Multiple sequence alignment - TraesCS4D01G054500

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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 TraesCS4D01G054500 chr4D 100.000 5615 0 0 1 5615 30221864 30216250 0.000000e+00 10370.0
1 TraesCS4D01G054500 chr4D 100.000 40 0 0 1933 1972 30219893 30219932 2.170000e-09 75.0
2 TraesCS4D01G054500 chr4A 91.919 3403 160 48 1970 5312 572831858 572835205 0.000000e+00 4654.0
3 TraesCS4D01G054500 chr4A 90.160 1941 93 51 67 1930 572829935 572831854 0.000000e+00 2436.0
4 TraesCS4D01G054500 chr4A 81.957 327 25 7 5313 5607 572835241 572835565 4.340000e-61 246.0
5 TraesCS4D01G054500 chr4B 92.382 2809 149 30 2833 5607 43110879 43108102 0.000000e+00 3941.0
6 TraesCS4D01G054500 chr4B 89.422 1938 99 43 71 1935 43113699 43111795 0.000000e+00 2346.0
7 TraesCS4D01G054500 chr4B 87.844 872 63 20 1970 2834 43111796 43110961 0.000000e+00 983.0
8 TraesCS4D01G054500 chr4B 89.796 98 10 0 283 380 27929276 27929179 5.910000e-25 126.0
9 TraesCS4D01G054500 chr1D 93.548 93 5 1 288 379 143955556 143955464 2.730000e-28 137.0
10 TraesCS4D01G054500 chr1D 94.286 35 2 0 521 555 279521555 279521589 3.000000e-03 54.7
11 TraesCS4D01G054500 chr1B 94.382 89 5 0 288 376 193283150 193283062 2.730000e-28 137.0
12 TraesCS4D01G054500 chr2A 92.632 95 6 1 288 381 53078427 53078521 9.810000e-28 135.0
13 TraesCS4D01G054500 chr2A 100.000 33 0 0 522 554 21557983 21557951 1.690000e-05 62.1
14 TraesCS4D01G054500 chrUn 92.391 92 7 0 283 374 15903926 15904017 1.270000e-26 132.0
15 TraesCS4D01G054500 chrUn 79.787 94 15 4 522 613 31703118 31703209 1.310000e-06 65.8
16 TraesCS4D01G054500 chr5D 90.816 98 9 0 284 381 330886145 330886242 1.270000e-26 132.0
17 TraesCS4D01G054500 chr5D 94.595 37 1 1 1943 1979 433063012 433062977 7.860000e-04 56.5
18 TraesCS4D01G054500 chr6D 87.850 107 12 1 271 377 78080275 78080170 2.120000e-24 124.0
19 TraesCS4D01G054500 chr6D 94.872 39 2 0 522 560 56934716 56934678 1.690000e-05 62.1
20 TraesCS4D01G054500 chr2D 100.000 34 0 0 522 555 54888864 54888831 4.700000e-06 63.9
21 TraesCS4D01G054500 chr3B 97.222 36 1 0 522 557 580887841 580887876 1.690000e-05 62.1
22 TraesCS4D01G054500 chr7B 92.105 38 3 0 525 562 464549286 464549249 3.000000e-03 54.7
23 TraesCS4D01G054500 chr5B 100.000 28 0 0 1952 1979 103464797 103464770 1.000000e-02 52.8
24 TraesCS4D01G054500 chr5B 100.000 28 0 0 1952 1979 105695965 105695938 1.000000e-02 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 TraesCS4D01G054500 chr4D 30216250 30221864 5614 True 10370.000000 10370 100.000000 1 5615 1 chr4D.!!$R1 5614
1 TraesCS4D01G054500 chr4A 572829935 572835565 5630 False 2445.333333 4654 88.012000 67 5607 3 chr4A.!!$F1 5540
2 TraesCS4D01G054500 chr4B 43108102 43113699 5597 True 2423.333333 3941 89.882667 71 5607 3 chr4B.!!$R2 5536

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
435 436 2.164624 CCTCCTAATAATCCCGAGCTCG 59.835 54.545 29.06 29.06 39.44 5.03 F
1330 1418 0.532862 CAACTGTCGTGGGTTCAGCT 60.533 55.000 0.00 0.00 33.12 4.24 F
1948 2056 0.106167 CATCTACTCCCTCCGTCCCA 60.106 60.000 0.00 0.00 0.00 4.37 F
2805 2920 0.674895 AAGAGTCGTGGATTGGCTGC 60.675 55.000 0.00 0.00 0.00 5.25 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1339 1427 0.881796 TTCTTCTGAGAGCGAGCGAA 59.118 50.000 0.00 0.0 32.44 4.70 R
2339 2452 1.883275 CAGGGGCGTCATGTGTTAAAA 59.117 47.619 0.00 0.0 0.00 1.52 R
2858 3056 3.149196 ACTGAATGCGAGGTTCACAATT 58.851 40.909 0.00 0.0 32.55 2.32 R
4640 4860 0.105760 AACCAATGGGGCTGACACAA 60.106 50.000 3.55 0.0 42.05 3.33 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
56 57 9.621629 TGACAAAAATAGAAGAAACTTAGGACA 57.378 29.630 0.00 0.00 0.00 4.02
59 60 9.346725 CAAAAATAGAAGAAACTTAGGACATGC 57.653 33.333 0.00 0.00 0.00 4.06
60 61 8.870075 AAAATAGAAGAAACTTAGGACATGCT 57.130 30.769 0.00 0.00 0.00 3.79
61 62 8.870075 AAATAGAAGAAACTTAGGACATGCTT 57.130 30.769 0.00 0.00 0.00 3.91
62 63 7.856145 ATAGAAGAAACTTAGGACATGCTTG 57.144 36.000 0.00 0.00 0.00 4.01
63 64 5.006386 AGAAGAAACTTAGGACATGCTTGG 58.994 41.667 4.44 0.00 0.00 3.61
64 65 4.373156 AGAAACTTAGGACATGCTTGGT 57.627 40.909 4.44 0.00 0.00 3.67
65 66 4.729868 AGAAACTTAGGACATGCTTGGTT 58.270 39.130 4.44 0.00 0.00 3.67
66 67 5.140454 AGAAACTTAGGACATGCTTGGTTT 58.860 37.500 4.44 3.76 0.00 3.27
67 68 4.853924 AACTTAGGACATGCTTGGTTTG 57.146 40.909 4.44 0.00 0.00 2.93
68 69 2.558359 ACTTAGGACATGCTTGGTTTGC 59.442 45.455 4.44 0.00 0.00 3.68
95 96 6.650390 GCCTACAAAATCCACAAATCAATGTT 59.350 34.615 0.00 0.00 0.00 2.71
114 115 8.772705 TCAATGTTTTGGCAAGTCATATTTTTC 58.227 29.630 15.70 0.00 33.44 2.29
147 148 3.636764 ACTTGTGGACAATTGGGAACTTC 59.363 43.478 10.83 0.00 35.02 3.01
198 199 4.955450 AGCAACCAATTGATAGCCAACATA 59.045 37.500 7.12 0.00 38.15 2.29
347 348 7.333528 AGTTCAATCTTAGTTCAAAACTGCA 57.666 32.000 2.65 0.00 42.84 4.41
435 436 2.164624 CCTCCTAATAATCCCGAGCTCG 59.835 54.545 29.06 29.06 39.44 5.03
603 631 8.308931 TCAGCTCATTAAAATTCTTTCAAGCAT 58.691 29.630 0.00 0.00 0.00 3.79
656 686 6.956202 TTTTTCCACGGAAATTTACAGGTA 57.044 33.333 11.92 0.00 42.71 3.08
657 687 7.527568 TTTTTCCACGGAAATTTACAGGTAT 57.472 32.000 11.92 0.00 42.71 2.73
658 688 6.503589 TTTCCACGGAAATTTACAGGTATG 57.496 37.500 7.17 0.00 38.95 2.39
659 689 5.168647 TCCACGGAAATTTACAGGTATGT 57.831 39.130 0.39 0.00 43.76 2.29
760 823 5.509622 GTGCATTTGAGCTCGAAATAAGAAC 59.490 40.000 20.22 11.25 34.99 3.01
773 836 5.907391 CGAAATAAGAACGTGGCAAATATCC 59.093 40.000 0.00 0.00 0.00 2.59
845 911 4.954875 CCTGCTCTATAAAACAGGGAGAG 58.045 47.826 0.00 0.00 44.90 3.20
988 1054 3.474570 CCAAGGAGCCCCGGAGAG 61.475 72.222 0.73 0.00 37.58 3.20
989 1055 3.474570 CAAGGAGCCCCGGAGAGG 61.475 72.222 0.73 0.00 37.58 3.69
990 1056 3.684628 AAGGAGCCCCGGAGAGGA 61.685 66.667 0.73 0.00 45.00 3.71
991 1057 3.254035 AAGGAGCCCCGGAGAGGAA 62.254 63.158 0.73 0.00 45.00 3.36
992 1058 3.157949 GGAGCCCCGGAGAGGAAG 61.158 72.222 0.73 0.00 45.00 3.46
1235 1318 1.533129 CGCCGTGATTCATCTCGTACA 60.533 52.381 9.67 0.00 40.86 2.90
1261 1344 3.733960 GACTGCCGCCCCGTTTTC 61.734 66.667 0.00 0.00 0.00 2.29
1330 1418 0.532862 CAACTGTCGTGGGTTCAGCT 60.533 55.000 0.00 0.00 33.12 4.24
1337 1425 2.876550 GTCGTGGGTTCAGCTTAAAAGT 59.123 45.455 0.00 0.00 0.00 2.66
1339 1427 4.694037 GTCGTGGGTTCAGCTTAAAAGTAT 59.306 41.667 0.00 0.00 0.00 2.12
1346 1435 5.248834 GTTCAGCTTAAAAGTATTCGCTCG 58.751 41.667 0.00 0.00 0.00 5.03
1371 1460 3.928618 GAAGAAAACTGCGCCGCCG 62.929 63.158 6.63 1.61 37.57 6.46
1436 1525 5.796502 TTGGATCTCCTGTCCCTAAAATT 57.203 39.130 0.00 0.00 34.76 1.82
1447 1546 9.182642 TCCTGTCCCTAAAATTATATCCTTCAT 57.817 33.333 0.00 0.00 0.00 2.57
1557 1657 6.088085 CCGTACATTTTTGTGATTCTCTTTGC 59.912 38.462 0.00 0.00 0.00 3.68
1586 1686 2.488153 GTGACCCTCTTTGTTATGTGGC 59.512 50.000 0.00 0.00 0.00 5.01
1588 1688 1.427368 ACCCTCTTTGTTATGTGGCCA 59.573 47.619 0.00 0.00 0.00 5.36
1595 1695 2.715749 TGTTATGTGGCCATCAGAGG 57.284 50.000 9.72 0.00 32.29 3.69
1613 1713 6.929625 TCAGAGGTTCTTCAGTATTCTTCAG 58.070 40.000 0.00 0.00 0.00 3.02
1615 1715 7.233553 TCAGAGGTTCTTCAGTATTCTTCAGAA 59.766 37.037 0.00 0.00 38.56 3.02
1684 1792 1.673808 CCCTCCCGTACCACTGTAGC 61.674 65.000 0.00 0.00 0.00 3.58
1747 1855 5.661458 ACTTTGGGTAGATTCAGATACACG 58.339 41.667 0.00 0.00 0.00 4.49
1914 2022 1.515081 ACATGTTTTGTACCGGACCG 58.485 50.000 9.46 6.99 36.57 4.79
1931 2039 0.469917 CCGCCCCTTGTCACTATCAT 59.530 55.000 0.00 0.00 0.00 2.45
1933 2041 1.414181 CGCCCCTTGTCACTATCATCT 59.586 52.381 0.00 0.00 0.00 2.90
1934 2042 2.628178 CGCCCCTTGTCACTATCATCTA 59.372 50.000 0.00 0.00 0.00 1.98
1935 2043 3.553096 CGCCCCTTGTCACTATCATCTAC 60.553 52.174 0.00 0.00 0.00 2.59
1936 2044 3.643792 GCCCCTTGTCACTATCATCTACT 59.356 47.826 0.00 0.00 0.00 2.57
1937 2045 4.262249 GCCCCTTGTCACTATCATCTACTC 60.262 50.000 0.00 0.00 0.00 2.59
1938 2046 4.282195 CCCCTTGTCACTATCATCTACTCC 59.718 50.000 0.00 0.00 0.00 3.85
1939 2047 4.282195 CCCTTGTCACTATCATCTACTCCC 59.718 50.000 0.00 0.00 0.00 4.30
1940 2048 5.144100 CCTTGTCACTATCATCTACTCCCT 58.856 45.833 0.00 0.00 0.00 4.20
1941 2049 5.242838 CCTTGTCACTATCATCTACTCCCTC 59.757 48.000 0.00 0.00 0.00 4.30
1942 2050 4.730966 TGTCACTATCATCTACTCCCTCC 58.269 47.826 0.00 0.00 0.00 4.30
1943 2051 3.754323 GTCACTATCATCTACTCCCTCCG 59.246 52.174 0.00 0.00 0.00 4.63
1944 2052 3.394940 TCACTATCATCTACTCCCTCCGT 59.605 47.826 0.00 0.00 0.00 4.69
1945 2053 3.754323 CACTATCATCTACTCCCTCCGTC 59.246 52.174 0.00 0.00 0.00 4.79
1946 2054 2.296073 ATCATCTACTCCCTCCGTCC 57.704 55.000 0.00 0.00 0.00 4.79
1947 2055 0.185416 TCATCTACTCCCTCCGTCCC 59.815 60.000 0.00 0.00 0.00 4.46
1948 2056 0.106167 CATCTACTCCCTCCGTCCCA 60.106 60.000 0.00 0.00 0.00 4.37
1949 2057 0.861155 ATCTACTCCCTCCGTCCCAT 59.139 55.000 0.00 0.00 0.00 4.00
1950 2058 1.526315 TCTACTCCCTCCGTCCCATA 58.474 55.000 0.00 0.00 0.00 2.74
1951 2059 1.854939 TCTACTCCCTCCGTCCCATAA 59.145 52.381 0.00 0.00 0.00 1.90
1952 2060 2.449730 TCTACTCCCTCCGTCCCATAAT 59.550 50.000 0.00 0.00 0.00 1.28
1953 2061 2.191981 ACTCCCTCCGTCCCATAATT 57.808 50.000 0.00 0.00 0.00 1.40
1954 2062 3.339713 ACTCCCTCCGTCCCATAATTA 57.660 47.619 0.00 0.00 0.00 1.40
1955 2063 3.870559 ACTCCCTCCGTCCCATAATTAT 58.129 45.455 0.00 0.00 0.00 1.28
1956 2064 3.583086 ACTCCCTCCGTCCCATAATTATG 59.417 47.826 17.11 17.11 0.00 1.90
1968 2076 4.207891 CATAATTATGGGACGGAGGGAG 57.792 50.000 16.41 0.00 0.00 4.30
1973 2081 1.229131 ATGGGACGGAGGGAGTAGTA 58.771 55.000 0.00 0.00 0.00 1.82
2004 2113 5.054477 CCCTCCGTTTACACAACATATAGG 58.946 45.833 0.00 0.00 0.00 2.57
2005 2114 4.510340 CCTCCGTTTACACAACATATAGGC 59.490 45.833 0.00 0.00 0.00 3.93
2006 2115 5.087391 TCCGTTTACACAACATATAGGCA 57.913 39.130 0.00 0.00 0.00 4.75
2034 2145 6.775088 TCAACATCTTGTCAGAAAATATCGC 58.225 36.000 0.00 0.00 30.76 4.58
2035 2146 5.395325 ACATCTTGTCAGAAAATATCGCG 57.605 39.130 0.00 0.00 30.76 5.87
2046 2157 6.362551 TCAGAAAATATCGCGAGTTATAGTGC 59.637 38.462 16.66 0.00 0.00 4.40
2076 2187 4.136796 TCATGTTTCAACTCCAGTTCCAG 58.863 43.478 0.00 0.00 35.83 3.86
2112 2223 3.728385 AGAGGTTCTGGGAAGAAATGG 57.272 47.619 0.00 0.00 0.00 3.16
2147 2259 6.072508 TGCTTCTTTTGATGACCTTGATACAC 60.073 38.462 0.00 0.00 0.00 2.90
2230 2343 7.278461 TCTCTAGAATATGGTACTTGCTCAC 57.722 40.000 0.00 0.00 0.00 3.51
2262 2375 8.511604 ACCATAATTTCACGATTCTGAGATTT 57.488 30.769 0.00 0.00 30.01 2.17
2271 2384 5.236047 CACGATTCTGAGATTTCCATCTTCC 59.764 44.000 0.00 0.00 40.14 3.46
2292 2405 8.462016 TCTTCCTCTTTAGATTGCTAAATTTGC 58.538 33.333 0.00 3.44 43.56 3.68
2352 2465 7.995463 TGCCTTTTAAGTTTTAACACATGAC 57.005 32.000 0.00 0.00 0.00 3.06
2513 2626 6.018016 CCCTGCAAAAATTAAACCTTGTCAAG 60.018 38.462 5.53 5.53 0.00 3.02
2523 2636 9.807921 AATTAAACCTTGTCAAGATCCTTCTTA 57.192 29.630 14.42 0.00 40.28 2.10
2527 2640 6.784031 ACCTTGTCAAGATCCTTCTTATTGT 58.216 36.000 14.42 0.00 40.28 2.71
2528 2641 7.234355 ACCTTGTCAAGATCCTTCTTATTGTT 58.766 34.615 14.42 0.00 40.28 2.83
2529 2642 7.725844 ACCTTGTCAAGATCCTTCTTATTGTTT 59.274 33.333 14.42 0.00 40.28 2.83
2530 2643 9.231297 CCTTGTCAAGATCCTTCTTATTGTTTA 57.769 33.333 14.42 0.00 40.28 2.01
2532 2645 9.793259 TTGTCAAGATCCTTCTTATTGTTTACT 57.207 29.630 0.00 0.00 40.28 2.24
2533 2646 9.793259 TGTCAAGATCCTTCTTATTGTTTACTT 57.207 29.630 0.00 0.00 40.28 2.24
2557 2670 7.011828 TGTTTTAGTACAAGTGCAAGAGAAC 57.988 36.000 0.00 0.00 0.00 3.01
2578 2691 5.362105 ACGGCATATTGGTTTAGGAAGTA 57.638 39.130 0.00 0.00 0.00 2.24
2579 2692 5.365619 ACGGCATATTGGTTTAGGAAGTAG 58.634 41.667 0.00 0.00 0.00 2.57
2580 2693 5.104652 ACGGCATATTGGTTTAGGAAGTAGT 60.105 40.000 0.00 0.00 0.00 2.73
2594 2707 5.269991 AGGAAGTAGTAGTATCCTGCAACA 58.730 41.667 0.00 0.00 40.73 3.33
2702 2816 8.034313 ACATTCATTCACTTCTTATAGGCCTA 57.966 34.615 16.60 16.60 0.00 3.93
2705 2819 7.676683 TCATTCACTTCTTATAGGCCTAAGT 57.323 36.000 18.42 14.39 31.85 2.24
2805 2920 0.674895 AAGAGTCGTGGATTGGCTGC 60.675 55.000 0.00 0.00 0.00 5.25
2820 2935 1.522258 GGCTGCGTGTGAAAACATTTG 59.478 47.619 0.00 0.00 0.00 2.32
2821 2936 1.071305 GCTGCGTGTGAAAACATTTGC 60.071 47.619 0.00 0.00 0.00 3.68
2858 3056 6.782986 ACTGATATTGCTTTGCTATATGGGA 58.217 36.000 10.23 0.00 37.17 4.37
2870 3068 5.376625 TGCTATATGGGAATTGTGAACCTC 58.623 41.667 0.00 0.00 0.00 3.85
2871 3069 4.452455 GCTATATGGGAATTGTGAACCTCG 59.548 45.833 0.00 0.00 0.00 4.63
3004 3202 0.252284 ATGACGACCCCTCTCCAGTT 60.252 55.000 0.00 0.00 0.00 3.16
3262 3460 2.291741 GTGGACAAGGCTGAAAAGAGTG 59.708 50.000 0.00 0.00 0.00 3.51
3350 3548 1.625818 CAGTCAAGCTCCAGGTAACCT 59.374 52.381 0.00 0.00 37.17 3.50
3366 3564 3.848272 AACCTGTTGTTTGACACAGTG 57.152 42.857 0.00 0.00 36.48 3.66
3416 3624 6.429385 CCTAGCAATCCTAATCTTGATTCACC 59.571 42.308 0.00 0.00 0.00 4.02
3417 3625 4.818546 AGCAATCCTAATCTTGATTCACCG 59.181 41.667 0.00 0.00 0.00 4.94
3775 3983 8.932963 GTTGATTTTAATTTGCAAAAACAGTCG 58.067 29.630 17.19 0.00 31.85 4.18
4033 4242 2.009774 CTGTACATGGCCTTCTTTCCG 58.990 52.381 3.32 0.00 0.00 4.30
4040 4249 0.251209 GGCCTTCTTTCCGTTCCCTT 60.251 55.000 0.00 0.00 0.00 3.95
4041 4250 1.003928 GGCCTTCTTTCCGTTCCCTTA 59.996 52.381 0.00 0.00 0.00 2.69
4138 4355 1.669440 CAAGCACTGCAAATGGGCT 59.331 52.632 3.30 0.00 36.13 5.19
4194 4411 1.001641 ATGGCAAGCAGGTGAGACC 60.002 57.895 0.00 0.00 38.99 3.85
4196 4413 2.743928 GCAAGCAGGTGAGACCCG 60.744 66.667 0.00 0.00 39.75 5.28
4249 4467 0.109532 TCCGACCAATGACAGCCAAA 59.890 50.000 0.00 0.00 0.00 3.28
4251 4469 0.110238 CGACCAATGACAGCCAAACG 60.110 55.000 0.00 0.00 0.00 3.60
4254 4472 3.006940 GACCAATGACAGCCAAACGATA 58.993 45.455 0.00 0.00 0.00 2.92
4348 4568 2.028658 TCAGCTTGTAGAGTTGAGCCAG 60.029 50.000 0.00 0.00 40.21 4.85
4368 4588 2.436911 AGATGATCTGTGCATGCAGGTA 59.563 45.455 23.41 9.57 37.12 3.08
4374 4594 2.026915 TCTGTGCATGCAGGTAGTTCAT 60.027 45.455 23.41 0.00 37.12 2.57
4788 5010 9.793259 AGAGATAAATGAAAAAGAACTGGTGTA 57.207 29.630 0.00 0.00 0.00 2.90
4830 5052 8.844690 GTCTGAATTTGAATTTGACTCGAAATC 58.155 33.333 12.23 0.00 33.47 2.17
4870 5092 9.910511 GTGGTATACTAAATGAACATAAACGTG 57.089 33.333 2.25 0.00 0.00 4.49
4895 5133 8.553153 TGGTCATTTTTATTACAGGACCTCATA 58.447 33.333 0.00 0.00 42.84 2.15
4914 5152 1.725803 AAAGAGGGTACGGTTCCTGT 58.274 50.000 7.34 1.59 32.74 4.00
4927 5165 4.700213 ACGGTTCCTGTGATTTCATAAAGG 59.300 41.667 0.00 0.00 0.00 3.11
4983 5221 1.929230 CCGAAAACCAAAACCACACC 58.071 50.000 0.00 0.00 0.00 4.16
5001 5239 5.920273 CCACACCACAACTTGATTGATTAAC 59.080 40.000 0.00 0.00 41.23 2.01
5016 5254 5.966636 TGATTAACGGACAATCAATCGAG 57.033 39.130 6.23 0.00 38.98 4.04
5022 5260 3.262420 CGGACAATCAATCGAGAAACCT 58.738 45.455 0.00 0.00 0.00 3.50
5039 5277 6.805713 AGAAACCTAACAATGACCACAAAAG 58.194 36.000 0.00 0.00 0.00 2.27
5042 5280 6.783708 ACCTAACAATGACCACAAAAGAAA 57.216 33.333 0.00 0.00 0.00 2.52
5045 5283 7.763985 ACCTAACAATGACCACAAAAGAAAAAG 59.236 33.333 0.00 0.00 0.00 2.27
5049 5287 8.614469 ACAATGACCACAAAAGAAAAAGAAAA 57.386 26.923 0.00 0.00 0.00 2.29
5118 5359 1.524961 CCAACATGCCCGCTACCTA 59.475 57.895 0.00 0.00 0.00 3.08
5123 5364 0.753262 CATGCCCGCTACCTAGAGTT 59.247 55.000 0.00 0.00 0.00 3.01
5156 5397 2.892852 CAAGAAGGAAGAACAATGCCCA 59.107 45.455 0.00 0.00 0.00 5.36
5202 5443 2.398498 CCTCGCCGATCAATAGAACTG 58.602 52.381 0.00 0.00 0.00 3.16
5215 5456 4.974645 ATAGAACTGTCACCCAGAAACA 57.025 40.909 0.00 0.00 44.49 2.83
5222 5463 1.903404 CACCCAGAAACAGCCCACC 60.903 63.158 0.00 0.00 0.00 4.61
5224 5465 1.077265 CCCAGAAACAGCCCACCAT 59.923 57.895 0.00 0.00 0.00 3.55
5278 5529 6.177610 TCGATATTTGGCCACTTTTAGAAGT 58.822 36.000 3.88 0.00 46.85 3.01
5298 5549 5.675684 AGTTTTTGACATGGTTTTCACCT 57.324 34.783 0.00 0.00 44.61 4.00
5300 5551 5.046663 AGTTTTTGACATGGTTTTCACCTGT 60.047 36.000 0.00 0.00 44.61 4.00
5376 5663 9.725019 ATTTTTGGAAGGAAACCAATTAAGATC 57.275 29.630 0.00 0.00 45.09 2.75
5378 5665 4.947388 TGGAAGGAAACCAATTAAGATCCG 59.053 41.667 0.00 0.00 34.25 4.18
5400 5687 3.071874 TCGATTGAAGCCAAATGGAGT 57.928 42.857 2.98 0.00 35.67 3.85
5414 5701 6.337356 CCAAATGGAGTAACTTTTGTTGTGT 58.663 36.000 0.00 0.00 39.39 3.72
5415 5702 6.255453 CCAAATGGAGTAACTTTTGTTGTGTG 59.745 38.462 0.00 0.00 39.39 3.82
5417 5704 5.968528 TGGAGTAACTTTTGTTGTGTGTT 57.031 34.783 0.00 0.00 43.41 3.32
5420 5718 5.969435 GGAGTAACTTTTGTTGTGTGTTAGC 59.031 40.000 0.00 0.00 43.41 3.09
5458 5756 2.803451 ACGAGCGCAATTGAACAAAAA 58.197 38.095 11.47 0.00 0.00 1.94
5460 5758 2.533535 CGAGCGCAATTGAACAAAAACA 59.466 40.909 11.47 0.00 0.00 2.83
5519 5817 4.702831 CCATGCACCTGTGTATACATGTA 58.297 43.478 9.18 8.27 34.49 2.29
5524 5842 9.002600 CATGCACCTGTGTATACATGTATAAAT 57.997 33.333 23.88 5.66 34.49 1.40
5607 5925 5.008619 TCACACATCAAAATGCAACAACT 57.991 34.783 0.00 0.00 36.26 3.16
5608 5926 6.141560 TCACACATCAAAATGCAACAACTA 57.858 33.333 0.00 0.00 36.26 2.24
5609 5927 6.207928 TCACACATCAAAATGCAACAACTAG 58.792 36.000 0.00 0.00 36.26 2.57
5610 5928 5.978919 CACACATCAAAATGCAACAACTAGT 59.021 36.000 0.00 0.00 36.26 2.57
5611 5929 5.978919 ACACATCAAAATGCAACAACTAGTG 59.021 36.000 0.00 0.00 36.26 2.74
5612 5930 4.984161 ACATCAAAATGCAACAACTAGTGC 59.016 37.500 0.00 0.00 36.26 4.40
5613 5931 3.976169 TCAAAATGCAACAACTAGTGCC 58.024 40.909 0.00 0.00 0.00 5.01
5614 5932 3.382865 TCAAAATGCAACAACTAGTGCCA 59.617 39.130 0.00 0.00 0.00 4.92
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
30 31 9.621629 TGTCCTAAGTTTCTTCTATTTTTGTCA 57.378 29.630 0.00 0.00 0.00 3.58
33 34 9.346725 GCATGTCCTAAGTTTCTTCTATTTTTG 57.653 33.333 0.00 0.00 0.00 2.44
34 35 9.301897 AGCATGTCCTAAGTTTCTTCTATTTTT 57.698 29.630 0.00 0.00 0.00 1.94
35 36 8.870075 AGCATGTCCTAAGTTTCTTCTATTTT 57.130 30.769 0.00 0.00 0.00 1.82
36 37 8.734386 CAAGCATGTCCTAAGTTTCTTCTATTT 58.266 33.333 0.00 0.00 0.00 1.40
37 38 7.337942 CCAAGCATGTCCTAAGTTTCTTCTATT 59.662 37.037 0.00 0.00 0.00 1.73
38 39 6.825721 CCAAGCATGTCCTAAGTTTCTTCTAT 59.174 38.462 0.00 0.00 0.00 1.98
39 40 6.173339 CCAAGCATGTCCTAAGTTTCTTCTA 58.827 40.000 0.00 0.00 0.00 2.10
40 41 5.006386 CCAAGCATGTCCTAAGTTTCTTCT 58.994 41.667 0.00 0.00 0.00 2.85
41 42 4.762251 ACCAAGCATGTCCTAAGTTTCTTC 59.238 41.667 0.00 0.00 0.00 2.87
42 43 4.729868 ACCAAGCATGTCCTAAGTTTCTT 58.270 39.130 0.00 0.00 0.00 2.52
43 44 4.373156 ACCAAGCATGTCCTAAGTTTCT 57.627 40.909 0.00 0.00 0.00 2.52
44 45 5.222631 CAAACCAAGCATGTCCTAAGTTTC 58.777 41.667 0.00 0.00 0.00 2.78
45 46 4.501400 GCAAACCAAGCATGTCCTAAGTTT 60.501 41.667 0.00 0.00 0.00 2.66
46 47 3.005791 GCAAACCAAGCATGTCCTAAGTT 59.994 43.478 0.00 0.00 0.00 2.66
47 48 2.558359 GCAAACCAAGCATGTCCTAAGT 59.442 45.455 0.00 0.00 0.00 2.24
48 49 2.557924 TGCAAACCAAGCATGTCCTAAG 59.442 45.455 0.00 0.00 37.02 2.18
49 50 2.557924 CTGCAAACCAAGCATGTCCTAA 59.442 45.455 0.00 0.00 41.82 2.69
50 51 2.161855 CTGCAAACCAAGCATGTCCTA 58.838 47.619 0.00 0.00 41.82 2.94
51 52 0.963962 CTGCAAACCAAGCATGTCCT 59.036 50.000 0.00 0.00 41.82 3.85
52 53 0.668401 GCTGCAAACCAAGCATGTCC 60.668 55.000 0.00 0.00 41.82 4.02
53 54 0.668401 GGCTGCAAACCAAGCATGTC 60.668 55.000 0.50 0.00 41.82 3.06
54 55 1.117142 AGGCTGCAAACCAAGCATGT 61.117 50.000 8.09 0.00 41.82 3.21
55 56 0.889994 TAGGCTGCAAACCAAGCATG 59.110 50.000 8.09 0.00 41.82 4.06
56 57 0.890683 GTAGGCTGCAAACCAAGCAT 59.109 50.000 8.09 0.00 41.82 3.79
57 58 0.467106 TGTAGGCTGCAAACCAAGCA 60.467 50.000 1.69 0.00 40.19 3.91
58 59 0.673437 TTGTAGGCTGCAAACCAAGC 59.327 50.000 15.89 0.00 0.00 4.01
59 60 3.451141 TTTTGTAGGCTGCAAACCAAG 57.549 42.857 26.94 0.00 35.82 3.61
60 61 3.244044 GGATTTTGTAGGCTGCAAACCAA 60.244 43.478 26.94 15.30 35.82 3.67
61 62 2.298729 GGATTTTGTAGGCTGCAAACCA 59.701 45.455 26.94 15.97 35.82 3.67
62 63 2.298729 TGGATTTTGTAGGCTGCAAACC 59.701 45.455 26.94 24.39 35.82 3.27
63 64 3.243704 TGTGGATTTTGTAGGCTGCAAAC 60.244 43.478 26.94 17.63 35.82 2.93
64 65 2.961741 TGTGGATTTTGTAGGCTGCAAA 59.038 40.909 24.06 24.06 34.47 3.68
65 66 2.591923 TGTGGATTTTGTAGGCTGCAA 58.408 42.857 14.27 14.27 0.00 4.08
66 67 2.284754 TGTGGATTTTGTAGGCTGCA 57.715 45.000 0.00 0.00 0.00 4.41
67 68 3.658757 TTTGTGGATTTTGTAGGCTGC 57.341 42.857 0.00 0.00 0.00 5.25
68 69 5.389859 TGATTTGTGGATTTTGTAGGCTG 57.610 39.130 0.00 0.00 0.00 4.85
95 96 8.074972 GCAATTTGAAAAATATGACTTGCCAAA 58.925 29.630 0.00 0.00 32.45 3.28
114 115 3.529533 TGTCCACAAGTTTGGCAATTTG 58.470 40.909 18.04 18.04 36.48 2.32
147 148 0.543277 TGCATTGCCCACCTCTAGAG 59.457 55.000 13.18 13.18 0.00 2.43
295 296 4.870221 AGTTCAAAACCGTGACACTTAC 57.130 40.909 3.68 0.00 0.00 2.34
347 348 6.099845 ACTCCCTTCGATCCATAATAAGTGTT 59.900 38.462 0.00 0.00 0.00 3.32
387 388 8.410912 ACATTTTTCGTTTAGTAGGCTTCTTTT 58.589 29.630 0.00 0.00 0.00 2.27
510 520 6.879993 TCATGAAAATTTGCAGCCATACAAAT 59.120 30.769 4.87 0.00 45.84 2.32
760 823 5.043248 GGAGAAAATTGGATATTTGCCACG 58.957 41.667 0.00 0.00 34.56 4.94
773 836 5.786392 GTCACGATTAGACGGAGAAAATTG 58.214 41.667 0.00 0.00 37.61 2.32
972 1038 3.474570 CCTCTCCGGGGCTCCTTG 61.475 72.222 0.00 0.00 0.00 3.61
988 1054 2.052104 CGCCCATGGTTTCCCTTCC 61.052 63.158 11.73 0.00 0.00 3.46
989 1055 2.710902 GCGCCCATGGTTTCCCTTC 61.711 63.158 11.73 0.00 0.00 3.46
990 1056 2.679996 GCGCCCATGGTTTCCCTT 60.680 61.111 11.73 0.00 0.00 3.95
991 1057 4.759205 GGCGCCCATGGTTTCCCT 62.759 66.667 18.11 0.00 0.00 4.20
1316 1399 2.876550 ACTTTTAAGCTGAACCCACGAC 59.123 45.455 0.00 0.00 0.00 4.34
1330 1418 4.740268 TGAGAGCGAGCGAATACTTTTAA 58.260 39.130 0.00 0.00 0.00 1.52
1337 1425 2.289565 TCTTCTGAGAGCGAGCGAATA 58.710 47.619 0.00 0.00 0.00 1.75
1339 1427 0.881796 TTCTTCTGAGAGCGAGCGAA 59.118 50.000 0.00 0.00 32.44 4.70
1346 1435 1.136113 GCGCAGTTTTCTTCTGAGAGC 60.136 52.381 0.30 0.00 35.36 4.09
1371 1460 2.414161 GGAACAGCAAGAAACGTATGGC 60.414 50.000 0.00 0.00 0.00 4.40
1447 1546 3.788142 AGGGGGAATTCTGCAATAGAGAA 59.212 43.478 5.23 0.00 36.61 2.87
1557 1657 8.576442 ACATAACAAAGAGGGTCACAAAAATAG 58.424 33.333 0.00 0.00 0.00 1.73
1586 1686 6.232581 AGAATACTGAAGAACCTCTGATGG 57.767 41.667 0.00 0.00 0.00 3.51
1588 1688 7.398618 TCTGAAGAATACTGAAGAACCTCTGAT 59.601 37.037 0.00 0.00 0.00 2.90
1595 1695 9.604626 CAAACATTCTGAAGAATACTGAAGAAC 57.395 33.333 5.26 0.00 42.41 3.01
1613 1713 5.175673 GCCAAAACTAGCAAGTCAAACATTC 59.824 40.000 0.00 0.00 33.75 2.67
1615 1715 4.342092 AGCCAAAACTAGCAAGTCAAACAT 59.658 37.500 0.00 0.00 33.75 2.71
1684 1792 8.991243 TTTATTTGAATTCAATGCAGAGAAGG 57.009 30.769 21.10 0.00 35.55 3.46
1759 1867 7.401080 CCTTTTAACAATGAAAGCAACACAAG 58.599 34.615 0.00 0.00 32.36 3.16
1779 1887 4.133820 GCCAAACCATAAACAAGCCTTTT 58.866 39.130 0.00 0.00 0.00 2.27
1914 2022 3.643792 AGTAGATGATAGTGACAAGGGGC 59.356 47.826 0.00 0.00 0.00 5.80
1931 2039 1.526315 TATGGGACGGAGGGAGTAGA 58.474 55.000 0.00 0.00 0.00 2.59
1933 2041 3.339713 AATTATGGGACGGAGGGAGTA 57.660 47.619 0.00 0.00 0.00 2.59
1934 2042 2.191981 AATTATGGGACGGAGGGAGT 57.808 50.000 0.00 0.00 0.00 3.85
1935 2043 4.207891 CATAATTATGGGACGGAGGGAG 57.792 50.000 16.41 0.00 0.00 4.30
1947 2055 3.583086 ACTCCCTCCGTCCCATAATTATG 59.417 47.826 17.11 17.11 0.00 1.90
1948 2056 3.870559 ACTCCCTCCGTCCCATAATTAT 58.129 45.455 0.00 0.00 0.00 1.28
1949 2057 3.339713 ACTCCCTCCGTCCCATAATTA 57.660 47.619 0.00 0.00 0.00 1.40
1950 2058 2.191981 ACTCCCTCCGTCCCATAATT 57.808 50.000 0.00 0.00 0.00 1.40
1951 2059 2.179424 ACTACTCCCTCCGTCCCATAAT 59.821 50.000 0.00 0.00 0.00 1.28
1952 2060 1.572415 ACTACTCCCTCCGTCCCATAA 59.428 52.381 0.00 0.00 0.00 1.90
1953 2061 1.229131 ACTACTCCCTCCGTCCCATA 58.771 55.000 0.00 0.00 0.00 2.74
1954 2062 1.229131 TACTACTCCCTCCGTCCCAT 58.771 55.000 0.00 0.00 0.00 4.00
1955 2063 1.229131 ATACTACTCCCTCCGTCCCA 58.771 55.000 0.00 0.00 0.00 4.37
1956 2064 2.158490 AGAATACTACTCCCTCCGTCCC 60.158 54.545 0.00 0.00 0.00 4.46
1957 2065 3.226682 AGAATACTACTCCCTCCGTCC 57.773 52.381 0.00 0.00 0.00 4.79
1958 2066 4.036616 GTCAAGAATACTACTCCCTCCGTC 59.963 50.000 0.00 0.00 0.00 4.79
1959 2067 3.952967 GTCAAGAATACTACTCCCTCCGT 59.047 47.826 0.00 0.00 0.00 4.69
1960 2068 3.318557 GGTCAAGAATACTACTCCCTCCG 59.681 52.174 0.00 0.00 0.00 4.63
1961 2069 3.642377 GGGTCAAGAATACTACTCCCTCC 59.358 52.174 0.00 0.00 0.00 4.30
1962 2070 4.548669 AGGGTCAAGAATACTACTCCCTC 58.451 47.826 0.00 0.00 35.95 4.30
1963 2071 4.548669 GAGGGTCAAGAATACTACTCCCT 58.451 47.826 0.00 0.00 39.87 4.20
1964 2072 3.642377 GGAGGGTCAAGAATACTACTCCC 59.358 52.174 0.00 0.00 36.16 4.30
1965 2073 3.318557 CGGAGGGTCAAGAATACTACTCC 59.681 52.174 0.00 0.00 37.49 3.85
1966 2074 3.952967 ACGGAGGGTCAAGAATACTACTC 59.047 47.826 0.00 0.00 0.00 2.59
1967 2075 3.978610 ACGGAGGGTCAAGAATACTACT 58.021 45.455 0.00 0.00 0.00 2.57
1968 2076 4.732672 AACGGAGGGTCAAGAATACTAC 57.267 45.455 0.00 0.00 0.00 2.73
1973 2081 3.071892 TGTGTAAACGGAGGGTCAAGAAT 59.928 43.478 0.00 0.00 0.00 2.40
2004 2113 1.467734 CTGACAAGATGTTGAGCCTGC 59.532 52.381 9.96 0.00 37.10 4.85
2005 2114 3.049708 TCTGACAAGATGTTGAGCCTG 57.950 47.619 9.96 2.99 37.10 4.85
2006 2115 3.777106 TTCTGACAAGATGTTGAGCCT 57.223 42.857 9.96 0.00 37.10 4.58
2034 2145 5.188327 TGAGAATGAGGCACTATAACTCG 57.812 43.478 0.00 0.00 41.55 4.18
2035 2146 6.520272 ACATGAGAATGAGGCACTATAACTC 58.480 40.000 0.00 0.00 41.55 3.01
2046 2157 5.005740 TGGAGTTGAAACATGAGAATGAGG 58.994 41.667 0.00 0.00 0.00 3.86
2076 2187 7.355778 CAGAACCTCTTTTCTGTGTTCATAAC 58.644 38.462 4.94 0.00 45.12 1.89
2124 2235 6.430925 TGGTGTATCAAGGTCATCAAAAGAAG 59.569 38.462 0.00 0.00 0.00 2.85
2125 2236 6.303054 TGGTGTATCAAGGTCATCAAAAGAA 58.697 36.000 0.00 0.00 0.00 2.52
2126 2237 5.875224 TGGTGTATCAAGGTCATCAAAAGA 58.125 37.500 0.00 0.00 0.00 2.52
2147 2259 5.122239 TCTGAATGTCTGCGTCTTAAAATGG 59.878 40.000 0.00 0.00 0.00 3.16
2230 2343 8.338259 CAGAATCGTGAAATTATGGTTTCCTAG 58.662 37.037 0.00 0.00 37.31 3.02
2262 2375 5.965033 AGCAATCTAAAGAGGAAGATGGA 57.035 39.130 0.00 0.00 32.79 3.41
2333 2446 5.507650 GGGGCGTCATGTGTTAAAACTTAAA 60.508 40.000 0.00 0.00 0.00 1.52
2334 2447 4.023021 GGGGCGTCATGTGTTAAAACTTAA 60.023 41.667 0.00 0.00 0.00 1.85
2335 2448 3.502979 GGGGCGTCATGTGTTAAAACTTA 59.497 43.478 0.00 0.00 0.00 2.24
2336 2449 2.295070 GGGGCGTCATGTGTTAAAACTT 59.705 45.455 0.00 0.00 0.00 2.66
2337 2450 1.883926 GGGGCGTCATGTGTTAAAACT 59.116 47.619 0.00 0.00 0.00 2.66
2338 2451 1.883926 AGGGGCGTCATGTGTTAAAAC 59.116 47.619 0.00 0.00 0.00 2.43
2339 2452 1.883275 CAGGGGCGTCATGTGTTAAAA 59.117 47.619 0.00 0.00 0.00 1.52
2532 2645 7.469260 GTTCTCTTGCACTTGTACTAAAACAA 58.531 34.615 0.00 0.00 37.75 2.83
2533 2646 6.237996 CGTTCTCTTGCACTTGTACTAAAACA 60.238 38.462 0.00 0.00 0.00 2.83
2534 2647 6.127403 CGTTCTCTTGCACTTGTACTAAAAC 58.873 40.000 0.00 0.00 0.00 2.43
2548 2661 2.017049 ACCAATATGCCGTTCTCTTGC 58.983 47.619 0.00 0.00 0.00 4.01
2557 2670 5.365619 ACTACTTCCTAAACCAATATGCCG 58.634 41.667 0.00 0.00 0.00 5.69
2588 2701 2.992543 GTGAAAGTGCTTTTGTGTTGCA 59.007 40.909 0.00 0.00 32.11 4.08
2594 2707 6.426328 TGTTTTTCATGTGAAAGTGCTTTTGT 59.574 30.769 8.07 0.00 43.90 2.83
2667 2780 8.627208 AGAAGTGAATGAATGTTGACTACAAT 57.373 30.769 0.00 0.00 40.89 2.71
2752 2867 3.495001 CGTGATGCAGAGTCGTAGATAGA 59.505 47.826 0.00 0.00 40.67 1.98
2767 2882 4.611943 TCTTAAGAGATAGTGCGTGATGC 58.388 43.478 0.00 0.00 46.70 3.91
2842 3040 5.199723 TCACAATTCCCATATAGCAAAGCA 58.800 37.500 0.00 0.00 0.00 3.91
2845 3043 6.194235 AGGTTCACAATTCCCATATAGCAAA 58.806 36.000 0.00 0.00 0.00 3.68
2848 3046 4.452455 CGAGGTTCACAATTCCCATATAGC 59.548 45.833 0.00 0.00 0.00 2.97
2858 3056 3.149196 ACTGAATGCGAGGTTCACAATT 58.851 40.909 0.00 0.00 32.55 2.32
2870 3068 5.220557 TCATGACATAACAACTGAATGCG 57.779 39.130 0.00 0.00 0.00 4.73
2871 3069 8.470040 AAATTCATGACATAACAACTGAATGC 57.530 30.769 0.00 0.00 33.03 3.56
2916 3114 5.552178 ACTCCTCAAAAGATACCTGTGAAC 58.448 41.667 0.00 0.00 0.00 3.18
2917 3115 5.825593 ACTCCTCAAAAGATACCTGTGAA 57.174 39.130 0.00 0.00 0.00 3.18
3004 3202 3.704566 CACTACCACCAGCCATAGTTCTA 59.295 47.826 0.00 0.00 0.00 2.10
3192 3390 7.962441 ACATAAAGTTGGCTTTGGATTTTAGT 58.038 30.769 3.17 0.00 44.00 2.24
3262 3460 3.551454 CCAAGCATGCACACTATAATGGC 60.551 47.826 21.98 0.00 0.00 4.40
3350 3548 6.682746 ACATTTAACACTGTGTCAAACAACA 58.317 32.000 14.68 0.00 38.67 3.33
3392 3599 6.146837 CGGTGAATCAAGATTAGGATTGCTAG 59.853 42.308 0.00 0.00 34.06 3.42
3395 3602 4.576463 ACGGTGAATCAAGATTAGGATTGC 59.424 41.667 0.00 0.00 34.06 3.56
3563 3771 8.748412 CAATGATGAAAAAGGTATCCAGGTTAA 58.252 33.333 0.00 0.00 0.00 2.01
3775 3983 8.488651 TGAGATAAACCGAAGAAACTAAATCC 57.511 34.615 0.00 0.00 0.00 3.01
4033 4242 7.992754 ATCAGATGCATAAGAATAAGGGAAC 57.007 36.000 0.00 0.00 0.00 3.62
4138 4355 0.750249 TTGAAGCGAGAGTCACCACA 59.250 50.000 0.00 0.00 0.00 4.17
4141 4358 1.433534 CCTTTGAAGCGAGAGTCACC 58.566 55.000 0.00 0.00 0.00 4.02
4194 4411 3.557577 TGTTGATGTTTTGATGCTCGG 57.442 42.857 0.00 0.00 0.00 4.63
4249 4467 0.747255 AGCATCGGCACTCTTATCGT 59.253 50.000 0.00 0.00 44.61 3.73
4251 4469 3.060602 GGTTAGCATCGGCACTCTTATC 58.939 50.000 0.00 0.00 44.61 1.75
4254 4472 0.613260 TGGTTAGCATCGGCACTCTT 59.387 50.000 0.00 0.00 44.61 2.85
4348 4568 1.676746 ACCTGCATGCACAGATCATC 58.323 50.000 18.46 0.00 40.25 2.92
4368 4588 1.750399 GATGGCCGGCACATGAACT 60.750 57.895 30.85 8.21 0.00 3.01
4640 4860 0.105760 AACCAATGGGGCTGACACAA 60.106 50.000 3.55 0.00 42.05 3.33
4642 4862 1.535204 CCAACCAATGGGGCTGACAC 61.535 60.000 3.55 0.00 46.27 3.67
4643 4863 1.228831 CCAACCAATGGGGCTGACA 60.229 57.895 3.55 0.00 46.27 3.58
4644 4864 3.698765 CCAACCAATGGGGCTGAC 58.301 61.111 3.55 0.00 46.27 3.51
4784 5006 7.147976 TCAGACACATATGCATGATACTACAC 58.852 38.462 10.16 0.00 35.96 2.90
4788 5010 8.565416 CAAATTCAGACACATATGCATGATACT 58.435 33.333 10.16 0.00 35.96 2.12
4830 5052 5.734720 AGTATACCACAGTCAGATGTTTGG 58.265 41.667 0.00 0.00 0.00 3.28
4870 5092 7.881775 ATGAGGTCCTGTAATAAAAATGACC 57.118 36.000 0.00 0.00 40.81 4.02
4895 5133 1.346722 CACAGGAACCGTACCCTCTTT 59.653 52.381 0.00 0.00 0.00 2.52
4905 5143 4.941263 TCCTTTATGAAATCACAGGAACCG 59.059 41.667 5.69 0.00 30.93 4.44
4927 5165 9.141400 CTTATAAACCGAGCCAACTATATTCTC 57.859 37.037 0.00 0.00 0.00 2.87
4983 5221 5.996219 TGTCCGTTAATCAATCAAGTTGTG 58.004 37.500 2.11 0.00 38.95 3.33
5001 5239 3.262420 AGGTTTCTCGATTGATTGTCCG 58.738 45.455 0.00 0.00 0.00 4.79
5016 5254 6.801575 TCTTTTGTGGTCATTGTTAGGTTTC 58.198 36.000 0.00 0.00 0.00 2.78
5022 5260 9.712305 TTTCTTTTTCTTTTGTGGTCATTGTTA 57.288 25.926 0.00 0.00 0.00 2.41
5049 5287 6.019075 GCGGCTTTGTTGTTTTTATCTCTTTT 60.019 34.615 0.00 0.00 0.00 2.27
5118 5359 2.365617 TCTTGAAGGCGTCTCAAACTCT 59.634 45.455 1.41 0.00 0.00 3.24
5123 5364 1.691976 TCCTTCTTGAAGGCGTCTCAA 59.308 47.619 21.16 0.00 39.80 3.02
5178 5419 0.673985 CTATTGATCGGCGAGGGTCA 59.326 55.000 17.22 11.90 0.00 4.02
5202 5443 1.150536 TGGGCTGTTTCTGGGTGAC 59.849 57.895 0.00 0.00 0.00 3.67
5215 5456 1.002134 CAAGGTTCGATGGTGGGCT 60.002 57.895 0.00 0.00 0.00 5.19
5222 5463 1.543429 GCCCTATCCCAAGGTTCGATG 60.543 57.143 0.00 0.00 34.56 3.84
5224 5465 1.342672 GGCCCTATCCCAAGGTTCGA 61.343 60.000 0.00 0.00 34.56 3.71
5278 5529 5.413309 ACAGGTGAAAACCATGTCAAAAA 57.587 34.783 0.00 0.00 0.00 1.94
5374 5661 2.620251 TTGGCTTCAATCGATCGGAT 57.380 45.000 16.41 4.75 36.78 4.18
5375 5662 2.394930 TTTGGCTTCAATCGATCGGA 57.605 45.000 16.41 1.35 0.00 4.55
5376 5663 2.287188 CCATTTGGCTTCAATCGATCGG 60.287 50.000 16.41 0.00 0.00 4.18
5378 5665 3.629398 ACTCCATTTGGCTTCAATCGATC 59.371 43.478 0.00 0.00 34.44 3.69
5400 5687 4.142665 TGCGCTAACACACAACAAAAGTTA 60.143 37.500 9.73 0.00 0.00 2.24
5414 5701 0.238025 TACGTCGTCTTGCGCTAACA 59.762 50.000 9.73 0.00 41.07 2.41
5415 5702 1.252015 CATACGTCGTCTTGCGCTAAC 59.748 52.381 9.73 2.92 41.07 2.34
5417 5704 0.248336 CCATACGTCGTCTTGCGCTA 60.248 55.000 9.73 0.00 41.07 4.26
5420 5718 1.186030 GTACCATACGTCGTCTTGCG 58.814 55.000 0.00 0.00 43.01 4.85
5440 5738 4.713854 ATGTTTTTGTTCAATTGCGCTC 57.286 36.364 9.73 0.00 0.00 5.03
5444 5742 9.286946 TGAATTTGAATGTTTTTGTTCAATTGC 57.713 25.926 0.00 0.00 42.12 3.56
5458 5756 9.598517 TTTTAGCACTCTTTTGAATTTGAATGT 57.401 25.926 0.00 0.00 0.00 2.71
5496 5794 2.036958 TGTATACACAGGTGCATGGC 57.963 50.000 0.08 0.00 0.00 4.40


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

AutoCloner maintained by Alex Coulton.