Multiple sequence alignment - TraesCS7A01G366900

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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 TraesCS7A01G366900 chr7A 100.000 2378 0 0 1 2378 540749667 540747290 0.000000e+00 4392.0
1 TraesCS7A01G366900 chr7A 89.362 94 10 0 998 1091 540766704 540766611 4.150000e-23 119.0
2 TraesCS7A01G366900 chr7A 92.157 51 4 0 658 708 540748968 540748918 3.280000e-09 73.1
3 TraesCS7A01G366900 chr7A 92.157 51 4 0 700 750 540749010 540748960 3.280000e-09 73.1
4 TraesCS7A01G366900 chr7D 89.194 583 47 9 1196 1777 459475900 459476467 0.000000e+00 713.0
5 TraesCS7A01G366900 chr7D 87.310 591 41 10 1802 2378 459476769 459477339 0.000000e+00 645.0
6 TraesCS7A01G366900 chr7D 83.721 516 41 21 700 1186 459475242 459475743 4.660000e-122 448.0
7 TraesCS7A01G366900 chr7D 93.548 248 15 1 1 248 459473085 459473331 3.730000e-98 368.0
8 TraesCS7A01G366900 chr2A 89.398 415 42 2 1966 2378 758682311 758681897 2.710000e-144 521.0
9 TraesCS7A01G366900 chr2A 85.579 423 54 7 1960 2377 685747930 685748350 1.010000e-118 436.0
10 TraesCS7A01G366900 chr2A 100.000 41 0 0 1798 1838 359076436 359076396 2.530000e-10 76.8
11 TraesCS7A01G366900 chr7B 85.598 493 40 11 704 1183 481660361 481660835 2.750000e-134 488.0
12 TraesCS7A01G366900 chr7B 93.145 248 16 1 1 248 481623990 481624236 1.740000e-96 363.0
13 TraesCS7A01G366900 chr7B 90.476 231 17 1 1516 1741 481661348 481661578 1.380000e-77 300.0
14 TraesCS7A01G366900 chr1D 82.270 423 55 11 1975 2377 435747851 435747429 4.860000e-92 348.0
15 TraesCS7A01G366900 chr1D 100.000 28 0 0 1798 1825 51822997 51823024 4.000000e-03 52.8
16 TraesCS7A01G366900 chr1D 100.000 28 0 0 1798 1825 180377276 180377303 4.000000e-03 52.8
17 TraesCS7A01G366900 chr1D 100.000 28 0 0 1798 1825 244760088 244760061 4.000000e-03 52.8
18 TraesCS7A01G366900 chr1D 100.000 28 0 0 1798 1825 254468385 254468358 4.000000e-03 52.8
19 TraesCS7A01G366900 chr3D 86.782 174 17 2 2080 2253 582814701 582814868 3.120000e-44 189.0
20 TraesCS7A01G366900 chrUn 100.000 28 0 0 1798 1825 298934960 298934987 4.000000e-03 52.8
21 TraesCS7A01G366900 chrUn 100.000 28 0 0 1798 1825 357609614 357609641 4.000000e-03 52.8
22 TraesCS7A01G366900 chrUn 100.000 28 0 0 1798 1825 472495339 472495366 4.000000e-03 52.8


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 TraesCS7A01G366900 chr7A 540747290 540749667 2377 True 1512.733333 4392 94.771333 1 2378 3 chr7A.!!$R2 2377
1 TraesCS7A01G366900 chr7D 459473085 459477339 4254 False 543.500000 713 88.443250 1 2378 4 chr7D.!!$F1 2377
2 TraesCS7A01G366900 chr7B 481660361 481661578 1217 False 394.000000 488 88.037000 704 1741 2 chr7B.!!$F2 1037

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
345 1766 0.100682 TGCTACCGATCGAGTTGCTC 59.899 55.0 27.97 12.75 36.98 4.26 F
364 1785 0.322546 CGGGGAGGAAGGTTTTGGAG 60.323 60.0 0.00 0.00 0.00 3.86 F
932 2472 0.392336 GGCTGGCCTAGAGTCATCAG 59.608 60.0 3.32 0.00 0.00 2.90 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1192 2740 0.034896 GAACCCTCAGTTTCAGGCGA 59.965 55.0 0.00 0.0 39.4 5.54 R
1193 2741 0.250295 TGAACCCTCAGTTTCAGGCG 60.250 55.0 0.00 0.0 39.4 5.52 R
2085 4106 0.308376 TGCGGCGGAAAAACTACAAC 59.692 50.0 9.78 0.0 0.0 3.32 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
44 45 1.902508 TGCTGGAGACTACTGGAAAGG 59.097 52.381 0.00 0.00 0.00 3.11
83 84 4.466015 GGCAAATTCCCTTGGAGATTGTTA 59.534 41.667 10.00 0.00 34.10 2.41
98 99 5.819991 AGATTGTTACCATCCAACATCAGT 58.180 37.500 0.00 0.00 35.89 3.41
116 117 6.098838 ACATCAGTATAGTCAATCTGGAGCAA 59.901 38.462 0.00 0.00 0.00 3.91
131 132 2.941720 GGAGCAATTTGAGAGCGAAGAT 59.058 45.455 0.00 0.00 0.00 2.40
135 136 6.090628 GGAGCAATTTGAGAGCGAAGATATAG 59.909 42.308 0.00 0.00 0.00 1.31
142 143 1.478916 GAGCGAAGATATAGAGCCCCC 59.521 57.143 0.00 0.00 0.00 5.40
143 144 0.173708 GCGAAGATATAGAGCCCCCG 59.826 60.000 0.00 0.00 0.00 5.73
145 146 1.893801 CGAAGATATAGAGCCCCCGTT 59.106 52.381 0.00 0.00 0.00 4.44
149 150 1.489560 ATATAGAGCCCCCGTTGCCC 61.490 60.000 0.00 0.00 0.00 5.36
167 168 2.163613 GCCCGCTTTTAGCTTGTTGTAT 59.836 45.455 0.00 0.00 39.60 2.29
169 170 3.171277 CCGCTTTTAGCTTGTTGTATGC 58.829 45.455 0.00 0.00 39.60 3.14
202 203 6.710295 AGTTCCTTTAAATTTGGCAATGAACC 59.290 34.615 0.00 0.00 0.00 3.62
289 1710 0.106918 TTGCGTGGAACTTGGGAAGT 60.107 50.000 0.00 0.00 45.46 3.01
291 1712 0.818040 GCGTGGAACTTGGGAAGTGT 60.818 55.000 0.00 0.00 41.91 3.55
297 1718 3.288092 GGAACTTGGGAAGTGTGAAACT 58.712 45.455 0.00 0.00 41.91 2.66
298 1719 3.066760 GGAACTTGGGAAGTGTGAAACTG 59.933 47.826 0.00 0.00 41.91 3.16
299 1720 3.644966 ACTTGGGAAGTGTGAAACTGA 57.355 42.857 0.00 0.00 41.01 3.41
300 1721 4.170468 ACTTGGGAAGTGTGAAACTGAT 57.830 40.909 0.00 0.00 41.01 2.90
304 1725 5.497464 TGGGAAGTGTGAAACTGATGATA 57.503 39.130 0.00 0.00 39.81 2.15
320 1741 5.927819 TGATGATAGCATGGTATGAACACA 58.072 37.500 21.63 12.90 34.11 3.72
345 1766 0.100682 TGCTACCGATCGAGTTGCTC 59.899 55.000 27.97 12.75 36.98 4.26
359 1780 1.423794 TTGCTCGGGGAGGAAGGTTT 61.424 55.000 0.00 0.00 35.21 3.27
364 1785 0.322546 CGGGGAGGAAGGTTTTGGAG 60.323 60.000 0.00 0.00 0.00 3.86
377 1800 6.149129 AGGTTTTGGAGATGAAACTGAAAC 57.851 37.500 0.00 0.00 36.32 2.78
378 1801 4.976116 GGTTTTGGAGATGAAACTGAAACG 59.024 41.667 0.00 0.00 36.32 3.60
381 1804 4.079980 TGGAGATGAAACTGAAACGGAA 57.920 40.909 0.00 0.00 0.00 4.30
386 1895 6.293955 GGAGATGAAACTGAAACGGAATCAAA 60.294 38.462 0.00 0.00 0.00 2.69
394 1903 6.805713 ACTGAAACGGAATCAAAGTTGAAAT 58.194 32.000 0.00 0.00 41.13 2.17
411 1920 3.192422 TGAAATGCCAATAGAACCGTTGG 59.808 43.478 0.00 0.00 46.03 3.77
417 1926 2.097466 CCAATAGAACCGTTGGTCATGC 59.903 50.000 0.00 0.00 39.97 4.06
418 1927 2.746904 CAATAGAACCGTTGGTCATGCA 59.253 45.455 0.00 0.00 33.12 3.96
421 1930 1.164411 GAACCGTTGGTCATGCATGA 58.836 50.000 25.42 25.42 33.12 3.07
434 1943 4.575236 GTCATGCATGAGTGTCAATCTGAT 59.425 41.667 29.38 0.00 37.51 2.90
437 1946 2.286242 GCATGAGTGTCAATCTGATGCG 60.286 50.000 9.08 0.00 41.00 4.73
444 1953 2.487762 TGTCAATCTGATGCGTTTTCCC 59.512 45.455 0.00 0.00 0.00 3.97
445 1954 1.737236 TCAATCTGATGCGTTTTCCCG 59.263 47.619 0.00 0.00 0.00 5.14
483 1992 7.681939 AATCTGGCAACTTAAATTTCTACGA 57.318 32.000 0.00 0.00 37.61 3.43
484 1993 6.476243 TCTGGCAACTTAAATTTCTACGAC 57.524 37.500 0.00 0.00 37.61 4.34
486 1995 4.456566 TGGCAACTTAAATTTCTACGACCC 59.543 41.667 0.00 0.00 37.61 4.46
487 1996 4.456566 GGCAACTTAAATTTCTACGACCCA 59.543 41.667 0.00 0.00 0.00 4.51
488 1997 5.124936 GGCAACTTAAATTTCTACGACCCAT 59.875 40.000 0.00 0.00 0.00 4.00
489 1998 6.349860 GGCAACTTAAATTTCTACGACCCATT 60.350 38.462 0.00 0.00 0.00 3.16
490 1999 7.088272 GCAACTTAAATTTCTACGACCCATTT 58.912 34.615 0.00 0.00 0.00 2.32
515 2024 7.647907 TTTTACGTATTCTCAGACTGGTTTC 57.352 36.000 1.81 0.00 0.00 2.78
516 2025 6.585695 TTACGTATTCTCAGACTGGTTTCT 57.414 37.500 1.81 0.00 0.00 2.52
517 2026 5.061920 ACGTATTCTCAGACTGGTTTCTC 57.938 43.478 1.81 0.00 0.00 2.87
518 2027 4.523173 ACGTATTCTCAGACTGGTTTCTCA 59.477 41.667 1.81 0.00 0.00 3.27
519 2028 5.098893 CGTATTCTCAGACTGGTTTCTCAG 58.901 45.833 1.81 0.00 40.40 3.35
520 2029 5.106118 CGTATTCTCAGACTGGTTTCTCAGA 60.106 44.000 1.81 0.00 38.11 3.27
521 2030 4.592485 TTCTCAGACTGGTTTCTCAGAC 57.408 45.455 1.81 0.00 38.11 3.51
522 2031 2.554462 TCTCAGACTGGTTTCTCAGACG 59.446 50.000 1.81 0.00 38.11 4.18
523 2032 2.294791 CTCAGACTGGTTTCTCAGACGT 59.705 50.000 1.81 0.00 38.11 4.34
524 2033 3.483421 TCAGACTGGTTTCTCAGACGTA 58.517 45.455 1.81 0.00 38.11 3.57
525 2034 4.079970 TCAGACTGGTTTCTCAGACGTAT 58.920 43.478 1.81 0.00 38.11 3.06
526 2035 4.523173 TCAGACTGGTTTCTCAGACGTATT 59.477 41.667 1.81 0.00 38.11 1.89
527 2036 4.859798 CAGACTGGTTTCTCAGACGTATTC 59.140 45.833 0.00 0.00 38.11 1.75
528 2037 4.767928 AGACTGGTTTCTCAGACGTATTCT 59.232 41.667 0.00 0.00 38.11 2.40
539 2048 1.480954 GACGTATTCTCAGGGGAAGCA 59.519 52.381 0.00 0.00 0.00 3.91
562 2071 3.319122 ACCTTTTGCTAAGAAACTGCCTG 59.681 43.478 1.35 0.00 0.00 4.85
605 2118 7.526142 AGAAAAGGAATGGAAAAGGACTTAC 57.474 36.000 0.00 0.00 0.00 2.34
608 2121 3.329814 AGGAATGGAAAAGGACTTACCGT 59.670 43.478 0.00 0.00 44.74 4.83
615 2128 4.153655 GGAAAAGGACTTACCGTGATGTTC 59.846 45.833 0.00 0.00 44.74 3.18
631 2153 6.454981 CGTGATGTTCGTTGTATTTATGCTCA 60.455 38.462 0.00 0.00 0.00 4.26
638 2160 4.034048 CGTTGTATTTATGCTCACTGGGAC 59.966 45.833 0.00 0.00 0.00 4.46
650 2172 4.626287 GCTCACTGGGACCAAGATATTTGA 60.626 45.833 1.72 0.00 0.00 2.69
653 2175 5.009631 CACTGGGACCAAGATATTTGACAA 58.990 41.667 1.72 0.00 0.00 3.18
661 2183 7.040409 GGACCAAGATATTTGACAACTCTGTTT 60.040 37.037 0.00 0.00 35.30 2.83
662 2184 8.237811 ACCAAGATATTTGACAACTCTGTTTT 57.762 30.769 0.00 0.00 35.30 2.43
663 2185 8.137437 ACCAAGATATTTGACAACTCTGTTTTG 58.863 33.333 0.00 0.00 35.30 2.44
664 2186 8.352201 CCAAGATATTTGACAACTCTGTTTTGA 58.648 33.333 0.00 0.00 35.30 2.69
665 2187 9.173939 CAAGATATTTGACAACTCTGTTTTGAC 57.826 33.333 0.00 0.00 35.30 3.18
666 2188 8.682936 AGATATTTGACAACTCTGTTTTGACT 57.317 30.769 0.00 0.00 35.30 3.41
667 2189 9.125026 AGATATTTGACAACTCTGTTTTGACTT 57.875 29.630 0.00 0.00 35.30 3.01
668 2190 9.173939 GATATTTGACAACTCTGTTTTGACTTG 57.826 33.333 0.00 0.00 35.30 3.16
669 2191 5.957842 TTGACAACTCTGTTTTGACTTGT 57.042 34.783 0.00 0.00 35.30 3.16
670 2192 7.441890 TTTGACAACTCTGTTTTGACTTGTA 57.558 32.000 0.00 0.00 35.30 2.41
671 2193 6.417191 TGACAACTCTGTTTTGACTTGTAC 57.583 37.500 0.00 0.00 35.30 2.90
672 2194 6.170506 TGACAACTCTGTTTTGACTTGTACT 58.829 36.000 0.00 0.00 35.30 2.73
673 2195 6.092122 TGACAACTCTGTTTTGACTTGTACTG 59.908 38.462 0.00 0.00 35.30 2.74
674 2196 5.938125 ACAACTCTGTTTTGACTTGTACTGT 59.062 36.000 0.00 0.00 28.57 3.55
675 2197 6.128282 ACAACTCTGTTTTGACTTGTACTGTG 60.128 38.462 0.00 0.00 28.57 3.66
676 2198 5.488341 ACTCTGTTTTGACTTGTACTGTGT 58.512 37.500 0.00 0.00 0.00 3.72
677 2199 6.636705 ACTCTGTTTTGACTTGTACTGTGTA 58.363 36.000 0.00 0.00 0.00 2.90
678 2200 6.534079 ACTCTGTTTTGACTTGTACTGTGTAC 59.466 38.462 0.00 1.33 0.00 2.90
679 2201 6.399743 TCTGTTTTGACTTGTACTGTGTACA 58.600 36.000 6.48 6.48 0.00 2.90
680 2202 6.874664 TCTGTTTTGACTTGTACTGTGTACAA 59.125 34.615 18.37 18.37 36.20 2.41
681 2203 7.388224 TCTGTTTTGACTTGTACTGTGTACAAA 59.612 33.333 19.45 6.95 37.04 2.83
682 2204 7.299586 TGTTTTGACTTGTACTGTGTACAAAC 58.700 34.615 19.45 16.60 37.04 2.93
683 2205 7.041303 TGTTTTGACTTGTACTGTGTACAAACA 60.041 33.333 19.45 18.24 37.04 2.83
684 2206 7.436430 TTTGACTTGTACTGTGTACAAACAA 57.564 32.000 22.61 22.61 37.36 2.83
685 2207 7.436430 TTGACTTGTACTGTGTACAAACAAA 57.564 32.000 23.34 15.92 37.36 2.83
686 2208 6.833839 TGACTTGTACTGTGTACAAACAAAC 58.166 36.000 19.45 11.74 37.36 2.93
687 2209 6.128227 TGACTTGTACTGTGTACAAACAAACC 60.128 38.462 19.45 9.15 37.36 3.27
688 2210 5.941647 ACTTGTACTGTGTACAAACAAACCT 59.058 36.000 19.45 0.63 37.36 3.50
689 2211 6.093082 ACTTGTACTGTGTACAAACAAACCTC 59.907 38.462 19.45 0.00 37.36 3.85
690 2212 5.736813 TGTACTGTGTACAAACAAACCTCT 58.263 37.500 7.95 0.00 37.36 3.69
691 2213 5.583061 TGTACTGTGTACAAACAAACCTCTG 59.417 40.000 7.95 0.00 37.36 3.35
692 2214 3.377172 ACTGTGTACAAACAAACCTCTGC 59.623 43.478 0.00 0.00 37.36 4.26
693 2215 3.348119 TGTGTACAAACAAACCTCTGCA 58.652 40.909 0.00 0.00 37.36 4.41
694 2216 3.951037 TGTGTACAAACAAACCTCTGCAT 59.049 39.130 0.00 0.00 37.36 3.96
695 2217 5.126779 TGTGTACAAACAAACCTCTGCATA 58.873 37.500 0.00 0.00 37.36 3.14
696 2218 5.008217 TGTGTACAAACAAACCTCTGCATAC 59.992 40.000 0.00 0.00 37.36 2.39
697 2219 5.008217 GTGTACAAACAAACCTCTGCATACA 59.992 40.000 0.00 0.00 37.36 2.29
698 2220 5.767665 TGTACAAACAAACCTCTGCATACAT 59.232 36.000 0.00 0.00 30.91 2.29
699 2221 5.789643 ACAAACAAACCTCTGCATACATT 57.210 34.783 0.00 0.00 0.00 2.71
700 2222 5.531634 ACAAACAAACCTCTGCATACATTG 58.468 37.500 0.00 0.00 0.00 2.82
701 2223 5.068987 ACAAACAAACCTCTGCATACATTGT 59.931 36.000 0.00 0.00 0.00 2.71
702 2224 6.264292 ACAAACAAACCTCTGCATACATTGTA 59.736 34.615 0.00 0.00 0.00 2.41
715 2237 9.313118 CTGCATACATTGTATTGACTTGTACTA 57.687 33.333 6.58 0.00 31.82 1.82
717 2239 8.266682 GCATACATTGTATTGACTTGTACTACG 58.733 37.037 6.58 0.00 31.82 3.51
740 2269 5.351465 CGTAGAAACAAACCTCTGCATACAT 59.649 40.000 0.00 0.00 0.00 2.29
743 2272 5.536161 AGAAACAAACCTCTGCATACATTGT 59.464 36.000 0.00 0.00 0.00 2.71
745 2274 7.394359 AGAAACAAACCTCTGCATACATTGTAT 59.606 33.333 3.40 3.40 0.00 2.29
750 2279 5.126067 ACCTCTGCATACATTGTATTGACC 58.874 41.667 6.58 0.00 0.00 4.02
755 2284 1.942677 TACATTGTATTGACCGCCGG 58.057 50.000 0.00 0.00 0.00 6.13
795 2324 3.118847 AGTGGAGTAGAGTCGTCGTATGA 60.119 47.826 0.00 0.00 0.00 2.15
796 2325 3.620374 GTGGAGTAGAGTCGTCGTATGAA 59.380 47.826 0.00 0.00 0.00 2.57
799 2328 5.046529 GGAGTAGAGTCGTCGTATGAAGTA 58.953 45.833 0.00 0.00 0.00 2.24
817 2350 5.048782 TGAAGTATGAACACATGCCTTTCAC 60.049 40.000 6.42 0.00 32.21 3.18
844 2380 1.912971 GTCGGGGAAGGTTAGGCAT 59.087 57.895 0.00 0.00 0.00 4.40
845 2381 0.463833 GTCGGGGAAGGTTAGGCATG 60.464 60.000 0.00 0.00 0.00 4.06
846 2382 1.152963 CGGGGAAGGTTAGGCATGG 60.153 63.158 0.00 0.00 0.00 3.66
847 2383 1.632018 CGGGGAAGGTTAGGCATGGA 61.632 60.000 0.00 0.00 0.00 3.41
848 2384 0.853530 GGGGAAGGTTAGGCATGGAT 59.146 55.000 0.00 0.00 0.00 3.41
849 2385 1.479389 GGGGAAGGTTAGGCATGGATG 60.479 57.143 0.00 0.00 0.00 3.51
850 2386 1.479389 GGGAAGGTTAGGCATGGATGG 60.479 57.143 0.00 0.00 0.00 3.51
851 2387 1.494721 GGAAGGTTAGGCATGGATGGA 59.505 52.381 0.00 0.00 0.00 3.41
857 2393 3.087031 GTTAGGCATGGATGGATGGATG 58.913 50.000 0.00 0.00 0.00 3.51
858 2394 0.408309 AGGCATGGATGGATGGATGG 59.592 55.000 0.00 0.00 0.00 3.51
860 2396 1.542492 GCATGGATGGATGGATGGAC 58.458 55.000 0.00 0.00 0.00 4.02
862 2398 2.556782 GCATGGATGGATGGATGGACAT 60.557 50.000 0.00 0.00 0.00 3.06
909 2449 5.685520 TTGCCGGTTATATATAGCATCCA 57.314 39.130 1.90 0.19 0.00 3.41
910 2450 5.276461 TGCCGGTTATATATAGCATCCAG 57.724 43.478 1.90 0.00 0.00 3.86
911 2451 4.959839 TGCCGGTTATATATAGCATCCAGA 59.040 41.667 1.90 0.00 0.00 3.86
912 2452 5.602561 TGCCGGTTATATATAGCATCCAGAT 59.397 40.000 1.90 0.00 0.00 2.90
915 2455 5.928839 CGGTTATATATAGCATCCAGATGGC 59.071 44.000 9.58 2.52 39.16 4.40
916 2456 6.239430 CGGTTATATATAGCATCCAGATGGCT 60.239 42.308 9.58 9.13 39.16 4.75
932 2472 0.392336 GGCTGGCCTAGAGTCATCAG 59.608 60.000 3.32 0.00 0.00 2.90
943 2483 2.699846 AGAGTCATCAGGGATCAGCTTC 59.300 50.000 0.00 0.00 0.00 3.86
945 2485 3.894427 GAGTCATCAGGGATCAGCTTCTA 59.106 47.826 0.00 0.00 0.00 2.10
950 2490 5.899547 TCATCAGGGATCAGCTTCTAGTTTA 59.100 40.000 0.00 0.00 0.00 2.01
960 2500 9.167311 GATCAGCTTCTAGTTTAAGAAATTCCA 57.833 33.333 0.00 0.00 35.14 3.53
963 2503 6.371825 AGCTTCTAGTTTAAGAAATTCCACGG 59.628 38.462 0.00 0.00 35.14 4.94
970 2510 1.995376 AGAAATTCCACGGCCAACTT 58.005 45.000 2.24 0.00 0.00 2.66
993 2535 1.070445 CATCTTGCCTGGCTAGAGAGG 59.930 57.143 30.64 21.99 42.66 3.69
1027 2569 2.647158 GCTCCCCGGTCGTCTCTTT 61.647 63.158 0.00 0.00 0.00 2.52
1053 2595 2.110967 GGTGCTGCTCATGTCGCAT 61.111 57.895 11.68 0.00 36.70 4.73
1091 2633 1.153549 CTTTCTTCTCCTCCGCCGG 60.154 63.158 0.00 0.00 0.00 6.13
1183 2731 2.176273 GCCGCTGCAGGTACAGATG 61.176 63.158 17.12 0.00 40.25 2.90
1184 2732 2.176273 CCGCTGCAGGTACAGATGC 61.176 63.158 17.12 9.33 40.25 3.91
1185 2733 2.176273 CGCTGCAGGTACAGATGCC 61.176 63.158 17.12 0.00 41.85 4.40
1186 2734 1.078214 GCTGCAGGTACAGATGCCA 60.078 57.895 17.12 3.10 41.85 4.92
1187 2735 0.677731 GCTGCAGGTACAGATGCCAA 60.678 55.000 17.12 0.00 41.85 4.52
1188 2736 1.376543 CTGCAGGTACAGATGCCAAG 58.623 55.000 5.57 3.27 41.85 3.61
1189 2737 0.983467 TGCAGGTACAGATGCCAAGA 59.017 50.000 12.64 0.00 41.85 3.02
1192 2740 3.019564 GCAGGTACAGATGCCAAGATTT 58.980 45.455 5.83 0.00 36.41 2.17
1193 2741 3.065925 GCAGGTACAGATGCCAAGATTTC 59.934 47.826 5.83 0.00 36.41 2.17
1194 2742 3.310774 CAGGTACAGATGCCAAGATTTCG 59.689 47.826 0.00 0.00 31.71 3.46
1229 2928 0.602638 TCATGTCACACGCTTGGACC 60.603 55.000 8.59 0.00 0.00 4.46
1234 2933 0.249868 TCACACGCTTGGACCTGAAG 60.250 55.000 0.00 0.00 0.00 3.02
1251 2950 1.131315 GAAGCTGACAAGATTTCGCCC 59.869 52.381 0.00 0.00 30.45 6.13
1302 3001 1.737735 CGAAGGCTCATGCGACACA 60.738 57.895 0.00 0.00 40.82 3.72
1320 3019 2.168521 CACACCTCAACCTGTATCGGAT 59.831 50.000 0.00 0.00 0.00 4.18
1328 3027 2.530701 ACCTGTATCGGATGATCCTCC 58.469 52.381 10.18 6.95 35.99 4.30
1352 3051 1.153549 GAGCTCGCAAAGACCCGAT 60.154 57.895 0.00 0.00 32.52 4.18
1369 3068 1.808411 GATGCACGGAGTTCCTGAAA 58.192 50.000 0.00 0.00 41.61 2.69
1374 3073 0.841289 ACGGAGTTCCTGAAAACCCA 59.159 50.000 0.00 0.00 37.78 4.51
1442 3141 7.365497 TCATCACATCCGGATATAGCAATAT 57.635 36.000 18.63 0.00 0.00 1.28
1483 3183 2.769663 TGGGTCCTACACACCATGTATC 59.230 50.000 0.00 0.00 43.01 2.24
1499 3199 5.305128 CCATGTATCCCCAAATTGTTAGCAT 59.695 40.000 0.00 0.00 0.00 3.79
1501 3201 4.578516 TGTATCCCCAAATTGTTAGCATCG 59.421 41.667 0.00 0.00 0.00 3.84
1509 3209 2.910688 TTGTTAGCATCGGATCCCTC 57.089 50.000 6.06 0.00 0.00 4.30
1510 3210 0.673985 TGTTAGCATCGGATCCCTCG 59.326 55.000 6.06 0.00 0.00 4.63
1525 3253 0.178767 CCTCGTGCATCAATCTCCCA 59.821 55.000 0.00 0.00 0.00 4.37
1543 3271 2.165030 CCCAATGCTCATTTCTTTCGCT 59.835 45.455 0.00 0.00 0.00 4.93
1594 3322 4.894784 GACCAACTCTTACAAGGTCATCA 58.105 43.478 0.00 0.00 46.15 3.07
1617 3345 8.814733 TCATTACATAAACTGAAAATTACGCG 57.185 30.769 3.53 3.53 0.00 6.01
1644 3377 4.270325 GTCTTTGGGTAAATCGATCTTCCG 59.730 45.833 0.00 0.00 0.00 4.30
1660 3393 2.432628 CGCCTGGACTCGTCAACC 60.433 66.667 0.00 0.00 0.00 3.77
1730 3463 3.648339 TCAGAGCCATTGAAAAGTTGC 57.352 42.857 0.00 0.00 0.00 4.17
1777 3510 2.932614 CTCGGAGCTCTTTGTATGTTGG 59.067 50.000 14.64 0.00 0.00 3.77
1779 3512 2.615493 CGGAGCTCTTTGTATGTTGGGT 60.615 50.000 14.64 0.00 0.00 4.51
1780 3513 3.010420 GGAGCTCTTTGTATGTTGGGTC 58.990 50.000 14.64 0.00 0.00 4.46
1781 3514 3.307762 GGAGCTCTTTGTATGTTGGGTCT 60.308 47.826 14.64 0.00 0.00 3.85
1782 3515 4.081087 GGAGCTCTTTGTATGTTGGGTCTA 60.081 45.833 14.64 0.00 0.00 2.59
1783 3516 5.396884 GGAGCTCTTTGTATGTTGGGTCTAT 60.397 44.000 14.64 0.00 0.00 1.98
1786 3519 6.069963 AGCTCTTTGTATGTTGGGTCTATCTT 60.070 38.462 0.00 0.00 0.00 2.40
1787 3520 6.599638 GCTCTTTGTATGTTGGGTCTATCTTT 59.400 38.462 0.00 0.00 0.00 2.52
1788 3521 7.414540 GCTCTTTGTATGTTGGGTCTATCTTTG 60.415 40.741 0.00 0.00 0.00 2.77
1790 3523 8.598916 TCTTTGTATGTTGGGTCTATCTTTGTA 58.401 33.333 0.00 0.00 0.00 2.41
1795 3528 5.416083 TGTTGGGTCTATCTTTGTATGTCG 58.584 41.667 0.00 0.00 0.00 4.35
1796 3529 4.665833 TGGGTCTATCTTTGTATGTCGG 57.334 45.455 0.00 0.00 0.00 4.79
1799 3532 4.100498 GGGTCTATCTTTGTATGTCGGGAA 59.900 45.833 0.00 0.00 0.00 3.97
1800 3533 5.048507 GGTCTATCTTTGTATGTCGGGAAC 58.951 45.833 0.00 0.00 0.00 3.62
1819 3829 9.090103 TCGGGAACTAATCACAATATCTATCTT 57.910 33.333 0.00 0.00 0.00 2.40
1860 3870 9.560860 AAAAAGAGGGGGACTTAATGATTTATT 57.439 29.630 0.00 0.00 0.00 1.40
1861 3871 8.768501 AAAGAGGGGGACTTAATGATTTATTC 57.231 34.615 0.00 0.00 0.00 1.75
1862 3872 6.534634 AGAGGGGGACTTAATGATTTATTCG 58.465 40.000 0.00 0.00 0.00 3.34
1863 3873 6.101296 AGAGGGGGACTTAATGATTTATTCGT 59.899 38.462 0.00 0.00 0.00 3.85
1864 3874 6.669631 AGGGGGACTTAATGATTTATTCGTT 58.330 36.000 0.00 0.00 37.36 3.85
1865 3875 6.771267 AGGGGGACTTAATGATTTATTCGTTC 59.229 38.462 0.00 0.00 35.22 3.95
1866 3876 6.016527 GGGGGACTTAATGATTTATTCGTTCC 60.017 42.308 0.00 0.00 35.22 3.62
1867 3877 6.016527 GGGGACTTAATGATTTATTCGTTCCC 60.017 42.308 0.00 0.00 39.25 3.97
1868 3878 6.771267 GGGACTTAATGATTTATTCGTTCCCT 59.229 38.462 0.00 0.00 35.22 4.20
1869 3879 7.255139 GGGACTTAATGATTTATTCGTTCCCTG 60.255 40.741 0.00 0.00 35.22 4.45
1870 3880 7.255139 GGACTTAATGATTTATTCGTTCCCTGG 60.255 40.741 0.00 0.00 35.22 4.45
1871 3881 7.343357 ACTTAATGATTTATTCGTTCCCTGGA 58.657 34.615 0.00 0.00 35.22 3.86
1892 3902 7.361286 CCTGGAACTAGAAGTAGAAATTGTTGC 60.361 40.741 0.00 0.00 0.00 4.17
1896 3906 5.638234 ACTAGAAGTAGAAATTGTTGCGGAC 59.362 40.000 0.00 0.00 0.00 4.79
1913 3923 9.150348 TGTTGCGGACATATATATCATGTAAAG 57.850 33.333 3.50 1.15 36.76 1.85
1915 3925 8.926715 TGCGGACATATATATCATGTAAAGAC 57.073 34.615 3.50 0.00 36.76 3.01
1917 3927 9.025020 GCGGACATATATATCATGTAAAGACAG 57.975 37.037 3.50 0.00 39.50 3.51
1931 3941 6.061441 TGTAAAGACAGCTTTTGAGGAATGA 58.939 36.000 0.00 0.00 41.43 2.57
1946 3956 2.106166 GGAATGAGCCAGATCTGACCAT 59.894 50.000 24.62 18.50 0.00 3.55
1953 3963 2.941720 GCCAGATCTGACCATTTCTCAC 59.058 50.000 24.62 0.00 0.00 3.51
1955 3965 4.582869 CCAGATCTGACCATTTCTCACAA 58.417 43.478 24.62 0.00 0.00 3.33
1960 3970 3.394274 TCTGACCATTTCTCACAAGGGAA 59.606 43.478 0.00 0.00 31.70 3.97
1982 4003 2.200373 TCAGGGAAAAGCTTGGCTAC 57.800 50.000 0.00 0.00 38.25 3.58
2037 4058 2.253154 CGTGTGACGCGTGTCCTA 59.747 61.111 25.28 12.02 44.86 2.94
2039 4060 1.008194 GTGTGACGCGTGTCCTACA 60.008 57.895 25.28 20.19 44.86 2.74
2068 4089 9.780186 GCTCACCTAGTATTATCTTTTATGGTT 57.220 33.333 0.00 0.00 0.00 3.67
2085 4106 3.539604 TGGTTTTGCAATTGAACCCTTG 58.460 40.909 22.74 0.00 41.64 3.61
2096 4117 6.315144 GCAATTGAACCCTTGTTGTAGTTTTT 59.685 34.615 10.34 0.00 33.97 1.94
2106 4127 1.240256 TGTAGTTTTTCCGCCGCAAT 58.760 45.000 0.00 0.00 0.00 3.56
2128 4149 3.170791 ACTCGTATGTTGCAGGATCTG 57.829 47.619 0.00 0.00 34.12 2.90
2135 4156 1.211212 TGTTGCAGGATCTGGATCTGG 59.789 52.381 9.96 4.68 37.92 3.86
2147 4168 1.583986 GATCTGGATCCCTCGAGCG 59.416 63.158 9.90 0.00 31.76 5.03
2148 4169 2.485188 GATCTGGATCCCTCGAGCGC 62.485 65.000 9.90 0.00 31.76 5.92
2180 4201 1.222113 GTTCCACCTAGGCTCCTGC 59.778 63.158 9.30 0.00 37.29 4.85
2225 4246 8.761575 ACATTATTTATGTTGCAAAAGTCCTG 57.238 30.769 0.00 0.00 45.19 3.86
2260 4281 6.545504 TCTATGTTGCAAGAAAGTGAAGAC 57.454 37.500 0.00 0.00 0.00 3.01
2261 4282 6.054941 TCTATGTTGCAAGAAAGTGAAGACA 58.945 36.000 0.00 0.00 0.00 3.41
2302 4326 3.396560 TGTCTCTGCAACATGAACTCTG 58.603 45.455 0.00 0.00 0.00 3.35
2325 4349 1.915141 CAAGGAGGGTTCTGCAACAT 58.085 50.000 0.00 0.00 33.70 2.71
2327 4351 1.915141 AGGAGGGTTCTGCAACATTG 58.085 50.000 0.00 0.00 33.70 2.82
2328 4352 0.890683 GGAGGGTTCTGCAACATTGG 59.109 55.000 0.00 0.00 33.70 3.16
2329 4353 0.244721 GAGGGTTCTGCAACATTGGC 59.755 55.000 0.00 0.00 33.70 4.52
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
22 23 2.310779 TTCCAGTAGTCTCCAGCAGT 57.689 50.000 0.00 0.00 0.00 4.40
83 84 6.560003 TTGACTATACTGATGTTGGATGGT 57.440 37.500 0.00 0.00 0.00 3.55
98 99 7.795047 TCTCAAATTGCTCCAGATTGACTATA 58.205 34.615 0.00 0.00 0.00 1.31
116 117 5.337169 GGGCTCTATATCTTCGCTCTCAAAT 60.337 44.000 0.00 0.00 0.00 2.32
131 132 2.144738 GGGCAACGGGGGCTCTATA 61.145 63.158 2.39 0.00 37.60 1.31
149 150 4.850487 TTGGCATACAACAAGCTAAAAGCG 60.850 41.667 0.00 0.00 39.33 4.68
167 168 8.093927 CCAAATTTAAAGGAACTAGATTTGGCA 58.906 33.333 11.59 0.00 41.59 4.92
169 170 8.093927 TGCCAAATTTAAAGGAACTAGATTTGG 58.906 33.333 16.68 16.68 45.46 3.28
202 203 4.342862 ACTGGATTCATACCATCCTTCG 57.657 45.455 0.82 0.00 40.99 3.79
236 237 5.350640 GCAGCGTAGGAAACTTTACTTGTAT 59.649 40.000 0.00 0.00 43.67 2.29
274 1695 2.341846 TCACACTTCCCAAGTTCCAC 57.658 50.000 0.00 0.00 40.46 4.02
289 1710 4.847198 ACCATGCTATCATCAGTTTCACA 58.153 39.130 0.00 0.00 0.00 3.58
291 1712 6.829849 TCATACCATGCTATCATCAGTTTCA 58.170 36.000 0.00 0.00 0.00 2.69
297 1718 5.927819 TGTGTTCATACCATGCTATCATCA 58.072 37.500 0.00 0.00 0.00 3.07
298 1719 6.564686 CGTTGTGTTCATACCATGCTATCATC 60.565 42.308 0.00 0.00 0.00 2.92
299 1720 5.237127 CGTTGTGTTCATACCATGCTATCAT 59.763 40.000 0.00 0.00 0.00 2.45
300 1721 4.570369 CGTTGTGTTCATACCATGCTATCA 59.430 41.667 0.00 0.00 0.00 2.15
304 1725 2.778299 ACGTTGTGTTCATACCATGCT 58.222 42.857 0.00 0.00 0.00 3.79
320 1741 1.068055 ACTCGATCGGTAGCAAACGTT 60.068 47.619 16.41 0.00 0.00 3.99
345 1766 0.322546 CTCCAAAACCTTCCTCCCCG 60.323 60.000 0.00 0.00 0.00 5.73
359 1780 4.079980 TCCGTTTCAGTTTCATCTCCAA 57.920 40.909 0.00 0.00 0.00 3.53
364 1785 6.438763 ACTTTGATTCCGTTTCAGTTTCATC 58.561 36.000 0.00 0.00 0.00 2.92
377 1800 3.911868 TGGCATTTCAACTTTGATTCCG 58.088 40.909 0.00 0.00 37.00 4.30
378 1801 7.322664 TCTATTGGCATTTCAACTTTGATTCC 58.677 34.615 0.00 0.00 37.00 3.01
381 1804 7.099120 GGTTCTATTGGCATTTCAACTTTGAT 58.901 34.615 0.00 0.00 37.00 2.57
386 1895 4.079253 ACGGTTCTATTGGCATTTCAACT 58.921 39.130 0.00 0.00 0.00 3.16
411 1920 3.937079 TCAGATTGACACTCATGCATGAC 59.063 43.478 25.42 15.78 32.50 3.06
417 1926 2.934553 ACGCATCAGATTGACACTCATG 59.065 45.455 0.00 0.00 0.00 3.07
418 1927 3.257469 ACGCATCAGATTGACACTCAT 57.743 42.857 0.00 0.00 0.00 2.90
421 1930 3.189287 GGAAAACGCATCAGATTGACACT 59.811 43.478 0.00 0.00 0.00 3.55
456 1965 9.191995 CGTAGAAATTTAAGTTGCCAGATTTTT 57.808 29.630 0.00 0.00 0.00 1.94
458 1967 8.021396 GTCGTAGAAATTTAAGTTGCCAGATTT 58.979 33.333 0.00 0.00 39.69 2.17
463 1972 4.456566 GGGTCGTAGAAATTTAAGTTGCCA 59.543 41.667 0.00 0.00 39.69 4.92
465 1974 5.616488 TGGGTCGTAGAAATTTAAGTTGC 57.384 39.130 0.00 0.00 39.69 4.17
490 1999 7.929785 AGAAACCAGTCTGAGAATACGTAAAAA 59.070 33.333 0.00 0.00 0.00 1.94
501 2010 2.554462 CGTCTGAGAAACCAGTCTGAGA 59.446 50.000 0.00 0.00 35.78 3.27
502 2011 2.294791 ACGTCTGAGAAACCAGTCTGAG 59.705 50.000 0.00 0.00 35.71 3.35
504 2013 2.802787 ACGTCTGAGAAACCAGTCTG 57.197 50.000 0.00 0.00 35.71 3.51
505 2014 4.767928 AGAATACGTCTGAGAAACCAGTCT 59.232 41.667 0.00 0.00 34.29 3.24
506 2015 5.061920 AGAATACGTCTGAGAAACCAGTC 57.938 43.478 0.00 0.00 34.29 3.51
507 2016 4.523173 TGAGAATACGTCTGAGAAACCAGT 59.477 41.667 0.00 0.00 36.41 4.00
508 2017 5.060662 TGAGAATACGTCTGAGAAACCAG 57.939 43.478 0.00 0.00 36.41 4.00
509 2018 4.082190 CCTGAGAATACGTCTGAGAAACCA 60.082 45.833 0.00 0.00 39.82 3.67
510 2019 4.425520 CCTGAGAATACGTCTGAGAAACC 58.574 47.826 0.00 0.00 39.82 3.27
511 2020 4.425520 CCCTGAGAATACGTCTGAGAAAC 58.574 47.826 0.00 0.00 39.82 2.78
512 2021 3.447586 CCCCTGAGAATACGTCTGAGAAA 59.552 47.826 0.00 0.00 39.82 2.52
513 2022 3.024547 CCCCTGAGAATACGTCTGAGAA 58.975 50.000 0.00 0.00 39.82 2.87
514 2023 2.241430 TCCCCTGAGAATACGTCTGAGA 59.759 50.000 0.00 0.00 39.82 3.27
515 2024 2.656002 TCCCCTGAGAATACGTCTGAG 58.344 52.381 0.00 0.00 37.34 3.35
516 2025 2.820728 TCCCCTGAGAATACGTCTGA 57.179 50.000 0.00 0.00 36.41 3.27
517 2026 2.482142 GCTTCCCCTGAGAATACGTCTG 60.482 54.545 0.00 0.00 36.41 3.51
518 2027 1.757699 GCTTCCCCTGAGAATACGTCT 59.242 52.381 0.00 0.00 40.25 4.18
519 2028 1.480954 TGCTTCCCCTGAGAATACGTC 59.519 52.381 0.00 0.00 0.00 4.34
520 2029 1.568504 TGCTTCCCCTGAGAATACGT 58.431 50.000 0.00 0.00 0.00 3.57
521 2030 2.280628 GTTGCTTCCCCTGAGAATACG 58.719 52.381 0.00 0.00 0.00 3.06
522 2031 2.239907 AGGTTGCTTCCCCTGAGAATAC 59.760 50.000 0.00 0.00 0.00 1.89
523 2032 2.562296 AGGTTGCTTCCCCTGAGAATA 58.438 47.619 0.00 0.00 0.00 1.75
524 2033 1.376649 AGGTTGCTTCCCCTGAGAAT 58.623 50.000 0.00 0.00 0.00 2.40
525 2034 1.149101 AAGGTTGCTTCCCCTGAGAA 58.851 50.000 0.00 0.00 0.00 2.87
526 2035 1.149101 AAAGGTTGCTTCCCCTGAGA 58.851 50.000 0.00 0.00 0.00 3.27
527 2036 1.615392 CAAAAGGTTGCTTCCCCTGAG 59.385 52.381 0.00 0.00 0.00 3.35
528 2037 1.703411 CAAAAGGTTGCTTCCCCTGA 58.297 50.000 0.00 0.00 0.00 3.86
539 2048 3.960755 AGGCAGTTTCTTAGCAAAAGGTT 59.039 39.130 0.00 0.00 0.00 3.50
562 2071 5.705609 TTCTTTTATTCACTCCTGTTGCC 57.294 39.130 0.00 0.00 0.00 4.52
578 2090 7.437713 AGTCCTTTTCCATTCCTTTTCTTTT 57.562 32.000 0.00 0.00 0.00 2.27
605 2118 4.961551 GCATAAATACAACGAACATCACGG 59.038 41.667 0.00 0.00 34.93 4.94
608 2121 6.593770 AGTGAGCATAAATACAACGAACATCA 59.406 34.615 0.00 0.00 0.00 3.07
615 2128 4.034048 GTCCCAGTGAGCATAAATACAACG 59.966 45.833 0.00 0.00 0.00 4.10
631 2153 4.927267 TGTCAAATATCTTGGTCCCAGT 57.073 40.909 0.00 0.00 0.00 4.00
638 2160 8.352201 TCAAAACAGAGTTGTCAAATATCTTGG 58.648 33.333 0.00 0.00 36.23 3.61
653 2175 5.488341 ACACAGTACAAGTCAAAACAGAGT 58.512 37.500 0.00 0.00 0.00 3.24
661 2183 7.299586 GTTTGTTTGTACACAGTACAAGTCAA 58.700 34.615 22.73 22.73 38.47 3.18
662 2184 6.128227 GGTTTGTTTGTACACAGTACAAGTCA 60.128 38.462 18.58 17.89 38.47 3.41
663 2185 6.093082 AGGTTTGTTTGTACACAGTACAAGTC 59.907 38.462 18.58 16.20 38.47 3.01
664 2186 5.941647 AGGTTTGTTTGTACACAGTACAAGT 59.058 36.000 18.58 0.00 38.47 3.16
665 2187 6.315393 AGAGGTTTGTTTGTACACAGTACAAG 59.685 38.462 18.58 0.00 38.47 3.16
666 2188 6.092944 CAGAGGTTTGTTTGTACACAGTACAA 59.907 38.462 16.30 16.30 35.84 2.41
667 2189 5.583061 CAGAGGTTTGTTTGTACACAGTACA 59.417 40.000 5.94 5.94 32.98 2.90
668 2190 5.503520 GCAGAGGTTTGTTTGTACACAGTAC 60.504 44.000 0.00 0.51 32.98 2.73
669 2191 4.573201 GCAGAGGTTTGTTTGTACACAGTA 59.427 41.667 0.00 0.00 32.98 2.74
670 2192 3.377172 GCAGAGGTTTGTTTGTACACAGT 59.623 43.478 0.00 0.00 32.98 3.55
671 2193 3.376859 TGCAGAGGTTTGTTTGTACACAG 59.623 43.478 0.00 0.00 32.98 3.66
672 2194 3.348119 TGCAGAGGTTTGTTTGTACACA 58.652 40.909 0.00 0.00 32.98 3.72
673 2195 4.568152 ATGCAGAGGTTTGTTTGTACAC 57.432 40.909 0.00 0.00 32.98 2.90
674 2196 5.126779 TGTATGCAGAGGTTTGTTTGTACA 58.873 37.500 0.00 0.00 0.00 2.90
675 2197 5.682943 TGTATGCAGAGGTTTGTTTGTAC 57.317 39.130 0.00 0.00 0.00 2.90
676 2198 6.264292 ACAATGTATGCAGAGGTTTGTTTGTA 59.736 34.615 0.00 0.00 0.00 2.41
677 2199 5.068987 ACAATGTATGCAGAGGTTTGTTTGT 59.931 36.000 0.00 0.00 0.00 2.83
678 2200 5.531634 ACAATGTATGCAGAGGTTTGTTTG 58.468 37.500 0.00 0.00 0.00 2.93
679 2201 5.789643 ACAATGTATGCAGAGGTTTGTTT 57.210 34.783 0.00 0.00 0.00 2.83
680 2202 7.176515 TCAATACAATGTATGCAGAGGTTTGTT 59.823 33.333 6.67 0.00 29.19 2.83
681 2203 6.658816 TCAATACAATGTATGCAGAGGTTTGT 59.341 34.615 6.67 5.30 30.74 2.83
682 2204 6.968904 GTCAATACAATGTATGCAGAGGTTTG 59.031 38.462 6.67 0.00 0.00 2.93
683 2205 6.886459 AGTCAATACAATGTATGCAGAGGTTT 59.114 34.615 6.67 0.00 0.00 3.27
684 2206 6.418101 AGTCAATACAATGTATGCAGAGGTT 58.582 36.000 6.67 0.00 0.00 3.50
685 2207 5.994250 AGTCAATACAATGTATGCAGAGGT 58.006 37.500 6.67 0.00 0.00 3.85
686 2208 6.317140 ACAAGTCAATACAATGTATGCAGAGG 59.683 38.462 6.67 0.00 0.00 3.69
687 2209 7.312657 ACAAGTCAATACAATGTATGCAGAG 57.687 36.000 6.67 0.00 0.00 3.35
688 2210 8.040727 AGTACAAGTCAATACAATGTATGCAGA 58.959 33.333 6.67 3.39 34.63 4.26
689 2211 8.201554 AGTACAAGTCAATACAATGTATGCAG 57.798 34.615 6.67 1.07 34.63 4.41
690 2212 9.093970 GTAGTACAAGTCAATACAATGTATGCA 57.906 33.333 6.67 0.00 34.63 3.96
691 2213 8.266682 CGTAGTACAAGTCAATACAATGTATGC 58.733 37.037 6.67 1.32 34.63 3.14
692 2214 9.297586 ACGTAGTACAAGTCAATACAATGTATG 57.702 33.333 6.67 2.12 41.94 2.39
694 2216 9.992910 CTACGTAGTACAAGTCAATACAATGTA 57.007 33.333 14.66 0.00 45.11 2.29
695 2217 8.733458 TCTACGTAGTACAAGTCAATACAATGT 58.267 33.333 21.53 0.00 45.11 2.71
696 2218 9.563898 TTCTACGTAGTACAAGTCAATACAATG 57.436 33.333 21.53 0.00 45.11 2.82
698 2220 9.398170 GTTTCTACGTAGTACAAGTCAATACAA 57.602 33.333 21.53 1.34 45.11 2.41
699 2221 8.567104 TGTTTCTACGTAGTACAAGTCAATACA 58.433 33.333 21.53 7.78 45.11 2.29
700 2222 8.955061 TGTTTCTACGTAGTACAAGTCAATAC 57.045 34.615 21.53 5.41 45.11 1.89
701 2223 9.964303 TTTGTTTCTACGTAGTACAAGTCAATA 57.036 29.630 27.85 18.30 45.11 1.90
702 2224 8.758715 GTTTGTTTCTACGTAGTACAAGTCAAT 58.241 33.333 27.85 0.00 45.11 2.57
715 2237 3.188159 TGCAGAGGTTTGTTTCTACGT 57.812 42.857 0.00 0.00 0.00 3.57
717 2239 6.743575 ATGTATGCAGAGGTTTGTTTCTAC 57.256 37.500 0.00 0.00 0.00 2.59
740 2269 1.376166 CCACCGGCGGTCAATACAA 60.376 57.895 31.82 0.00 31.02 2.41
755 2284 0.171455 CTCACGTCCTACTCTGCCAC 59.829 60.000 0.00 0.00 0.00 5.01
763 2292 2.937799 CTCTACTCCACTCACGTCCTAC 59.062 54.545 0.00 0.00 0.00 3.18
764 2293 2.570752 ACTCTACTCCACTCACGTCCTA 59.429 50.000 0.00 0.00 0.00 2.94
765 2294 1.351683 ACTCTACTCCACTCACGTCCT 59.648 52.381 0.00 0.00 0.00 3.85
766 2295 1.738908 GACTCTACTCCACTCACGTCC 59.261 57.143 0.00 0.00 0.00 4.79
767 2296 1.394227 CGACTCTACTCCACTCACGTC 59.606 57.143 0.00 0.00 0.00 4.34
795 2324 4.826733 TGTGAAAGGCATGTGTTCATACTT 59.173 37.500 9.91 0.00 34.04 2.24
796 2325 4.216257 GTGTGAAAGGCATGTGTTCATACT 59.784 41.667 18.64 0.00 39.15 2.12
799 2328 2.030893 CGTGTGAAAGGCATGTGTTCAT 60.031 45.455 9.91 0.00 34.04 2.57
844 2380 1.202964 GCATGTCCATCCATCCATCCA 60.203 52.381 0.00 0.00 0.00 3.41
845 2381 1.542492 GCATGTCCATCCATCCATCC 58.458 55.000 0.00 0.00 0.00 3.51
846 2382 1.075050 AGGCATGTCCATCCATCCATC 59.925 52.381 8.58 0.00 37.29 3.51
847 2383 1.075050 GAGGCATGTCCATCCATCCAT 59.925 52.381 8.58 0.00 37.29 3.41
848 2384 0.475475 GAGGCATGTCCATCCATCCA 59.525 55.000 8.58 0.00 37.29 3.41
849 2385 0.604780 CGAGGCATGTCCATCCATCC 60.605 60.000 8.58 0.00 37.29 3.51
850 2386 0.604780 CCGAGGCATGTCCATCCATC 60.605 60.000 8.58 0.00 37.29 3.51
851 2387 1.453235 CCGAGGCATGTCCATCCAT 59.547 57.895 8.58 0.00 37.29 3.41
857 2393 4.899239 CCTCGCCGAGGCATGTCC 62.899 72.222 21.84 0.00 43.29 4.02
887 2427 5.423931 TCTGGATGCTATATATAACCGGCAA 59.576 40.000 0.00 0.00 33.44 4.52
891 2431 5.928839 GCCATCTGGATGCTATATATAACCG 59.071 44.000 0.00 0.00 37.49 4.44
909 2449 0.031716 TGACTCTAGGCCAGCCATCT 60.032 55.000 12.03 0.00 38.92 2.90
910 2450 1.001860 GATGACTCTAGGCCAGCCATC 59.998 57.143 12.03 3.58 38.92 3.51
911 2451 1.055040 GATGACTCTAGGCCAGCCAT 58.945 55.000 12.03 0.00 38.92 4.40
912 2452 0.325577 TGATGACTCTAGGCCAGCCA 60.326 55.000 12.03 0.00 38.92 4.75
915 2455 1.047002 CCCTGATGACTCTAGGCCAG 58.953 60.000 5.01 0.00 0.00 4.85
916 2456 0.636647 TCCCTGATGACTCTAGGCCA 59.363 55.000 5.01 0.00 0.00 5.36
920 2460 3.499338 AGCTGATCCCTGATGACTCTAG 58.501 50.000 0.00 0.00 0.00 2.43
921 2461 3.609256 AGCTGATCCCTGATGACTCTA 57.391 47.619 0.00 0.00 0.00 2.43
922 2462 2.475339 AGCTGATCCCTGATGACTCT 57.525 50.000 0.00 0.00 0.00 3.24
932 2472 8.512966 AATTTCTTAAACTAGAAGCTGATCCC 57.487 34.615 0.00 0.00 35.69 3.85
943 2483 4.698304 TGGCCGTGGAATTTCTTAAACTAG 59.302 41.667 0.00 0.00 0.00 2.57
945 2485 3.492337 TGGCCGTGGAATTTCTTAAACT 58.508 40.909 0.00 0.00 0.00 2.66
950 2490 1.995376 AGTTGGCCGTGGAATTTCTT 58.005 45.000 0.00 0.00 0.00 2.52
960 2500 1.238439 CAAGATGACAAGTTGGCCGT 58.762 50.000 6.18 0.00 0.00 5.68
963 2503 1.068055 CAGGCAAGATGACAAGTTGGC 60.068 52.381 15.17 15.17 44.76 4.52
970 2510 1.483827 CTCTAGCCAGGCAAGATGACA 59.516 52.381 15.80 0.00 0.00 3.58
993 2535 2.899339 GCAAGCGCCATCCTCTCC 60.899 66.667 2.29 0.00 0.00 3.71
1183 2731 1.541588 AGTTTCAGGCGAAATCTTGGC 59.458 47.619 7.54 0.00 42.90 4.52
1184 2732 2.813754 TCAGTTTCAGGCGAAATCTTGG 59.186 45.455 7.54 0.00 42.90 3.61
1185 2733 3.120060 CCTCAGTTTCAGGCGAAATCTTG 60.120 47.826 7.54 7.32 42.90 3.02
1186 2734 3.077359 CCTCAGTTTCAGGCGAAATCTT 58.923 45.455 7.54 0.00 42.90 2.40
1187 2735 2.616510 CCCTCAGTTTCAGGCGAAATCT 60.617 50.000 7.54 5.13 42.90 2.40
1188 2736 1.740025 CCCTCAGTTTCAGGCGAAATC 59.260 52.381 7.54 3.45 42.90 2.17
1189 2737 1.073923 ACCCTCAGTTTCAGGCGAAAT 59.926 47.619 7.54 0.00 42.90 2.17
1192 2740 0.034896 GAACCCTCAGTTTCAGGCGA 59.965 55.000 0.00 0.00 39.40 5.54
1193 2741 0.250295 TGAACCCTCAGTTTCAGGCG 60.250 55.000 0.00 0.00 39.40 5.52
1194 2742 1.815003 CATGAACCCTCAGTTTCAGGC 59.185 52.381 0.00 0.00 39.40 4.85
1201 2900 1.270305 CGTGTGACATGAACCCTCAGT 60.270 52.381 0.00 0.00 34.23 3.41
1229 2928 2.159599 GGCGAAATCTTGTCAGCTTCAG 60.160 50.000 0.00 0.00 0.00 3.02
1234 2933 1.425428 CGGGCGAAATCTTGTCAGC 59.575 57.895 0.00 0.00 0.00 4.26
1278 2977 1.523938 GCATGAGCCTTCGGGTACC 60.524 63.158 2.17 2.17 39.50 3.34
1279 2978 1.883084 CGCATGAGCCTTCGGGTAC 60.883 63.158 0.00 0.00 37.52 3.34
1282 2981 2.892425 GTCGCATGAGCCTTCGGG 60.892 66.667 0.00 0.00 37.52 5.14
1287 2986 2.046892 GGTGTGTCGCATGAGCCT 60.047 61.111 0.00 0.00 37.52 4.58
1298 2997 1.275291 CCGATACAGGTTGAGGTGTGT 59.725 52.381 0.00 0.00 0.00 3.72
1302 3001 2.747177 TCATCCGATACAGGTTGAGGT 58.253 47.619 0.00 0.00 35.67 3.85
1328 3027 1.080501 TCTTTGCGAGCTCCAGACG 60.081 57.895 8.47 0.00 0.00 4.18
1330 3029 1.293498 GGTCTTTGCGAGCTCCAGA 59.707 57.895 8.47 1.80 37.18 3.86
1336 3035 3.093278 CATCGGGTCTTTGCGAGC 58.907 61.111 0.00 0.00 39.41 5.03
1352 3051 1.305201 GTTTTCAGGAACTCCGTGCA 58.695 50.000 0.00 0.00 42.08 4.57
1369 3068 4.123545 GCACGGGCCCTATGGGTT 62.124 66.667 22.43 0.00 46.51 4.11
1374 3073 4.626081 GCATCGCACGGGCCCTAT 62.626 66.667 22.43 4.55 36.38 2.57
1382 3081 1.585668 CAACTTCTCTAGCATCGCACG 59.414 52.381 0.00 0.00 0.00 5.34
1393 3092 7.872113 ACACAAGAAAAATCTCAACTTCTCT 57.128 32.000 0.00 0.00 0.00 3.10
1442 3141 9.816787 GGACCCAATACAATTAAGGGATAATTA 57.183 33.333 2.29 0.00 41.27 1.40
1483 3183 2.374184 TCCGATGCTAACAATTTGGGG 58.626 47.619 0.78 0.00 0.00 4.96
1499 3199 1.326951 TTGATGCACGAGGGATCCGA 61.327 55.000 5.45 0.00 43.18 4.55
1501 3201 1.071385 AGATTGATGCACGAGGGATCC 59.929 52.381 1.92 1.92 43.18 3.36
1509 3209 1.268896 GCATTGGGAGATTGATGCACG 60.269 52.381 0.00 0.00 43.23 5.34
1510 3210 2.029623 AGCATTGGGAGATTGATGCAC 58.970 47.619 9.49 0.00 45.47 4.57
1525 3253 4.771590 TTCAGCGAAAGAAATGAGCATT 57.228 36.364 0.00 0.00 0.00 3.56
1560 3288 7.802738 TGTAAGAGTTGGTCGATTTAAACATG 58.197 34.615 0.00 0.00 0.00 3.21
1594 3322 6.689669 GGCGCGTAATTTTCAGTTTATGTAAT 59.310 34.615 8.43 0.00 0.00 1.89
1617 3345 2.706890 TCGATTTACCCAAAGACTGGC 58.293 47.619 0.00 0.00 44.90 4.85
1777 3510 4.931661 TCCCGACATACAAAGATAGACC 57.068 45.455 0.00 0.00 0.00 3.85
1779 3512 7.649533 TTAGTTCCCGACATACAAAGATAGA 57.350 36.000 0.00 0.00 0.00 1.98
1780 3513 8.141909 TGATTAGTTCCCGACATACAAAGATAG 58.858 37.037 0.00 0.00 0.00 2.08
1781 3514 7.924412 GTGATTAGTTCCCGACATACAAAGATA 59.076 37.037 0.00 0.00 0.00 1.98
1782 3515 6.761714 GTGATTAGTTCCCGACATACAAAGAT 59.238 38.462 0.00 0.00 0.00 2.40
1783 3516 6.103997 GTGATTAGTTCCCGACATACAAAGA 58.896 40.000 0.00 0.00 0.00 2.52
1786 3519 5.408880 TGTGATTAGTTCCCGACATACAA 57.591 39.130 0.00 0.00 0.00 2.41
1787 3520 5.408880 TTGTGATTAGTTCCCGACATACA 57.591 39.130 0.00 0.00 0.00 2.29
1788 3521 8.088981 AGATATTGTGATTAGTTCCCGACATAC 58.911 37.037 0.00 0.00 0.00 2.39
1790 3523 7.067496 AGATATTGTGATTAGTTCCCGACAT 57.933 36.000 0.00 0.00 0.00 3.06
1863 3873 7.017254 ACAATTTCTACTTCTAGTTCCAGGGAA 59.983 37.037 0.00 0.00 0.00 3.97
1864 3874 6.500751 ACAATTTCTACTTCTAGTTCCAGGGA 59.499 38.462 0.00 0.00 0.00 4.20
1865 3875 6.712276 ACAATTTCTACTTCTAGTTCCAGGG 58.288 40.000 0.00 0.00 0.00 4.45
1866 3876 7.361286 GCAACAATTTCTACTTCTAGTTCCAGG 60.361 40.741 0.00 0.00 0.00 4.45
1867 3877 7.522374 GCAACAATTTCTACTTCTAGTTCCAG 58.478 38.462 0.00 0.00 0.00 3.86
1868 3878 6.147164 CGCAACAATTTCTACTTCTAGTTCCA 59.853 38.462 0.00 0.00 0.00 3.53
1869 3879 6.402226 CCGCAACAATTTCTACTTCTAGTTCC 60.402 42.308 0.00 0.00 0.00 3.62
1870 3880 6.367969 TCCGCAACAATTTCTACTTCTAGTTC 59.632 38.462 0.00 0.00 0.00 3.01
1871 3881 6.147328 GTCCGCAACAATTTCTACTTCTAGTT 59.853 38.462 0.00 0.00 0.00 2.24
1892 3902 9.025020 GCTGTCTTTACATGATATATATGTCCG 57.975 37.037 0.00 1.66 39.36 4.79
1913 3923 2.163211 GGCTCATTCCTCAAAAGCTGTC 59.837 50.000 0.00 0.00 33.50 3.51
1915 3925 2.163815 CTGGCTCATTCCTCAAAAGCTG 59.836 50.000 0.00 0.00 33.50 4.24
1917 3927 2.440409 TCTGGCTCATTCCTCAAAAGC 58.560 47.619 0.00 0.00 0.00 3.51
1931 3941 2.842496 TGAGAAATGGTCAGATCTGGCT 59.158 45.455 25.69 6.90 35.13 4.75
1946 3956 4.141041 TCCCTGATTTTCCCTTGTGAGAAA 60.141 41.667 0.00 0.00 0.00 2.52
1953 3963 3.580022 AGCTTTTCCCTGATTTTCCCTTG 59.420 43.478 0.00 0.00 0.00 3.61
1955 3965 3.549898 AGCTTTTCCCTGATTTTCCCT 57.450 42.857 0.00 0.00 0.00 4.20
1960 3970 2.613129 AGCCAAGCTTTTCCCTGATTT 58.387 42.857 0.00 0.00 33.89 2.17
2008 4029 3.403057 CACACGGACGAAGCGGTG 61.403 66.667 0.00 11.42 42.63 4.94
2009 4030 3.598715 TCACACGGACGAAGCGGT 61.599 61.111 0.00 0.00 0.00 5.68
2037 4058 5.081315 AGATAATACTAGGTGAGCCCTGT 57.919 43.478 0.00 0.00 45.81 4.00
2056 4077 7.174772 GGGTTCAATTGCAAAACCATAAAAGAT 59.825 33.333 25.48 0.00 43.46 2.40
2058 4079 6.486320 AGGGTTCAATTGCAAAACCATAAAAG 59.514 34.615 25.48 0.88 43.46 2.27
2068 4089 4.213564 ACAACAAGGGTTCAATTGCAAA 57.786 36.364 1.71 0.00 34.21 3.68
2075 4096 5.393243 CGGAAAAACTACAACAAGGGTTCAA 60.393 40.000 0.00 0.00 34.21 2.69
2079 4100 2.359848 GCGGAAAAACTACAACAAGGGT 59.640 45.455 0.00 0.00 0.00 4.34
2085 4106 0.308376 TGCGGCGGAAAAACTACAAC 59.692 50.000 9.78 0.00 0.00 3.32
2096 4117 0.386476 ATACGAGTTATTGCGGCGGA 59.614 50.000 9.78 1.34 0.00 5.54
2106 4127 4.441495 CCAGATCCTGCAACATACGAGTTA 60.441 45.833 0.00 0.00 0.00 2.24
2135 4156 1.880340 CAACTGCGCTCGAGGGATC 60.880 63.158 31.36 15.82 0.00 3.36
2170 4191 2.541233 AGAGAAAGAGCAGGAGCCTA 57.459 50.000 0.00 0.00 43.56 3.93
2204 4225 5.621104 CGGCAGGACTTTTGCAACATAAATA 60.621 40.000 0.00 0.00 43.28 1.40
2225 4246 3.189080 TGCAACATAGATGATATTGCGGC 59.811 43.478 10.13 0.00 46.81 6.53
2283 4307 3.758755 ACAGAGTTCATGTTGCAGAGA 57.241 42.857 0.00 0.00 0.00 3.10
2302 4326 0.823356 TGCAGAACCCTCCTTGCAAC 60.823 55.000 0.00 0.00 0.00 4.17
2309 4333 0.890683 CCAATGTTGCAGAACCCTCC 59.109 55.000 0.00 0.00 0.00 4.30
2325 4349 4.282957 TCCTCATTATTGCAACAAAGCCAA 59.717 37.500 0.00 0.00 0.00 4.52
2327 4351 4.176271 GTCCTCATTATTGCAACAAAGCC 58.824 43.478 0.00 0.00 0.00 4.35
2328 4352 4.808558 TGTCCTCATTATTGCAACAAAGC 58.191 39.130 0.00 0.00 0.00 3.51
2329 4353 6.449698 ACTTGTCCTCATTATTGCAACAAAG 58.550 36.000 0.00 0.00 0.00 2.77


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

AutoCloner maintained by Alex Coulton.