Multiple sequence alignment - TraesCS4D01G020700

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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 TraesCS4D01G020700 chr4D 100.000 2402 0 0 1 2402 8941036 8938635 0.000000e+00 4436.0
1 TraesCS4D01G020700 chr4A 85.474 1370 70 52 743 2053 594392366 594393665 0.000000e+00 1308.0
2 TraesCS4D01G020700 chr4A 88.245 638 43 22 6 636 594391322 594391934 0.000000e+00 734.0
3 TraesCS4D01G020700 chr4B 87.133 1158 77 40 359 1477 16878528 16877404 0.000000e+00 1247.0
4 TraesCS4D01G020700 chr4B 94.074 135 5 1 155 286 16878670 16878536 4.050000e-48 202.0
5 TraesCS4D01G020700 chr4B 91.589 107 8 1 5 110 16878770 16878664 1.920000e-31 147.0
6 TraesCS4D01G020700 chr4B 81.176 170 12 13 1582 1742 16877319 16877161 4.190000e-23 119.0
7 TraesCS4D01G020700 chr5A 86.441 118 14 2 1130 1246 7472362 7472478 6.970000e-26 128.0
8 TraesCS4D01G020700 chr5A 97.143 35 1 0 2144 2178 704831662 704831628 2.580000e-05 60.2
9 TraesCS4D01G020700 chr5B 87.500 104 11 2 1144 1246 9289637 9289739 4.190000e-23 119.0
10 TraesCS4D01G020700 chr5B 100.000 29 0 0 658 686 710618042 710618070 1.000000e-03 54.7
11 TraesCS4D01G020700 chr6B 100.000 28 0 0 657 684 11317287 11317260 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 TraesCS4D01G020700 chr4D 8938635 8941036 2401 True 4436.00 4436 100.0000 1 2402 1 chr4D.!!$R1 2401
1 TraesCS4D01G020700 chr4A 594391322 594393665 2343 False 1021.00 1308 86.8595 6 2053 2 chr4A.!!$F1 2047
2 TraesCS4D01G020700 chr4B 16877161 16878770 1609 True 428.75 1247 88.4930 5 1742 4 chr4B.!!$R1 1737

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
986 1336 0.39086 ATCACATCGACTGCTAGCCC 59.609 55.0 13.29 0.27 0.0 5.19 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2071 2529 0.036875 TCGCAGTCTCAGACTCTGGA 59.963 55.0 3.6 0.0 41.37 3.86 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
137 141 1.850755 TCCTCCCGCCCTTTTCCTT 60.851 57.895 0.00 0.00 0.00 3.36
188 192 0.396556 TGCTACTCACTCCGGCCATA 60.397 55.000 2.24 0.00 0.00 2.74
232 236 0.529119 GTGTACCTAATGCGACCCCG 60.529 60.000 0.00 0.00 39.16 5.73
347 351 0.684153 CCAAATTGGATGCCGACCCT 60.684 55.000 6.04 0.00 40.96 4.34
408 414 7.696992 ATTAAAAAGGGCGAGTTAAGATTGA 57.303 32.000 0.00 0.00 0.00 2.57
410 416 6.399639 AAAAAGGGCGAGTTAAGATTGAAA 57.600 33.333 0.00 0.00 0.00 2.69
412 422 4.287766 AGGGCGAGTTAAGATTGAAAGT 57.712 40.909 0.00 0.00 0.00 2.66
416 426 5.048991 GGGCGAGTTAAGATTGAAAGTTTGA 60.049 40.000 0.00 0.00 0.00 2.69
434 444 1.425448 TGATGATAGGGAGGCGAGAGA 59.575 52.381 0.00 0.00 0.00 3.10
439 449 1.279749 TAGGGAGGCGAGAGAGGTCA 61.280 60.000 0.00 0.00 0.00 4.02
554 567 2.637947 CAGAGATGAGAGGTCGAGACA 58.362 52.381 5.55 0.00 0.00 3.41
558 571 4.709397 AGAGATGAGAGGTCGAGACAATTT 59.291 41.667 5.55 0.00 0.00 1.82
561 574 4.179926 TGAGAGGTCGAGACAATTTGAG 57.820 45.455 2.79 0.00 0.00 3.02
563 576 2.900546 AGAGGTCGAGACAATTTGAGGT 59.099 45.455 2.79 0.00 0.00 3.85
581 594 4.402474 TGAGGTAGTGTAGATGACATGTGG 59.598 45.833 1.15 0.00 41.14 4.17
599 612 4.612412 GTTCGGGTCCACACGGCA 62.612 66.667 0.67 0.00 44.15 5.69
618 631 4.678044 CGGCAGTGATCATACTACACAAGT 60.678 45.833 0.00 0.00 42.62 3.16
619 632 5.449999 CGGCAGTGATCATACTACACAAGTA 60.450 44.000 0.00 0.00 44.76 2.24
631 751 5.967088 ACTACACAAGTAATACTGCAGAGG 58.033 41.667 23.35 0.00 36.36 3.69
655 834 2.481449 CCAAAATACTCCCTCCGTCTCG 60.481 54.545 0.00 0.00 0.00 4.04
678 857 1.961133 TTTTGGGACGGAGGGAGTAT 58.039 50.000 0.00 0.00 0.00 2.12
706 885 8.947115 AGATTCGACCGAGAGAAAATTAATTTT 58.053 29.630 22.95 22.95 42.24 1.82
727 908 3.206150 TCTCAGTGTTCAGTTTCTTGCC 58.794 45.455 0.00 0.00 0.00 4.52
810 1153 5.247340 CGTGCTTGCTTTTTACAAAGTTTG 58.753 37.500 14.13 14.13 41.51 2.93
830 1173 2.364970 TGTCAAGGGCAAAACAGGAATG 59.635 45.455 0.00 0.00 0.00 2.67
970 1320 1.565759 CCCTTCCCCTTCATCACATCA 59.434 52.381 0.00 0.00 0.00 3.07
971 1321 2.648059 CCTTCCCCTTCATCACATCAC 58.352 52.381 0.00 0.00 0.00 3.06
982 1332 3.381272 TCATCACATCACATCGACTGCTA 59.619 43.478 0.00 0.00 0.00 3.49
983 1333 3.427161 TCACATCACATCGACTGCTAG 57.573 47.619 0.00 0.00 0.00 3.42
984 1334 1.857217 CACATCACATCGACTGCTAGC 59.143 52.381 8.10 8.10 0.00 3.42
985 1335 1.202463 ACATCACATCGACTGCTAGCC 60.202 52.381 13.29 0.00 0.00 3.93
986 1336 0.390860 ATCACATCGACTGCTAGCCC 59.609 55.000 13.29 0.27 0.00 5.19
1289 1639 4.592192 GGCGCCGCTGATGCTCTA 62.592 66.667 12.58 0.00 36.97 2.43
1291 1641 3.026879 CGCCGCTGATGCTCTACG 61.027 66.667 0.00 0.00 36.97 3.51
1365 1724 2.690510 AGGAAGGGCAGGAGGAGC 60.691 66.667 0.00 0.00 0.00 4.70
1405 1779 5.036737 GCTACGGTGATCAAATTTGAATGG 58.963 41.667 23.91 13.78 41.13 3.16
1415 1789 3.925688 AATTTGAATGGTCGATCGACG 57.074 42.857 34.69 3.92 45.41 5.12
1416 1790 2.357327 TTTGAATGGTCGATCGACGT 57.643 45.000 34.69 25.36 45.41 4.34
1417 1791 1.904144 TTGAATGGTCGATCGACGTC 58.096 50.000 34.69 29.78 45.41 4.34
1462 1837 4.739046 AGCTTCTTGACGTTGATTCTTG 57.261 40.909 0.00 0.00 0.00 3.02
1464 1839 4.450419 AGCTTCTTGACGTTGATTCTTGAG 59.550 41.667 0.00 0.00 0.00 3.02
1465 1840 4.706527 CTTCTTGACGTTGATTCTTGAGC 58.293 43.478 0.00 0.00 0.00 4.26
1466 1841 3.995199 TCTTGACGTTGATTCTTGAGCT 58.005 40.909 0.00 0.00 0.00 4.09
1467 1842 4.380531 TCTTGACGTTGATTCTTGAGCTT 58.619 39.130 0.00 0.00 0.00 3.74
1468 1843 4.816385 TCTTGACGTTGATTCTTGAGCTTT 59.184 37.500 0.00 0.00 0.00 3.51
1469 1844 4.472691 TGACGTTGATTCTTGAGCTTTG 57.527 40.909 0.00 0.00 0.00 2.77
1470 1845 3.876914 TGACGTTGATTCTTGAGCTTTGT 59.123 39.130 0.00 0.00 0.00 2.83
1471 1846 4.335315 TGACGTTGATTCTTGAGCTTTGTT 59.665 37.500 0.00 0.00 0.00 2.83
1472 1847 4.601019 ACGTTGATTCTTGAGCTTTGTTG 58.399 39.130 0.00 0.00 0.00 3.33
1473 1848 3.423206 CGTTGATTCTTGAGCTTTGTTGC 59.577 43.478 0.00 0.00 0.00 4.17
1474 1849 4.362279 GTTGATTCTTGAGCTTTGTTGCA 58.638 39.130 0.00 0.00 34.99 4.08
1475 1850 4.652421 TGATTCTTGAGCTTTGTTGCAA 57.348 36.364 0.00 0.00 34.99 4.08
1476 1851 4.613944 TGATTCTTGAGCTTTGTTGCAAG 58.386 39.130 0.00 4.60 39.17 4.01
1477 1852 2.497107 TCTTGAGCTTTGTTGCAAGC 57.503 45.000 0.00 0.00 42.10 4.01
1525 1940 7.716998 GGTGTATGGATGATTGATTAACTGAGT 59.283 37.037 0.00 0.00 0.00 3.41
1553 1968 9.869844 CAACTACATACTACCTTATGTACGTAC 57.130 37.037 18.90 18.90 41.82 3.67
1576 1991 9.326413 GTACAAGTGTAATTATAGGCTGTGAAT 57.674 33.333 0.00 0.00 31.52 2.57
1577 1992 8.807948 ACAAGTGTAATTATAGGCTGTGAATT 57.192 30.769 0.00 2.92 0.00 2.17
1578 1993 9.899661 ACAAGTGTAATTATAGGCTGTGAATTA 57.100 29.630 0.00 1.93 0.00 1.40
1659 2074 4.699257 AGAAGTGGAGAAGATGTGAAATGC 59.301 41.667 0.00 0.00 0.00 3.56
1665 2080 7.395489 AGTGGAGAAGATGTGAAATGCTATTTT 59.605 33.333 0.00 0.00 0.00 1.82
1734 2159 2.174685 TGCCCTCCTTGCATACTCTA 57.825 50.000 0.00 0.00 32.85 2.43
1790 2247 2.991250 TGAGAAGATTAAGTGGCCAGC 58.009 47.619 5.11 0.39 0.00 4.85
1791 2248 1.936547 GAGAAGATTAAGTGGCCAGCG 59.063 52.381 5.11 0.00 0.00 5.18
1792 2249 1.279271 AGAAGATTAAGTGGCCAGCGT 59.721 47.619 5.11 1.93 0.00 5.07
1793 2250 2.500098 AGAAGATTAAGTGGCCAGCGTA 59.500 45.455 5.11 0.82 0.00 4.42
1794 2251 2.604046 AGATTAAGTGGCCAGCGTAG 57.396 50.000 5.11 0.00 0.00 3.51
1825 2282 1.278127 ACGGGTGCTTAGTGCTTACAT 59.722 47.619 0.00 0.00 43.37 2.29
1831 2288 6.568844 CGGGTGCTTAGTGCTTACATTAAAAA 60.569 38.462 0.00 0.00 43.37 1.94
1832 2289 7.320399 GGGTGCTTAGTGCTTACATTAAAAAT 58.680 34.615 0.00 0.00 43.37 1.82
1833 2290 8.463607 GGGTGCTTAGTGCTTACATTAAAAATA 58.536 33.333 0.00 0.00 43.37 1.40
1834 2291 9.503427 GGTGCTTAGTGCTTACATTAAAAATAG 57.497 33.333 0.00 0.00 43.37 1.73
1835 2292 9.010366 GTGCTTAGTGCTTACATTAAAAATAGC 57.990 33.333 0.00 0.00 43.37 2.97
1843 2300 6.129352 GCTTACATTAAAAATAGCGCTGATGC 60.129 38.462 22.90 4.55 0.00 3.91
1845 2302 5.276270 ACATTAAAAATAGCGCTGATGCTG 58.724 37.500 22.90 9.55 46.70 4.41
1853 2310 2.358957 AGCGCTGATGCTGTTCAAATA 58.641 42.857 10.39 0.00 45.28 1.40
1855 2312 4.129380 AGCGCTGATGCTGTTCAAATATA 58.871 39.130 10.39 0.00 45.28 0.86
1880 2337 3.790212 CAGCATGCACTAGATTCGATG 57.210 47.619 21.98 0.11 0.00 3.84
1890 2347 1.296867 GATTCGATGCGGCGTTGTG 60.297 57.895 9.37 0.00 0.00 3.33
1892 2349 1.966493 ATTCGATGCGGCGTTGTGTC 61.966 55.000 9.37 0.00 0.00 3.67
1907 2364 0.166814 GTGTCGCTGAATTGCTGGAC 59.833 55.000 0.00 0.00 0.00 4.02
1954 2411 1.228675 CTGCTTTGGCCTGGGTTCT 60.229 57.895 3.32 0.00 37.74 3.01
1955 2412 0.038166 CTGCTTTGGCCTGGGTTCTA 59.962 55.000 3.32 0.00 37.74 2.10
1958 2415 1.668419 CTTTGGCCTGGGTTCTATCG 58.332 55.000 3.32 0.00 0.00 2.92
1959 2416 0.254747 TTTGGCCTGGGTTCTATCGG 59.745 55.000 3.32 0.00 0.00 4.18
1960 2417 0.619255 TTGGCCTGGGTTCTATCGGA 60.619 55.000 3.32 0.00 0.00 4.55
1961 2418 0.619255 TGGCCTGGGTTCTATCGGAA 60.619 55.000 3.32 0.00 0.00 4.30
1962 2419 0.106894 GGCCTGGGTTCTATCGGAAG 59.893 60.000 0.00 0.00 34.23 3.46
1963 2420 0.831307 GCCTGGGTTCTATCGGAAGT 59.169 55.000 0.00 0.00 34.23 3.01
1964 2421 1.209747 GCCTGGGTTCTATCGGAAGTT 59.790 52.381 0.00 0.00 34.23 2.66
1965 2422 2.433239 GCCTGGGTTCTATCGGAAGTTA 59.567 50.000 0.00 0.00 34.23 2.24
1966 2423 3.118519 GCCTGGGTTCTATCGGAAGTTAA 60.119 47.826 0.00 0.00 34.23 2.01
1989 2447 2.476821 CACTCCGTTAAACAGACCGTT 58.523 47.619 0.00 0.00 40.50 4.44
2004 2462 1.947456 ACCGTTCTGCCTTTCTTCAAC 59.053 47.619 0.00 0.00 0.00 3.18
2010 2468 3.811083 TCTGCCTTTCTTCAACGGTTTA 58.189 40.909 0.00 0.00 0.00 2.01
2053 2511 1.217882 ACGTTTCAACAGAGCCTTCG 58.782 50.000 0.00 0.00 0.00 3.79
2054 2512 1.217882 CGTTTCAACAGAGCCTTCGT 58.782 50.000 0.00 0.00 0.00 3.85
2055 2513 2.223876 ACGTTTCAACAGAGCCTTCGTA 60.224 45.455 0.00 0.00 0.00 3.43
2056 2514 2.408704 CGTTTCAACAGAGCCTTCGTAG 59.591 50.000 0.00 0.00 0.00 3.51
2057 2515 3.391049 GTTTCAACAGAGCCTTCGTAGT 58.609 45.455 0.00 0.00 0.00 2.73
2058 2516 3.746045 TTCAACAGAGCCTTCGTAGTT 57.254 42.857 0.00 0.00 0.00 2.24
2059 2517 3.299340 TCAACAGAGCCTTCGTAGTTC 57.701 47.619 0.00 0.00 0.00 3.01
2060 2518 1.986378 CAACAGAGCCTTCGTAGTTCG 59.014 52.381 0.00 0.00 41.41 3.95
2061 2519 1.245732 ACAGAGCCTTCGTAGTTCGT 58.754 50.000 0.00 0.00 40.80 3.85
2062 2520 2.430465 ACAGAGCCTTCGTAGTTCGTA 58.570 47.619 0.00 0.00 40.80 3.43
2063 2521 2.419324 ACAGAGCCTTCGTAGTTCGTAG 59.581 50.000 0.00 0.00 40.80 3.51
2064 2522 2.419324 CAGAGCCTTCGTAGTTCGTAGT 59.581 50.000 0.00 0.00 40.80 2.73
2065 2523 2.677337 AGAGCCTTCGTAGTTCGTAGTC 59.323 50.000 0.00 0.00 40.80 2.59
2066 2524 1.742268 AGCCTTCGTAGTTCGTAGTCC 59.258 52.381 0.00 0.00 40.80 3.85
2067 2525 1.742268 GCCTTCGTAGTTCGTAGTCCT 59.258 52.381 0.00 0.00 40.80 3.85
2068 2526 2.939103 GCCTTCGTAGTTCGTAGTCCTA 59.061 50.000 0.00 0.00 40.80 2.94
2069 2527 3.242576 GCCTTCGTAGTTCGTAGTCCTAC 60.243 52.174 0.00 0.00 40.80 3.18
2070 2528 3.935203 CCTTCGTAGTTCGTAGTCCTACA 59.065 47.826 5.40 0.00 40.80 2.74
2071 2529 4.574013 CCTTCGTAGTTCGTAGTCCTACAT 59.426 45.833 5.40 0.00 40.80 2.29
2072 2530 5.277250 CCTTCGTAGTTCGTAGTCCTACATC 60.277 48.000 5.40 0.00 40.80 3.06
2073 2531 4.122776 TCGTAGTTCGTAGTCCTACATCC 58.877 47.826 5.40 0.00 40.80 3.51
2074 2532 3.873361 CGTAGTTCGTAGTCCTACATCCA 59.127 47.826 5.40 0.00 35.87 3.41
2075 2533 4.025061 CGTAGTTCGTAGTCCTACATCCAG 60.025 50.000 5.40 0.00 35.87 3.86
2076 2534 4.232188 AGTTCGTAGTCCTACATCCAGA 57.768 45.455 5.40 0.00 35.87 3.86
2077 2535 4.200874 AGTTCGTAGTCCTACATCCAGAG 58.799 47.826 5.40 0.00 35.87 3.35
2078 2536 3.928005 TCGTAGTCCTACATCCAGAGT 57.072 47.619 5.40 0.00 35.87 3.24
2079 2537 3.806380 TCGTAGTCCTACATCCAGAGTC 58.194 50.000 5.40 0.00 35.87 3.36
2080 2538 3.455177 TCGTAGTCCTACATCCAGAGTCT 59.545 47.826 5.40 0.00 35.87 3.24
2081 2539 3.562141 CGTAGTCCTACATCCAGAGTCTG 59.438 52.174 13.56 13.56 35.87 3.51
2082 2540 4.683671 CGTAGTCCTACATCCAGAGTCTGA 60.684 50.000 22.09 8.14 35.87 3.27
2083 2541 3.897239 AGTCCTACATCCAGAGTCTGAG 58.103 50.000 22.09 12.81 32.44 3.35
2084 2542 3.525609 AGTCCTACATCCAGAGTCTGAGA 59.474 47.826 22.09 16.32 32.44 3.27
2085 2543 3.630312 GTCCTACATCCAGAGTCTGAGAC 59.370 52.174 22.09 3.98 32.44 3.36
2086 2544 3.525609 TCCTACATCCAGAGTCTGAGACT 59.474 47.826 22.09 16.14 46.42 3.24
2087 2545 3.631686 CCTACATCCAGAGTCTGAGACTG 59.368 52.174 21.45 7.38 43.53 3.51
2088 2546 1.824230 ACATCCAGAGTCTGAGACTGC 59.176 52.381 21.45 11.45 43.53 4.40
2089 2547 1.102154 ATCCAGAGTCTGAGACTGCG 58.898 55.000 21.45 10.22 43.53 5.18
2090 2548 0.036875 TCCAGAGTCTGAGACTGCGA 59.963 55.000 21.45 9.15 43.53 5.10
2091 2549 0.451383 CCAGAGTCTGAGACTGCGAG 59.549 60.000 21.45 6.53 43.53 5.03
2092 2550 1.447945 CAGAGTCTGAGACTGCGAGA 58.552 55.000 21.45 0.00 43.53 4.04
2093 2551 1.809547 CAGAGTCTGAGACTGCGAGAA 59.190 52.381 21.45 0.00 43.53 2.87
2094 2552 1.810151 AGAGTCTGAGACTGCGAGAAC 59.190 52.381 21.45 3.36 43.53 3.01
2095 2553 1.810151 GAGTCTGAGACTGCGAGAACT 59.190 52.381 21.45 0.00 43.53 3.01
2096 2554 1.810151 AGTCTGAGACTGCGAGAACTC 59.190 52.381 15.39 0.00 41.76 3.01
2097 2555 1.537638 GTCTGAGACTGCGAGAACTCA 59.462 52.381 5.12 0.00 37.71 3.41
2098 2556 2.163412 GTCTGAGACTGCGAGAACTCAT 59.837 50.000 5.12 0.00 38.43 2.90
2099 2557 2.163211 TCTGAGACTGCGAGAACTCATG 59.837 50.000 0.00 0.00 38.43 3.07
2100 2558 2.162681 TGAGACTGCGAGAACTCATGA 58.837 47.619 0.00 0.00 35.01 3.07
2101 2559 2.095008 TGAGACTGCGAGAACTCATGAC 60.095 50.000 0.00 0.00 35.01 3.06
2102 2560 1.889170 AGACTGCGAGAACTCATGACA 59.111 47.619 0.00 0.00 0.00 3.58
2103 2561 1.989165 GACTGCGAGAACTCATGACAC 59.011 52.381 0.00 0.00 0.00 3.67
2104 2562 1.337260 ACTGCGAGAACTCATGACACC 60.337 52.381 0.00 0.00 0.00 4.16
2105 2563 0.969149 TGCGAGAACTCATGACACCT 59.031 50.000 0.00 0.00 0.00 4.00
2106 2564 1.344438 TGCGAGAACTCATGACACCTT 59.656 47.619 0.00 0.00 0.00 3.50
2107 2565 1.996191 GCGAGAACTCATGACACCTTC 59.004 52.381 0.00 0.00 0.00 3.46
2108 2566 2.610479 GCGAGAACTCATGACACCTTCA 60.610 50.000 0.00 0.00 39.11 3.02
2109 2567 3.249091 CGAGAACTCATGACACCTTCAG 58.751 50.000 0.00 0.00 37.77 3.02
2110 2568 3.594134 GAGAACTCATGACACCTTCAGG 58.406 50.000 0.00 0.00 37.77 3.86
2111 2569 2.079925 GAACTCATGACACCTTCAGGC 58.920 52.381 0.00 0.00 37.77 4.85
2112 2570 0.326264 ACTCATGACACCTTCAGGCC 59.674 55.000 0.00 0.00 37.77 5.19
2113 2571 0.617413 CTCATGACACCTTCAGGCCT 59.383 55.000 0.00 0.00 37.77 5.19
2114 2572 1.833630 CTCATGACACCTTCAGGCCTA 59.166 52.381 3.98 0.00 37.77 3.93
2115 2573 2.437281 CTCATGACACCTTCAGGCCTAT 59.563 50.000 3.98 0.00 37.77 2.57
2116 2574 2.846206 TCATGACACCTTCAGGCCTATT 59.154 45.455 3.98 0.00 37.77 1.73
2117 2575 3.266772 TCATGACACCTTCAGGCCTATTT 59.733 43.478 3.98 0.00 37.77 1.40
2118 2576 3.350219 TGACACCTTCAGGCCTATTTC 57.650 47.619 3.98 0.00 39.32 2.17
2119 2577 2.026262 TGACACCTTCAGGCCTATTTCC 60.026 50.000 3.98 0.00 39.32 3.13
2120 2578 1.285078 ACACCTTCAGGCCTATTTCCC 59.715 52.381 3.98 0.00 39.32 3.97
2121 2579 1.566231 CACCTTCAGGCCTATTTCCCT 59.434 52.381 3.98 0.00 39.32 4.20
2123 2581 1.685148 CTTCAGGCCTATTTCCCTGC 58.315 55.000 3.98 0.00 46.48 4.85
2124 2582 0.998928 TTCAGGCCTATTTCCCTGCA 59.001 50.000 3.98 0.00 46.48 4.41
2125 2583 0.998928 TCAGGCCTATTTCCCTGCAA 59.001 50.000 3.98 0.00 46.48 4.08
2126 2584 1.357420 TCAGGCCTATTTCCCTGCAAA 59.643 47.619 3.98 0.00 46.48 3.68
2127 2585 2.178580 CAGGCCTATTTCCCTGCAAAA 58.821 47.619 3.98 0.00 41.86 2.44
2128 2586 2.767960 CAGGCCTATTTCCCTGCAAAAT 59.232 45.455 3.98 0.84 41.86 1.82
2129 2587 3.198417 CAGGCCTATTTCCCTGCAAAATT 59.802 43.478 3.98 0.00 41.86 1.82
2130 2588 3.198417 AGGCCTATTTCCCTGCAAAATTG 59.802 43.478 1.29 0.00 0.00 2.32
2131 2589 3.055167 GGCCTATTTCCCTGCAAAATTGT 60.055 43.478 0.00 0.00 0.00 2.71
2132 2590 4.183865 GCCTATTTCCCTGCAAAATTGTC 58.816 43.478 0.43 0.00 0.00 3.18
2133 2591 4.758688 CCTATTTCCCTGCAAAATTGTCC 58.241 43.478 0.43 0.00 0.00 4.02
2134 2592 3.701205 ATTTCCCTGCAAAATTGTCCC 57.299 42.857 0.00 0.00 0.00 4.46
2135 2593 1.347062 TTCCCTGCAAAATTGTCCCC 58.653 50.000 0.00 0.00 0.00 4.81
2136 2594 0.544120 TCCCTGCAAAATTGTCCCCC 60.544 55.000 0.00 0.00 0.00 5.40
2137 2595 0.545071 CCCTGCAAAATTGTCCCCCT 60.545 55.000 0.00 0.00 0.00 4.79
2138 2596 1.272985 CCCTGCAAAATTGTCCCCCTA 60.273 52.381 0.00 0.00 0.00 3.53
2139 2597 2.534990 CCTGCAAAATTGTCCCCCTAA 58.465 47.619 0.00 0.00 0.00 2.69
2140 2598 2.903135 CCTGCAAAATTGTCCCCCTAAA 59.097 45.455 0.00 0.00 0.00 1.85
2141 2599 3.055891 CCTGCAAAATTGTCCCCCTAAAG 60.056 47.826 0.00 0.00 0.00 1.85
2142 2600 2.301583 TGCAAAATTGTCCCCCTAAAGC 59.698 45.455 0.00 0.00 0.00 3.51
2143 2601 2.354704 GCAAAATTGTCCCCCTAAAGCC 60.355 50.000 0.00 0.00 0.00 4.35
2144 2602 2.903135 CAAAATTGTCCCCCTAAAGCCA 59.097 45.455 0.00 0.00 0.00 4.75
2145 2603 3.490060 AAATTGTCCCCCTAAAGCCAT 57.510 42.857 0.00 0.00 0.00 4.40
2146 2604 3.490060 AATTGTCCCCCTAAAGCCATT 57.510 42.857 0.00 0.00 0.00 3.16
2147 2605 3.490060 ATTGTCCCCCTAAAGCCATTT 57.510 42.857 0.00 0.00 0.00 2.32
2148 2606 4.618378 ATTGTCCCCCTAAAGCCATTTA 57.382 40.909 0.00 0.00 0.00 1.40
2149 2607 4.405756 TTGTCCCCCTAAAGCCATTTAA 57.594 40.909 0.00 0.00 30.59 1.52
2150 2608 3.703921 TGTCCCCCTAAAGCCATTTAAC 58.296 45.455 0.00 0.00 30.59 2.01
2151 2609 3.076182 TGTCCCCCTAAAGCCATTTAACA 59.924 43.478 0.00 0.00 30.59 2.41
2152 2610 4.264623 TGTCCCCCTAAAGCCATTTAACAT 60.265 41.667 0.00 0.00 30.59 2.71
2153 2611 4.714802 GTCCCCCTAAAGCCATTTAACATT 59.285 41.667 0.00 0.00 30.59 2.71
2154 2612 5.188948 GTCCCCCTAAAGCCATTTAACATTT 59.811 40.000 0.00 0.00 30.59 2.32
2155 2613 5.423931 TCCCCCTAAAGCCATTTAACATTTC 59.576 40.000 0.00 0.00 30.59 2.17
2156 2614 5.425217 CCCCCTAAAGCCATTTAACATTTCT 59.575 40.000 0.00 0.00 30.59 2.52
2157 2615 6.406961 CCCCCTAAAGCCATTTAACATTTCTC 60.407 42.308 0.00 0.00 30.59 2.87
2158 2616 6.154363 CCCCTAAAGCCATTTAACATTTCTCA 59.846 38.462 0.00 0.00 30.59 3.27
2159 2617 7.310361 CCCCTAAAGCCATTTAACATTTCTCAA 60.310 37.037 0.00 0.00 30.59 3.02
2160 2618 8.093927 CCCTAAAGCCATTTAACATTTCTCAAA 58.906 33.333 0.00 0.00 30.59 2.69
2161 2619 9.657419 CCTAAAGCCATTTAACATTTCTCAAAT 57.343 29.630 0.00 0.00 30.59 2.32
2164 2622 9.995003 AAAGCCATTTAACATTTCTCAAATACA 57.005 25.926 0.00 0.00 0.00 2.29
2166 2624 9.590451 AGCCATTTAACATTTCTCAAATACATG 57.410 29.630 0.00 0.00 0.00 3.21
2167 2625 9.585099 GCCATTTAACATTTCTCAAATACATGA 57.415 29.630 0.00 0.00 0.00 3.07
2236 2694 9.980780 TCACATTGTACATTTTAACATACATCG 57.019 29.630 0.00 0.00 0.00 3.84
2237 2695 9.980780 CACATTGTACATTTTAACATACATCGA 57.019 29.630 0.00 0.00 0.00 3.59
2252 2710 9.634163 AACATACATCGATATTTTCTATACGCA 57.366 29.630 0.00 0.00 0.00 5.24
2253 2711 9.073368 ACATACATCGATATTTTCTATACGCAC 57.927 33.333 0.00 0.00 0.00 5.34
2254 2712 9.290483 CATACATCGATATTTTCTATACGCACT 57.710 33.333 0.00 0.00 0.00 4.40
2257 2715 9.343103 ACATCGATATTTTCTATACGCACTAAG 57.657 33.333 0.00 0.00 0.00 2.18
2258 2716 9.556030 CATCGATATTTTCTATACGCACTAAGA 57.444 33.333 0.00 0.00 0.00 2.10
2259 2717 9.776158 ATCGATATTTTCTATACGCACTAAGAG 57.224 33.333 0.00 0.00 0.00 2.85
2260 2718 8.996271 TCGATATTTTCTATACGCACTAAGAGA 58.004 33.333 0.00 0.00 0.00 3.10
2261 2719 9.608617 CGATATTTTCTATACGCACTAAGAGAA 57.391 33.333 0.00 0.00 0.00 2.87
2265 2723 9.817809 ATTTTCTATACGCACTAAGAGAATTCA 57.182 29.630 8.44 0.00 0.00 2.57
2266 2724 9.647797 TTTTCTATACGCACTAAGAGAATTCAA 57.352 29.630 8.44 0.00 0.00 2.69
2267 2725 9.817809 TTTCTATACGCACTAAGAGAATTCAAT 57.182 29.630 8.44 0.00 0.00 2.57
2268 2726 9.817809 TTCTATACGCACTAAGAGAATTCAATT 57.182 29.630 8.44 4.40 0.00 2.32
2269 2727 9.817809 TCTATACGCACTAAGAGAATTCAATTT 57.182 29.630 8.44 1.59 0.00 1.82
2272 2730 7.440523 ACGCACTAAGAGAATTCAATTTTCT 57.559 32.000 8.44 0.00 35.47 2.52
2273 2731 8.547967 ACGCACTAAGAGAATTCAATTTTCTA 57.452 30.769 8.44 0.00 33.13 2.10
2274 2732 9.167311 ACGCACTAAGAGAATTCAATTTTCTAT 57.833 29.630 8.44 0.00 33.13 1.98
2362 2820 9.737427 TTTTCATACACATTGTACATTTTTCGT 57.263 25.926 0.00 0.00 35.42 3.85
2369 2827 9.982291 ACACATTGTACATTTTTCGTATACATC 57.018 29.630 3.32 0.00 0.00 3.06
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 5.347635 CGACAAGTTTCGAATTGGACTGATA 59.652 40.000 14.28 0.00 41.78 2.15
1 2 4.152402 CGACAAGTTTCGAATTGGACTGAT 59.848 41.667 14.28 1.29 41.78 2.90
2 3 3.493129 CGACAAGTTTCGAATTGGACTGA 59.507 43.478 14.28 0.00 41.78 3.41
3 4 3.799035 CGACAAGTTTCGAATTGGACTG 58.201 45.455 14.28 6.19 41.78 3.51
188 192 3.644966 ATAATGTCACGGGTGTGGATT 57.355 42.857 0.00 0.00 46.42 3.01
232 236 4.739587 CCTTTGTAGTAGGAGAAGGGAC 57.260 50.000 0.00 0.00 34.58 4.46
347 351 0.537143 CCAGTACTGGCCAGCACAAA 60.537 55.000 32.86 12.70 44.73 2.83
385 390 7.513371 TTCAATCTTAACTCGCCCTTTTTAA 57.487 32.000 0.00 0.00 0.00 1.52
386 391 7.229907 ACTTTCAATCTTAACTCGCCCTTTTTA 59.770 33.333 0.00 0.00 0.00 1.52
387 392 6.040504 ACTTTCAATCTTAACTCGCCCTTTTT 59.959 34.615 0.00 0.00 0.00 1.94
392 397 5.048991 TCAAACTTTCAATCTTAACTCGCCC 60.049 40.000 0.00 0.00 0.00 6.13
408 414 3.199946 TCGCCTCCCTATCATCAAACTTT 59.800 43.478 0.00 0.00 0.00 2.66
410 416 2.366916 CTCGCCTCCCTATCATCAAACT 59.633 50.000 0.00 0.00 0.00 2.66
412 422 2.630098 CTCTCGCCTCCCTATCATCAAA 59.370 50.000 0.00 0.00 0.00 2.69
416 426 1.272425 CCTCTCTCGCCTCCCTATCAT 60.272 57.143 0.00 0.00 0.00 2.45
447 457 0.246360 TGTCATCCACACTACCGCAG 59.754 55.000 0.00 0.00 0.00 5.18
499 509 9.952030 TCCTTTGTAATATCACATTGTTCAGTA 57.048 29.630 0.00 0.00 0.00 2.74
500 510 8.862325 TCCTTTGTAATATCACATTGTTCAGT 57.138 30.769 0.00 0.00 0.00 3.41
554 567 7.550551 CACATGTCATCTACACTACCTCAAATT 59.449 37.037 0.00 0.00 42.09 1.82
558 571 4.402474 CCACATGTCATCTACACTACCTCA 59.598 45.833 0.00 0.00 42.09 3.86
561 574 3.451178 ACCCACATGTCATCTACACTACC 59.549 47.826 0.00 0.00 42.09 3.18
563 576 4.142249 CGAACCCACATGTCATCTACACTA 60.142 45.833 0.00 0.00 42.09 2.74
618 631 8.034313 AGTATTTTGGATCCTCTGCAGTATTA 57.966 34.615 14.67 0.00 0.00 0.98
619 632 6.904626 AGTATTTTGGATCCTCTGCAGTATT 58.095 36.000 14.67 0.00 0.00 1.89
631 751 3.388350 AGACGGAGGGAGTATTTTGGATC 59.612 47.826 0.00 0.00 0.00 3.36
655 834 2.092323 CTCCCTCCGTCCCAAAATTTC 58.908 52.381 0.00 0.00 0.00 2.17
678 857 9.595823 AATTAATTTTCTCTCGGTCGAATCTAA 57.404 29.630 0.00 0.00 0.00 2.10
702 881 6.268566 GCAAGAAACTGAACACTGAGAAAAT 58.731 36.000 0.00 0.00 0.00 1.82
706 885 3.206150 GGCAAGAAACTGAACACTGAGA 58.794 45.455 0.00 0.00 0.00 3.27
715 896 0.603707 CAGAGGCGGCAAGAAACTGA 60.604 55.000 13.08 0.00 0.00 3.41
718 899 1.916697 GCTCAGAGGCGGCAAGAAAC 61.917 60.000 13.08 0.00 0.00 2.78
727 908 7.804614 CTAATTACTAATTAGCTCAGAGGCG 57.195 40.000 12.54 0.00 42.58 5.52
759 1102 4.070009 CTGCCTATGATAATTGCTGCAGA 58.930 43.478 20.43 0.00 45.84 4.26
810 1153 2.867647 GCATTCCTGTTTTGCCCTTGAC 60.868 50.000 0.00 0.00 0.00 3.18
830 1173 2.088950 ACTCCAATGCTGCATTTTGC 57.911 45.000 24.28 0.00 45.29 3.68
970 1320 1.819229 CTGGGCTAGCAGTCGATGT 59.181 57.895 18.24 0.00 0.00 3.06
971 1321 4.746361 CTGGGCTAGCAGTCGATG 57.254 61.111 18.24 0.00 0.00 3.84
982 1332 0.987081 ATGATGACCTGAGCTGGGCT 60.987 55.000 0.00 0.00 43.88 5.19
983 1333 0.818445 CATGATGACCTGAGCTGGGC 60.818 60.000 0.00 0.00 35.14 5.36
984 1334 0.179026 CCATGATGACCTGAGCTGGG 60.179 60.000 0.00 0.00 0.00 4.45
985 1335 0.818445 GCCATGATGACCTGAGCTGG 60.818 60.000 0.00 0.00 0.00 4.85
986 1336 1.158484 CGCCATGATGACCTGAGCTG 61.158 60.000 0.00 0.00 0.00 4.24
1281 1631 1.654743 GCCGTCGTCGTAGAGCATC 60.655 63.158 0.71 0.00 36.95 3.91
1288 1638 2.127270 GTCGTTGCCGTCGTCGTA 60.127 61.111 0.71 0.00 35.01 3.43
1291 1641 3.456039 GTCGTCGTTGCCGTCGTC 61.456 66.667 0.00 0.00 44.09 4.20
1384 1758 5.163804 CGACCATTCAAATTTGATCACCGTA 60.164 40.000 21.10 5.37 37.00 4.02
1405 1779 2.494591 GCGTTGGACGTCGATCGAC 61.495 63.158 33.22 33.22 44.73 4.20
1415 1789 6.979238 AGTACAGATTCTTATTAGCGTTGGAC 59.021 38.462 0.00 0.00 0.00 4.02
1416 1790 7.108841 AGTACAGATTCTTATTAGCGTTGGA 57.891 36.000 0.00 0.00 0.00 3.53
1417 1791 7.115095 GCTAGTACAGATTCTTATTAGCGTTGG 59.885 40.741 0.00 0.00 0.00 3.77
1465 1840 1.067916 AAGGGCGCTTGCAACAAAG 59.932 52.632 16.16 0.00 41.71 2.77
1466 1841 1.227205 CAAGGGCGCTTGCAACAAA 60.227 52.632 27.84 0.00 41.71 2.83
1467 1842 1.103987 TACAAGGGCGCTTGCAACAA 61.104 50.000 35.51 17.78 41.71 2.83
1468 1843 1.103987 TTACAAGGGCGCTTGCAACA 61.104 50.000 35.51 19.65 41.71 3.33
1469 1844 0.387239 CTTACAAGGGCGCTTGCAAC 60.387 55.000 35.51 0.00 41.71 4.17
1470 1845 0.821711 ACTTACAAGGGCGCTTGCAA 60.822 50.000 35.51 29.23 41.71 4.08
1471 1846 0.821711 AACTTACAAGGGCGCTTGCA 60.822 50.000 35.51 25.00 41.71 4.08
1472 1847 0.313987 AAACTTACAAGGGCGCTTGC 59.686 50.000 35.51 0.00 37.83 4.01
1473 1848 1.606668 TCAAACTTACAAGGGCGCTTG 59.393 47.619 34.39 34.39 39.98 4.01
1474 1849 1.975660 TCAAACTTACAAGGGCGCTT 58.024 45.000 10.73 10.73 0.00 4.68
1475 1850 2.200373 ATCAAACTTACAAGGGCGCT 57.800 45.000 7.64 0.00 0.00 5.92
1476 1851 4.428615 TTAATCAAACTTACAAGGGCGC 57.571 40.909 0.00 0.00 0.00 6.53
1477 1852 5.105917 ACCATTAATCAAACTTACAAGGGCG 60.106 40.000 0.00 0.00 0.00 6.13
1525 1940 7.775093 ACGTACATAAGGTAGTATGTAGTTGGA 59.225 37.037 5.51 0.00 43.99 3.53
1576 1991 9.826574 GGTATACACTGTGATGGAATTTACTAA 57.173 33.333 15.86 0.00 0.00 2.24
1577 1992 8.983789 TGGTATACACTGTGATGGAATTTACTA 58.016 33.333 15.86 0.00 0.00 1.82
1578 1993 7.857456 TGGTATACACTGTGATGGAATTTACT 58.143 34.615 15.86 0.00 0.00 2.24
1579 1994 8.500753 TTGGTATACACTGTGATGGAATTTAC 57.499 34.615 15.86 0.97 0.00 2.01
1580 1995 9.693739 ATTTGGTATACACTGTGATGGAATTTA 57.306 29.630 15.86 0.00 0.00 1.40
1592 2007 7.984391 TGAAGCATAACATTTGGTATACACTG 58.016 34.615 5.01 0.00 0.00 3.66
1598 2013 7.333528 ACGATTGAAGCATAACATTTGGTAT 57.666 32.000 0.00 0.00 0.00 2.73
1599 2014 6.751514 ACGATTGAAGCATAACATTTGGTA 57.248 33.333 0.00 0.00 0.00 3.25
1600 2015 5.643379 ACGATTGAAGCATAACATTTGGT 57.357 34.783 0.00 0.00 0.00 3.67
1671 2086 3.930848 ACATATCACGTCTTTTTCGGACC 59.069 43.478 0.00 0.00 0.00 4.46
1674 2089 6.464834 GCTTAAACATATCACGTCTTTTTCGG 59.535 38.462 0.00 0.00 0.00 4.30
1683 2100 5.402568 CGATGCTAGCTTAAACATATCACGT 59.597 40.000 17.23 0.00 0.00 4.49
1684 2101 5.629435 TCGATGCTAGCTTAAACATATCACG 59.371 40.000 17.23 5.58 0.00 4.35
1718 2143 5.295950 CATCAAGTAGAGTATGCAAGGAGG 58.704 45.833 0.00 0.00 0.00 4.30
1734 2159 4.537135 TTCTAACTCGAAGGCATCAAGT 57.463 40.909 0.00 0.00 0.00 3.16
1779 2236 2.162338 AACGCTACGCTGGCCACTTA 62.162 55.000 0.00 0.00 0.00 2.24
1790 2247 1.135689 ACCCGTAACACTAACGCTACG 60.136 52.381 0.00 0.00 39.00 3.51
1791 2248 2.253603 CACCCGTAACACTAACGCTAC 58.746 52.381 0.00 0.00 39.00 3.58
1792 2249 1.402720 GCACCCGTAACACTAACGCTA 60.403 52.381 0.00 0.00 39.00 4.26
1793 2250 0.668401 GCACCCGTAACACTAACGCT 60.668 55.000 0.00 0.00 39.00 5.07
1794 2251 0.668401 AGCACCCGTAACACTAACGC 60.668 55.000 0.00 0.00 39.00 4.84
1795 2252 1.787012 AAGCACCCGTAACACTAACG 58.213 50.000 0.00 0.00 40.01 3.18
1796 2253 3.676646 CACTAAGCACCCGTAACACTAAC 59.323 47.826 0.00 0.00 0.00 2.34
1890 2347 1.129437 GAAGTCCAGCAATTCAGCGAC 59.871 52.381 0.00 0.00 40.15 5.19
1892 2349 1.129998 CTGAAGTCCAGCAATTCAGCG 59.870 52.381 0.57 0.00 42.32 5.18
1900 2357 0.321671 GCTGTACCTGAAGTCCAGCA 59.678 55.000 5.63 0.00 41.57 4.41
1907 2364 3.157932 GCTGAGTAGCTGTACCTGAAG 57.842 52.381 0.00 0.00 46.57 3.02
1929 2386 2.359230 GGCCAAAGCAGAGTCGCT 60.359 61.111 0.00 4.01 46.67 4.93
1954 2411 2.100252 CGGAGTGCCTTAACTTCCGATA 59.900 50.000 5.35 0.00 40.36 2.92
1955 2412 1.134788 CGGAGTGCCTTAACTTCCGAT 60.135 52.381 5.35 0.00 40.36 4.18
1958 2415 2.180432 AACGGAGTGCCTTAACTTCC 57.820 50.000 0.00 0.00 45.00 3.46
1959 2416 4.512571 TGTTTAACGGAGTGCCTTAACTTC 59.487 41.667 0.00 0.00 45.00 3.01
1960 2417 4.453751 TGTTTAACGGAGTGCCTTAACTT 58.546 39.130 0.00 0.00 45.00 2.66
1961 2418 4.062991 CTGTTTAACGGAGTGCCTTAACT 58.937 43.478 0.00 0.00 45.00 2.24
1962 2419 4.060205 TCTGTTTAACGGAGTGCCTTAAC 58.940 43.478 2.02 0.00 45.00 2.01
1963 2420 4.060205 GTCTGTTTAACGGAGTGCCTTAA 58.940 43.478 6.89 0.00 45.00 1.85
1964 2421 3.555586 GGTCTGTTTAACGGAGTGCCTTA 60.556 47.826 6.89 0.00 45.00 2.69
1965 2422 2.490991 GTCTGTTTAACGGAGTGCCTT 58.509 47.619 6.89 0.00 45.00 4.35
1966 2423 1.270678 GGTCTGTTTAACGGAGTGCCT 60.271 52.381 6.89 0.00 45.00 4.75
1989 2447 2.341846 AACCGTTGAAGAAAGGCAGA 57.658 45.000 0.00 0.00 34.25 4.26
2010 2468 1.319541 CGTCCGAGATCAGGTGGTAT 58.680 55.000 7.06 0.00 0.00 2.73
2041 2499 1.612463 ACGAACTACGAAGGCTCTGTT 59.388 47.619 0.00 0.00 45.77 3.16
2053 2511 5.121811 TCTGGATGTAGGACTACGAACTAC 58.878 45.833 5.14 0.00 38.85 2.73
2054 2512 5.104610 ACTCTGGATGTAGGACTACGAACTA 60.105 44.000 5.14 0.00 38.85 2.24
2055 2513 4.200874 CTCTGGATGTAGGACTACGAACT 58.799 47.826 5.14 0.00 38.85 3.01
2056 2514 3.946558 ACTCTGGATGTAGGACTACGAAC 59.053 47.826 5.14 0.00 38.85 3.95
2057 2515 4.080469 AGACTCTGGATGTAGGACTACGAA 60.080 45.833 5.14 0.00 38.85 3.85
2058 2516 3.455177 AGACTCTGGATGTAGGACTACGA 59.545 47.826 5.14 0.00 38.85 3.43
2059 2517 3.562141 CAGACTCTGGATGTAGGACTACG 59.438 52.174 5.14 0.00 38.85 3.51
2060 2518 4.783055 TCAGACTCTGGATGTAGGACTAC 58.217 47.826 6.20 2.57 32.99 2.73
2061 2519 4.722279 TCTCAGACTCTGGATGTAGGACTA 59.278 45.833 6.20 0.00 31.51 2.59
2062 2520 3.525609 TCTCAGACTCTGGATGTAGGACT 59.474 47.826 6.20 0.00 31.51 3.85
2063 2521 3.630312 GTCTCAGACTCTGGATGTAGGAC 59.370 52.174 6.20 1.54 31.51 3.85
2064 2522 3.525609 AGTCTCAGACTCTGGATGTAGGA 59.474 47.826 0.00 0.00 38.71 2.94
2065 2523 3.631686 CAGTCTCAGACTCTGGATGTAGG 59.368 52.174 3.60 0.00 41.37 3.18
2066 2524 3.066621 GCAGTCTCAGACTCTGGATGTAG 59.933 52.174 3.60 0.00 41.37 2.74
2067 2525 3.020274 GCAGTCTCAGACTCTGGATGTA 58.980 50.000 3.60 0.00 41.37 2.29
2068 2526 1.824230 GCAGTCTCAGACTCTGGATGT 59.176 52.381 3.60 0.00 41.37 3.06
2069 2527 1.202279 CGCAGTCTCAGACTCTGGATG 60.202 57.143 3.60 0.00 41.37 3.51
2070 2528 1.102154 CGCAGTCTCAGACTCTGGAT 58.898 55.000 3.60 0.00 41.37 3.41
2071 2529 0.036875 TCGCAGTCTCAGACTCTGGA 59.963 55.000 3.60 0.00 41.37 3.86
2072 2530 0.451383 CTCGCAGTCTCAGACTCTGG 59.549 60.000 3.60 0.00 41.37 3.86
2073 2531 1.447945 TCTCGCAGTCTCAGACTCTG 58.552 55.000 3.60 0.00 41.37 3.35
2074 2532 1.810151 GTTCTCGCAGTCTCAGACTCT 59.190 52.381 3.60 0.00 41.37 3.24
2075 2533 1.810151 AGTTCTCGCAGTCTCAGACTC 59.190 52.381 3.60 0.00 41.37 3.36
2076 2534 1.810151 GAGTTCTCGCAGTCTCAGACT 59.190 52.381 0.00 0.00 44.44 3.24
2077 2535 1.537638 TGAGTTCTCGCAGTCTCAGAC 59.462 52.381 0.00 0.00 33.77 3.51
2078 2536 1.897560 TGAGTTCTCGCAGTCTCAGA 58.102 50.000 0.00 0.00 33.77 3.27
2079 2537 2.163211 TCATGAGTTCTCGCAGTCTCAG 59.837 50.000 0.00 0.00 39.69 3.35
2080 2538 2.095008 GTCATGAGTTCTCGCAGTCTCA 60.095 50.000 0.00 0.00 40.43 3.27
2081 2539 2.095008 TGTCATGAGTTCTCGCAGTCTC 60.095 50.000 0.00 0.00 0.00 3.36
2082 2540 1.889170 TGTCATGAGTTCTCGCAGTCT 59.111 47.619 0.00 0.00 0.00 3.24
2083 2541 1.989165 GTGTCATGAGTTCTCGCAGTC 59.011 52.381 0.00 0.00 0.00 3.51
2084 2542 1.337260 GGTGTCATGAGTTCTCGCAGT 60.337 52.381 0.00 0.00 0.00 4.40
2085 2543 1.067283 AGGTGTCATGAGTTCTCGCAG 60.067 52.381 0.00 0.00 0.00 5.18
2086 2544 0.969149 AGGTGTCATGAGTTCTCGCA 59.031 50.000 0.00 0.00 0.00 5.10
2087 2545 1.996191 GAAGGTGTCATGAGTTCTCGC 59.004 52.381 0.00 0.00 0.00 5.03
2088 2546 3.249091 CTGAAGGTGTCATGAGTTCTCG 58.751 50.000 0.00 0.00 35.07 4.04
2089 2547 3.594134 CCTGAAGGTGTCATGAGTTCTC 58.406 50.000 0.00 0.00 35.07 2.87
2090 2548 2.289945 GCCTGAAGGTGTCATGAGTTCT 60.290 50.000 0.00 0.00 35.07 3.01
2091 2549 2.079925 GCCTGAAGGTGTCATGAGTTC 58.920 52.381 0.00 0.00 35.07 3.01
2092 2550 1.271597 GGCCTGAAGGTGTCATGAGTT 60.272 52.381 0.00 0.00 35.07 3.01
2093 2551 0.326264 GGCCTGAAGGTGTCATGAGT 59.674 55.000 0.00 0.00 35.07 3.41
2094 2552 0.617413 AGGCCTGAAGGTGTCATGAG 59.383 55.000 3.11 0.00 35.07 2.90
2095 2553 1.951209 TAGGCCTGAAGGTGTCATGA 58.049 50.000 17.99 0.00 35.07 3.07
2096 2554 3.287867 AATAGGCCTGAAGGTGTCATG 57.712 47.619 17.99 0.00 35.07 3.07
2097 2555 3.372025 GGAAATAGGCCTGAAGGTGTCAT 60.372 47.826 17.99 0.00 35.07 3.06
2098 2556 2.026262 GGAAATAGGCCTGAAGGTGTCA 60.026 50.000 17.99 0.00 37.57 3.58
2099 2557 2.644676 GGAAATAGGCCTGAAGGTGTC 58.355 52.381 17.99 2.71 37.57 3.67
2100 2558 1.285078 GGGAAATAGGCCTGAAGGTGT 59.715 52.381 17.99 0.00 37.57 4.16
2101 2559 1.566231 AGGGAAATAGGCCTGAAGGTG 59.434 52.381 17.99 0.00 37.57 4.00
2102 2560 1.566231 CAGGGAAATAGGCCTGAAGGT 59.434 52.381 17.99 0.00 37.57 3.50
2103 2561 1.752084 GCAGGGAAATAGGCCTGAAGG 60.752 57.143 17.99 0.00 38.53 3.46
2104 2562 1.064463 TGCAGGGAAATAGGCCTGAAG 60.064 52.381 17.99 0.00 32.65 3.02
2105 2563 0.998928 TGCAGGGAAATAGGCCTGAA 59.001 50.000 17.99 0.00 32.65 3.02
2106 2564 0.998928 TTGCAGGGAAATAGGCCTGA 59.001 50.000 17.99 0.00 32.65 3.86
2107 2565 1.851304 TTTGCAGGGAAATAGGCCTG 58.149 50.000 17.99 0.00 0.00 4.85
2108 2566 2.621556 TTTTGCAGGGAAATAGGCCT 57.378 45.000 11.78 11.78 0.00 5.19
2109 2567 3.055167 ACAATTTTGCAGGGAAATAGGCC 60.055 43.478 0.00 0.00 0.00 5.19
2110 2568 4.183865 GACAATTTTGCAGGGAAATAGGC 58.816 43.478 0.00 0.00 0.00 3.93
2111 2569 4.383010 GGGACAATTTTGCAGGGAAATAGG 60.383 45.833 0.00 0.00 0.00 2.57
2112 2570 4.383010 GGGGACAATTTTGCAGGGAAATAG 60.383 45.833 0.00 0.00 0.00 1.73
2113 2571 3.517500 GGGGACAATTTTGCAGGGAAATA 59.482 43.478 0.00 0.00 0.00 1.40
2114 2572 2.305635 GGGGACAATTTTGCAGGGAAAT 59.694 45.455 0.00 0.00 0.00 2.17
2115 2573 1.696884 GGGGACAATTTTGCAGGGAAA 59.303 47.619 0.00 0.00 0.00 3.13
2116 2574 1.347062 GGGGACAATTTTGCAGGGAA 58.653 50.000 0.00 0.00 0.00 3.97
2117 2575 0.544120 GGGGGACAATTTTGCAGGGA 60.544 55.000 0.00 0.00 0.00 4.20
2118 2576 0.545071 AGGGGGACAATTTTGCAGGG 60.545 55.000 0.00 0.00 0.00 4.45
2119 2577 2.230130 TAGGGGGACAATTTTGCAGG 57.770 50.000 0.00 0.00 0.00 4.85
2120 2578 3.617288 GCTTTAGGGGGACAATTTTGCAG 60.617 47.826 0.00 0.00 0.00 4.41
2121 2579 2.301583 GCTTTAGGGGGACAATTTTGCA 59.698 45.455 0.00 0.00 0.00 4.08
2122 2580 2.354704 GGCTTTAGGGGGACAATTTTGC 60.355 50.000 0.00 0.00 0.00 3.68
2123 2581 2.903135 TGGCTTTAGGGGGACAATTTTG 59.097 45.455 0.00 0.00 0.00 2.44
2124 2582 3.268034 TGGCTTTAGGGGGACAATTTT 57.732 42.857 0.00 0.00 0.00 1.82
2125 2583 3.490060 ATGGCTTTAGGGGGACAATTT 57.510 42.857 0.00 0.00 0.00 1.82
2126 2584 3.490060 AATGGCTTTAGGGGGACAATT 57.510 42.857 0.00 0.00 0.00 2.32
2127 2585 3.490060 AAATGGCTTTAGGGGGACAAT 57.510 42.857 0.00 0.00 0.00 2.71
2128 2586 4.090819 GTTAAATGGCTTTAGGGGGACAA 58.909 43.478 0.00 0.00 0.00 3.18
2129 2587 3.076182 TGTTAAATGGCTTTAGGGGGACA 59.924 43.478 0.00 0.00 0.00 4.02
2130 2588 3.703921 TGTTAAATGGCTTTAGGGGGAC 58.296 45.455 0.00 0.00 0.00 4.46
2131 2589 4.618378 ATGTTAAATGGCTTTAGGGGGA 57.382 40.909 0.00 0.00 0.00 4.81
2132 2590 5.425217 AGAAATGTTAAATGGCTTTAGGGGG 59.575 40.000 0.00 0.00 0.00 5.40
2133 2591 6.154363 TGAGAAATGTTAAATGGCTTTAGGGG 59.846 38.462 0.00 0.00 0.00 4.79
2134 2592 7.169158 TGAGAAATGTTAAATGGCTTTAGGG 57.831 36.000 0.00 0.00 0.00 3.53
2135 2593 9.657419 ATTTGAGAAATGTTAAATGGCTTTAGG 57.343 29.630 0.00 0.00 0.00 2.69
2138 2596 9.995003 TGTATTTGAGAAATGTTAAATGGCTTT 57.005 25.926 0.00 0.00 32.38 3.51
2140 2598 9.590451 CATGTATTTGAGAAATGTTAAATGGCT 57.410 29.630 0.00 0.00 32.38 4.75
2141 2599 9.585099 TCATGTATTTGAGAAATGTTAAATGGC 57.415 29.630 0.00 0.00 32.38 4.40
2210 2668 9.980780 CGATGTATGTTAAAATGTACAATGTGA 57.019 29.630 0.00 0.00 31.57 3.58
2211 2669 9.980780 TCGATGTATGTTAAAATGTACAATGTG 57.019 29.630 0.00 0.00 31.57 3.21
2226 2684 9.634163 TGCGTATAGAAAATATCGATGTATGTT 57.366 29.630 8.54 0.00 0.00 2.71
2227 2685 9.073368 GTGCGTATAGAAAATATCGATGTATGT 57.927 33.333 8.54 0.00 0.00 2.29
2228 2686 9.290483 AGTGCGTATAGAAAATATCGATGTATG 57.710 33.333 8.54 0.00 0.00 2.39
2231 2689 9.343103 CTTAGTGCGTATAGAAAATATCGATGT 57.657 33.333 8.54 0.00 0.00 3.06
2232 2690 9.556030 TCTTAGTGCGTATAGAAAATATCGATG 57.444 33.333 8.54 0.00 0.00 3.84
2233 2691 9.776158 CTCTTAGTGCGTATAGAAAATATCGAT 57.224 33.333 2.16 2.16 0.00 3.59
2234 2692 8.996271 TCTCTTAGTGCGTATAGAAAATATCGA 58.004 33.333 0.00 0.00 0.00 3.59
2235 2693 9.608617 TTCTCTTAGTGCGTATAGAAAATATCG 57.391 33.333 0.00 0.00 0.00 2.92
2239 2697 9.817809 TGAATTCTCTTAGTGCGTATAGAAAAT 57.182 29.630 7.05 0.00 0.00 1.82
2240 2698 9.647797 TTGAATTCTCTTAGTGCGTATAGAAAA 57.352 29.630 7.05 0.00 0.00 2.29
2241 2699 9.817809 ATTGAATTCTCTTAGTGCGTATAGAAA 57.182 29.630 7.05 0.00 0.00 2.52
2242 2700 9.817809 AATTGAATTCTCTTAGTGCGTATAGAA 57.182 29.630 7.05 0.00 0.00 2.10
2243 2701 9.817809 AAATTGAATTCTCTTAGTGCGTATAGA 57.182 29.630 7.05 0.00 0.00 1.98
2246 2704 9.167311 AGAAAATTGAATTCTCTTAGTGCGTAT 57.833 29.630 7.05 0.00 31.61 3.06
2247 2705 8.547967 AGAAAATTGAATTCTCTTAGTGCGTA 57.452 30.769 7.05 0.00 31.61 4.42
2248 2706 7.440523 AGAAAATTGAATTCTCTTAGTGCGT 57.559 32.000 7.05 0.00 31.61 5.24
2336 2794 9.737427 ACGAAAAATGTACAATGTGTATGAAAA 57.263 25.926 0.00 0.00 35.05 2.29
2343 2801 9.982291 GATGTATACGAAAAATGTACAATGTGT 57.018 29.630 0.00 0.00 29.00 3.72


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

AutoCloner maintained by Alex Coulton.