 0.00 3.16
7891 9769 2.255252 CGGACAAAAGGCTTGCGG 59.745 61.111 0.00 0.00 0.00 5.69
7892 9770 1.082104 GACGGACAAAAGGCTTGCG 60.082 57.895 0.00 0.00 0.00 4.85
7911 9972 1.745087 CCTAAAATCACTGGCGTGCAT 59.255 47.619 0.00 0.00 40.99 3.96
7915 9976 0.328258 AGCCCTAAAATCACTGGCGT 59.672 50.000 0.00 0.00 46.67 5.68
7933 9994 1.154131 CGGAGCGCCTATGATCGAG 60.154 63.158 2.29 0.00 0.00 4.04
7945 10006 3.814049 GATTGCTTCAATCGGAGCG 57.186 52.632 4.09 0.00 40.33 5.03
8080 10144 9.760077 CTTTCCAGTTGTACCGTCTATTATTAT 57.240 33.333 0.00 0.00 0.00 1.28
8081 10145 8.970020 TCTTTCCAGTTGTACCGTCTATTATTA 58.030 33.333 0.00 0.00 0.00 0.98
8211 10300 7.176285 TGCACATGTTTCTTTTCTTAATTGC 57.824 32.000 0.00 0.00 0.00 3.56
8216 10305 7.437862 GGACATTTGCACATGTTTCTTTTCTTA 59.562 33.333 18.99 0.00 37.52 2.10
8238 10327 4.498513 CGACTAGTTATTGCATACGGGACA 60.499 45.833 0.00 0.00 0.00 4.02
8258 10348 3.707793 AGATCTTATTTCTGGCGACGAC 58.292 45.455 0.00 0.00 0.00 4.34
8304 10394 1.989165 TCAAGTTGTTTTGTGTTGCGC 59.011 42.857 0.00 0.00 0.00 6.09
8305 10395 4.384247 TCTTTCAAGTTGTTTTGTGTTGCG 59.616 37.500 2.11 0.00 0.00 4.85
8331 10421 0.672401 TGGTTTGACGGCTTCGATCC 60.672 55.000 0.00 2.15 37.63 3.36
8357 10450 2.160417 CAGTCGGAAGAAGCAATTGACC 59.840 50.000 10.34 1.41 45.01 4.02
8358 10451 3.067106 TCAGTCGGAAGAAGCAATTGAC 58.933 45.455 10.34 0.30 45.01 3.18
8363 10456 1.138069 TGTGTCAGTCGGAAGAAGCAA 59.862 47.619 0.00 0.00 45.01 3.91
8421 10514 1.141053 GGCCTGTGAGGGTAGGTATTG 59.859 57.143 0.00 0.00 35.37 1.90
8424 10517 1.002533 GGGCCTGTGAGGGTAGGTA 59.997 63.158 0.84 0.00 35.37 3.08
8449 10542 2.417787 CGAGAATGTCTGATCCAGCACA 60.418 50.000 0.00 0.00 0.00 4.57
8467 10560 2.103263 CCCATCCTTTTCCTACCTCGAG 59.897 54.545 5.13 5.13 0.00 4.04
8486 10579 2.433239 TGCGTTAGAATAAGGTCTCCCC 59.567 50.000 0.00 0.00 0.00 4.81
8487 10580 3.814005 TGCGTTAGAATAAGGTCTCCC 57.186 47.619 0.00 0.00 0.00 4.30
8501 10596 2.068519 GATGATGGCGATGATGCGTTA 58.931 47.619 0.00 0.00 35.06 3.18
8528 10623 2.680339 GTTTGGTTCTCTAGCAGCATCC 59.320 50.000 0.00 0.00 35.32 3.51
8554 10650 3.712218 AGCTCTTGTAGGTCCTATTTCCC 59.288 47.826 0.82 0.00 0.00 3.97


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

AutoCloner maintained by Alex Coulton.