Multiple sequence alignment - TraesCS2D01G145200

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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 TraesCS2D01G145200 chr2D 100.000 2636 0 0 1 2636 86718016 86715381 0.000000e+00 4868.0
1 TraesCS2D01G145200 chr2D 96.117 103 4 0 2534 2636 5672218 5672116 4.510000e-38 169.0
2 TraesCS2D01G145200 chr2D 96.117 103 4 0 2534 2636 579754491 579754389 4.510000e-38 169.0
3 TraesCS2D01G145200 chr2D 96.117 103 4 0 2534 2636 622019190 622019292 4.510000e-38 169.0
4 TraesCS2D01G145200 chr2A 91.523 1852 79 25 1 1852 86989676 86987903 0.000000e+00 2479.0
5 TraesCS2D01G145200 chr2A 89.552 134 13 1 2402 2534 86987185 86987052 4.510000e-38 169.0
6 TraesCS2D01G145200 chr2A 96.117 103 4 0 2534 2636 98897544 98897442 4.510000e-38 169.0
7 TraesCS2D01G145200 chr2B 92.561 1519 93 9 210 1716 139571327 139569817 0.000000e+00 2161.0
8 TraesCS2D01G145200 chr2B 85.778 225 17 4 3 219 139571563 139571346 9.490000e-55 224.0
9 TraesCS2D01G145200 chr2B 88.060 134 15 1 2402 2534 139568983 139568850 9.770000e-35 158.0
10 TraesCS2D01G145200 chr2B 84.524 84 6 3 1769 1852 139569784 139569708 2.810000e-10 76.8
11 TraesCS2D01G145200 chr7D 96.117 103 4 0 2534 2636 580887549 580887651 4.510000e-38 169.0
12 TraesCS2D01G145200 chr7A 96.117 103 4 0 2534 2636 437074503 437074401 4.510000e-38 169.0
13 TraesCS2D01G145200 chr3A 96.117 103 4 0 2534 2636 64085365 64085263 4.510000e-38 169.0
14 TraesCS2D01G145200 chr1D 96.117 103 4 0 2534 2636 459856889 459856991 4.510000e-38 169.0
15 TraesCS2D01G145200 chr6A 96.040 101 4 0 2536 2636 4415365 4415465 5.840000e-37 165.0
16 TraesCS2D01G145200 chr5D 97.619 42 0 1 1994 2034 68253318 68253277 1.310000e-08 71.3
17 TraesCS2D01G145200 chr5B 97.619 42 0 1 1993 2033 74435097 74435056 1.310000e-08 71.3


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 TraesCS2D01G145200 chr2D 86715381 86718016 2635 True 4868.00 4868 100.00000 1 2636 1 chr2D.!!$R2 2635
1 TraesCS2D01G145200 chr2A 86987052 86989676 2624 True 1324.00 2479 90.53750 1 2534 2 chr2A.!!$R2 2533
2 TraesCS2D01G145200 chr2B 139568850 139571563 2713 True 654.95 2161 87.73075 3 2534 4 chr2B.!!$R1 2531

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
46 47 0.238289 CGCAGTTTACCAGCAACCTG 59.762 55.0 0.0 0.0 38.85 4.0 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1788 1846 0.040425 CGACGAACCAAAAGCCCAAG 60.04 55.0 0.0 0.0 0.0 3.61 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
46 47 0.238289 CGCAGTTTACCAGCAACCTG 59.762 55.000 0.00 0.00 38.85 4.00
47 48 1.604604 GCAGTTTACCAGCAACCTGA 58.395 50.000 0.00 0.00 41.77 3.86
48 49 1.537202 GCAGTTTACCAGCAACCTGAG 59.463 52.381 0.00 0.00 41.77 3.35
49 50 2.851195 CAGTTTACCAGCAACCTGAGT 58.149 47.619 0.00 0.00 41.77 3.41
52 53 0.690762 TTACCAGCAACCTGAGTCCC 59.309 55.000 0.00 0.00 41.77 4.46
55 56 1.002868 CAGCAACCTGAGTCCCCAG 60.003 63.158 0.00 0.00 41.77 4.45
94 95 0.320374 TTCATCGAAAGCCGGACACT 59.680 50.000 5.05 0.00 39.14 3.55
143 144 3.246226 CGATGCTTTAGTCCTCATTTCCG 59.754 47.826 0.00 0.00 0.00 4.30
145 146 3.861840 TGCTTTAGTCCTCATTTCCGAG 58.138 45.455 0.00 0.00 0.00 4.63
165 166 4.438608 CGAGGATGATCAGTCAGCTATAGC 60.439 50.000 17.33 17.33 40.55 2.97
168 169 2.587522 TGATCAGTCAGCTATAGCCGT 58.412 47.619 21.17 0.29 43.38 5.68
173 182 1.405821 AGTCAGCTATAGCCGTGTCAC 59.594 52.381 21.17 8.96 43.38 3.67
262 305 2.531522 ACATTGCCAAACCTTGCTTC 57.468 45.000 0.00 0.00 0.00 3.86
350 393 4.223700 ACATGTAGCAATCTCTTGGTCTCA 59.776 41.667 0.00 0.00 41.95 3.27
352 395 5.227569 TGTAGCAATCTCTTGGTCTCAAA 57.772 39.130 0.00 0.00 41.95 2.69
379 422 3.994392 GAGGTCAACGTCTGCAGATTTTA 59.006 43.478 21.47 5.29 0.00 1.52
380 423 3.746492 AGGTCAACGTCTGCAGATTTTAC 59.254 43.478 21.47 16.27 0.00 2.01
410 453 3.501445 GTGCAGCTTTCAGAACTGAGAAT 59.499 43.478 5.19 0.00 41.13 2.40
412 455 3.750130 GCAGCTTTCAGAACTGAGAATGA 59.250 43.478 5.19 0.00 41.13 2.57
413 456 4.378253 GCAGCTTTCAGAACTGAGAATGAC 60.378 45.833 5.19 0.00 41.13 3.06
414 457 4.753610 CAGCTTTCAGAACTGAGAATGACA 59.246 41.667 4.72 0.00 41.13 3.58
423 466 8.853126 TCAGAACTGAGAATGACAAATTTCAAT 58.147 29.630 0.00 0.00 34.14 2.57
426 469 9.635520 GAACTGAGAATGACAAATTTCAATCAT 57.364 29.630 4.11 4.11 33.18 2.45
427 470 9.635520 AACTGAGAATGACAAATTTCAATCATC 57.364 29.630 8.74 4.81 31.41 2.92
428 471 8.799367 ACTGAGAATGACAAATTTCAATCATCA 58.201 29.630 8.74 4.81 31.41 3.07
429 472 9.803315 CTGAGAATGACAAATTTCAATCATCAT 57.197 29.630 8.74 3.07 31.41 2.45
520 563 3.188786 GGCAGCGTCACGATCACC 61.189 66.667 0.00 0.00 0.00 4.02
613 656 4.780815 TCCCGAGACAATTAATCTGCAAT 58.219 39.130 0.00 0.00 0.00 3.56
614 657 5.924356 TCCCGAGACAATTAATCTGCAATA 58.076 37.500 0.00 0.00 0.00 1.90
710 753 7.978982 ACCTAATCAATCATGAAAACTCTTCG 58.021 34.615 0.00 0.00 39.49 3.79
765 808 9.892130 ATCAGGATCTTAGAAAAATTTCGTACT 57.108 29.630 0.00 0.00 41.92 2.73
816 859 1.546923 TCATCTTGCAAATGTGGGCAG 59.453 47.619 16.17 0.00 41.68 4.85
823 866 1.067000 GCAAATGTGGGCAGCATGTAA 60.067 47.619 0.00 0.00 39.31 2.41
824 867 2.419021 GCAAATGTGGGCAGCATGTAAT 60.419 45.455 0.00 0.00 39.31 1.89
833 876 4.222366 TGGGCAGCATGTAATTCAATTTGA 59.778 37.500 0.00 0.00 39.31 2.69
838 881 6.019318 GCAGCATGTAATTCAATTTGATCACC 60.019 38.462 0.00 0.00 39.31 4.02
872 915 6.515035 GCAATTTACAACCAAGACAAGCTACT 60.515 38.462 0.00 0.00 0.00 2.57
884 927 7.147811 CCAAGACAAGCTACTACTATTTCTCCT 60.148 40.741 0.00 0.00 0.00 3.69
976 1019 4.097135 GGCAAATTAGAGAAGAAAGGAGGC 59.903 45.833 0.00 0.00 0.00 4.70
1038 1081 0.389166 AAGCCGAGTCGAGCAAGAAG 60.389 55.000 22.32 3.33 0.00 2.85
1049 1092 2.266627 GCAAGAAGGCAGCAGCAGT 61.267 57.895 2.65 0.00 44.61 4.40
1076 1125 3.660111 AGCGACAAAAGTGGGCGC 61.660 61.111 4.17 4.17 46.55 6.53
1389 1438 1.185618 TCTCCAAGTACAGGCTGCGT 61.186 55.000 15.89 0.00 0.00 5.24
1655 1704 1.380785 TAGTCCGGCCGGTGATCTT 60.381 57.895 41.57 23.16 36.47 2.40
1706 1755 0.711118 GTTTGTGTTTTGCGTGCGTT 59.289 45.000 0.00 0.00 0.00 4.84
1710 1759 0.498095 GTGTTTTGCGTGCGTTCATG 59.502 50.000 0.00 0.00 0.00 3.07
1716 1765 1.195347 TGCGTGCGTTCATGTTTTTG 58.805 45.000 0.00 0.00 0.00 2.44
1720 1769 3.482760 GCGTGCGTTCATGTTTTTGTTTT 60.483 39.130 0.00 0.00 0.00 2.43
1721 1770 4.633011 CGTGCGTTCATGTTTTTGTTTTT 58.367 34.783 0.00 0.00 0.00 1.94
1790 1848 3.055719 CCGTTCGCATGTGGCCTT 61.056 61.111 3.32 0.00 40.31 4.35
1791 1849 2.176546 CGTTCGCATGTGGCCTTG 59.823 61.111 3.32 0.00 40.31 3.61
1792 1850 2.568090 GTTCGCATGTGGCCTTGG 59.432 61.111 3.32 0.00 40.31 3.61
1809 1867 2.548295 GGGCTTTTGGTTCGTCGCA 61.548 57.895 0.00 0.00 0.00 5.10
1918 2024 2.907458 AAGGACAGCTAAAGGGCATT 57.093 45.000 0.00 0.00 34.17 3.56
1921 2027 4.316025 AGGACAGCTAAAGGGCATTTTA 57.684 40.909 1.20 0.00 32.01 1.52
1922 2028 4.017126 AGGACAGCTAAAGGGCATTTTAC 58.983 43.478 1.20 0.00 32.01 2.01
1926 2032 5.005094 ACAGCTAAAGGGCATTTTACGTAA 58.995 37.500 3.29 3.29 32.01 3.18
1932 2038 8.565416 GCTAAAGGGCATTTTACGTAAGATAAT 58.435 33.333 10.68 4.69 34.87 1.28
1962 2069 6.795098 AAAGGAAAACAACAACCAAGAAAC 57.205 33.333 0.00 0.00 0.00 2.78
1967 2074 6.148645 GGAAAACAACAACCAAGAAACACAAT 59.851 34.615 0.00 0.00 0.00 2.71
1969 2076 8.785329 AAAACAACAACCAAGAAACACAATAT 57.215 26.923 0.00 0.00 0.00 1.28
1972 2079 7.725251 ACAACAACCAAGAAACACAATATGAT 58.275 30.769 0.00 0.00 0.00 2.45
1973 2080 7.652909 ACAACAACCAAGAAACACAATATGATG 59.347 33.333 0.00 0.00 0.00 3.07
1982 2089 6.803320 AGAAACACAATATGATGCAAAACGAG 59.197 34.615 0.00 0.00 0.00 4.18
1983 2090 5.627499 ACACAATATGATGCAAAACGAGT 57.373 34.783 0.00 0.00 0.00 4.18
1984 2091 6.735678 ACACAATATGATGCAAAACGAGTA 57.264 33.333 0.00 0.00 0.00 2.59
1985 2092 7.320443 ACACAATATGATGCAAAACGAGTAT 57.680 32.000 0.00 0.00 0.00 2.12
1986 2093 7.761409 ACACAATATGATGCAAAACGAGTATT 58.239 30.769 0.00 0.00 0.00 1.89
1987 2094 7.910162 ACACAATATGATGCAAAACGAGTATTC 59.090 33.333 0.00 0.00 0.00 1.75
1990 2097 9.803130 CAATATGATGCAAAACGAGTATTCTAG 57.197 33.333 0.00 0.00 0.00 2.43
1992 2099 5.972935 TGATGCAAAACGAGTATTCTAGGA 58.027 37.500 0.00 0.00 0.00 2.94
2040 2155 4.516698 TGACCATCTTCTTCTTTCACTTGC 59.483 41.667 0.00 0.00 0.00 4.01
2046 2161 2.899976 TCTTCTTTCACTTGCACGTCA 58.100 42.857 0.00 0.00 0.00 4.35
2050 2165 1.872952 CTTTCACTTGCACGTCATCCA 59.127 47.619 0.00 0.00 0.00 3.41
2068 2183 7.083858 GTCATCCATCGAAACTTGAAAATTGA 58.916 34.615 0.00 0.00 0.00 2.57
2074 2193 7.113965 CCATCGAAACTTGAAAATTGAAGTGAG 59.886 37.037 0.00 0.00 34.84 3.51
2077 2196 5.596836 AACTTGAAAATTGAAGTGAGCCA 57.403 34.783 0.00 0.00 34.84 4.75
2078 2197 5.596836 ACTTGAAAATTGAAGTGAGCCAA 57.403 34.783 0.00 0.00 33.36 4.52
2079 2198 6.165700 ACTTGAAAATTGAAGTGAGCCAAT 57.834 33.333 0.00 0.00 33.36 3.16
2080 2199 7.288810 ACTTGAAAATTGAAGTGAGCCAATA 57.711 32.000 0.00 0.00 33.36 1.90
2085 2204 8.296713 TGAAAATTGAAGTGAGCCAATAGTAAC 58.703 33.333 0.00 0.00 33.13 2.50
2091 2210 6.483974 TGAAGTGAGCCAATAGTAACGAAAAA 59.516 34.615 0.00 0.00 0.00 1.94
2094 2213 5.180680 GTGAGCCAATAGTAACGAAAAACCT 59.819 40.000 0.00 0.00 0.00 3.50
2101 2220 3.687200 AGTAACGAAAAACCTGCAAACG 58.313 40.909 0.00 0.00 0.00 3.60
2102 2221 1.273688 AACGAAAAACCTGCAAACGC 58.726 45.000 0.00 0.00 0.00 4.84
2106 2225 0.104120 AAAAACCTGCAAACGCCCTC 59.896 50.000 0.00 0.00 0.00 4.30
2110 2229 2.252260 CTGCAAACGCCCTCAACG 59.748 61.111 0.00 0.00 0.00 4.10
2113 2232 1.225376 TGCAAACGCCCTCAACGTAG 61.225 55.000 0.00 0.00 44.30 3.51
2116 2235 1.990563 CAAACGCCCTCAACGTAGTAG 59.009 52.381 0.00 0.00 45.00 2.57
2122 2241 2.167075 GCCCTCAACGTAGTAGGCTTTA 59.833 50.000 11.21 0.00 45.00 1.85
2129 2248 5.010922 TCAACGTAGTAGGCTTTAAAGACCA 59.989 40.000 17.71 0.28 45.00 4.02
2130 2249 4.814147 ACGTAGTAGGCTTTAAAGACCAC 58.186 43.478 17.71 14.37 41.94 4.16
2133 2252 5.873164 CGTAGTAGGCTTTAAAGACCACAAT 59.127 40.000 19.86 12.65 33.27 2.71
2134 2253 6.183360 CGTAGTAGGCTTTAAAGACCACAATG 60.183 42.308 19.86 6.53 33.27 2.82
2135 2254 5.876357 AGTAGGCTTTAAAGACCACAATGA 58.124 37.500 19.86 0.00 33.27 2.57
2153 2443 7.641411 CCACAATGATCATTCATCGTTAGAAAC 59.359 37.037 18.16 0.00 41.83 2.78
2154 2444 7.371615 CACAATGATCATTCATCGTTAGAAACG 59.628 37.037 18.16 5.86 44.18 3.60
2201 2502 4.513442 GCATCACCCTGTTTAGTACATGA 58.487 43.478 0.00 0.00 35.85 3.07
2204 2505 6.095440 GCATCACCCTGTTTAGTACATGATTT 59.905 38.462 0.00 0.00 33.71 2.17
2205 2506 7.362920 GCATCACCCTGTTTAGTACATGATTTT 60.363 37.037 0.00 0.00 33.71 1.82
2207 2508 7.881142 TCACCCTGTTTAGTACATGATTTTTG 58.119 34.615 0.00 0.00 35.85 2.44
2209 2510 8.141268 CACCCTGTTTAGTACATGATTTTTGTT 58.859 33.333 0.00 0.00 35.85 2.83
2219 2520 9.744468 AGTACATGATTTTTGTTTTTCACTACC 57.256 29.630 0.00 0.00 0.00 3.18
2222 2523 9.612066 ACATGATTTTTGTTTTTCACTACCATT 57.388 25.926 0.00 0.00 0.00 3.16
2232 2533 7.827236 TGTTTTTCACTACCATTATAGAGGGTG 59.173 37.037 0.00 0.00 36.14 4.61
2240 2541 4.412528 ACCATTATAGAGGGTGGGAGAAAC 59.587 45.833 0.00 0.00 36.05 2.78
2241 2542 4.660771 CCATTATAGAGGGTGGGAGAAACT 59.339 45.833 0.00 0.00 0.00 2.66
2242 2543 5.844516 CCATTATAGAGGGTGGGAGAAACTA 59.155 44.000 0.00 0.00 0.00 2.24
2261 2562 3.699038 ACTAAACCATGCCGCATAACAAT 59.301 39.130 5.31 0.00 0.00 2.71
2262 2563 4.884744 ACTAAACCATGCCGCATAACAATA 59.115 37.500 5.31 0.00 0.00 1.90
2263 2564 4.935352 AAACCATGCCGCATAACAATAT 57.065 36.364 5.31 0.00 0.00 1.28
2266 2574 3.253188 ACCATGCCGCATAACAATATGAC 59.747 43.478 5.31 0.00 41.25 3.06
2276 2584 5.853282 GCATAACAATATGACGCTGAAATCC 59.147 40.000 0.19 0.00 41.25 3.01
2278 2586 5.741388 AACAATATGACGCTGAAATCCTC 57.259 39.130 0.00 0.00 0.00 3.71
2279 2587 4.130118 ACAATATGACGCTGAAATCCTCC 58.870 43.478 0.00 0.00 0.00 4.30
2284 2592 1.452108 CGCTGAAATCCTCCCACCC 60.452 63.158 0.00 0.00 0.00 4.61
2293 2601 2.608988 CTCCCACCCAGAGCCAGT 60.609 66.667 0.00 0.00 0.00 4.00
2296 2604 2.667418 CCACCCAGAGCCAGTCAG 59.333 66.667 0.00 0.00 0.00 3.51
2299 2607 1.079256 ACCCAGAGCCAGTCAGCTA 59.921 57.895 0.00 0.00 45.15 3.32
2300 2608 0.545309 ACCCAGAGCCAGTCAGCTAA 60.545 55.000 0.00 0.00 45.15 3.09
2303 2611 2.356535 CCCAGAGCCAGTCAGCTAATTT 60.357 50.000 0.00 0.00 45.15 1.82
2320 2628 5.863935 GCTAATTTCCTTGATTTGACACACC 59.136 40.000 0.00 0.00 0.00 4.16
2323 2631 4.647424 TTCCTTGATTTGACACACCAAC 57.353 40.909 0.00 0.00 0.00 3.77
2344 2652 8.141909 ACCAACTGTTTAAATCTAAAGAAAGCC 58.858 33.333 0.00 0.00 0.00 4.35
2371 2679 1.220749 TGGCAACATCTACCCTCGC 59.779 57.895 0.00 0.00 46.17 5.03
2372 2680 1.220749 GGCAACATCTACCCTCGCA 59.779 57.895 0.00 0.00 0.00 5.10
2373 2681 0.811616 GGCAACATCTACCCTCGCAG 60.812 60.000 0.00 0.00 0.00 5.18
2374 2682 0.175760 GCAACATCTACCCTCGCAGA 59.824 55.000 0.00 0.00 0.00 4.26
2375 2683 1.927895 CAACATCTACCCTCGCAGAC 58.072 55.000 0.00 0.00 0.00 3.51
2376 2684 0.824759 AACATCTACCCTCGCAGACC 59.175 55.000 0.00 0.00 0.00 3.85
2377 2685 1.043673 ACATCTACCCTCGCAGACCC 61.044 60.000 0.00 0.00 0.00 4.46
2378 2686 0.757188 CATCTACCCTCGCAGACCCT 60.757 60.000 0.00 0.00 0.00 4.34
2379 2687 0.032017 ATCTACCCTCGCAGACCCTT 60.032 55.000 0.00 0.00 0.00 3.95
2380 2688 0.683504 TCTACCCTCGCAGACCCTTC 60.684 60.000 0.00 0.00 0.00 3.46
2381 2689 2.005960 CTACCCTCGCAGACCCTTCG 62.006 65.000 0.00 0.00 0.00 3.79
2382 2690 2.776370 TACCCTCGCAGACCCTTCGT 62.776 60.000 0.00 0.00 0.00 3.85
2383 2691 2.657237 CCTCGCAGACCCTTCGTT 59.343 61.111 0.00 0.00 0.00 3.85
2384 2692 1.738099 CCTCGCAGACCCTTCGTTG 60.738 63.158 0.00 0.00 0.00 4.10
2385 2693 1.738099 CTCGCAGACCCTTCGTTGG 60.738 63.158 0.00 0.00 0.00 3.77
2386 2694 2.154798 CTCGCAGACCCTTCGTTGGA 62.155 60.000 0.00 0.00 0.00 3.53
2387 2695 1.738099 CGCAGACCCTTCGTTGGAG 60.738 63.158 0.00 0.00 0.00 3.86
2388 2696 1.371558 GCAGACCCTTCGTTGGAGT 59.628 57.895 0.00 0.00 0.00 3.85
2389 2697 0.250338 GCAGACCCTTCGTTGGAGTT 60.250 55.000 0.00 0.00 0.00 3.01
2390 2698 1.512926 CAGACCCTTCGTTGGAGTTG 58.487 55.000 0.00 0.00 0.00 3.16
2391 2699 0.396811 AGACCCTTCGTTGGAGTTGG 59.603 55.000 0.00 0.00 0.00 3.77
2392 2700 0.395312 GACCCTTCGTTGGAGTTGGA 59.605 55.000 0.00 0.00 0.00 3.53
2393 2701 1.003233 GACCCTTCGTTGGAGTTGGAT 59.997 52.381 0.00 0.00 0.00 3.41
2394 2702 1.003233 ACCCTTCGTTGGAGTTGGATC 59.997 52.381 0.00 0.00 0.00 3.36
2395 2703 1.003118 CCCTTCGTTGGAGTTGGATCA 59.997 52.381 0.00 0.00 0.00 2.92
2396 2704 2.552155 CCCTTCGTTGGAGTTGGATCAA 60.552 50.000 0.00 0.00 0.00 2.57
2397 2705 3.146066 CCTTCGTTGGAGTTGGATCAAA 58.854 45.455 0.00 0.00 0.00 2.69
2398 2706 3.758554 CCTTCGTTGGAGTTGGATCAAAT 59.241 43.478 0.00 0.00 0.00 2.32
2399 2707 4.379813 CCTTCGTTGGAGTTGGATCAAATG 60.380 45.833 0.00 0.00 0.00 2.32
2400 2708 4.014569 TCGTTGGAGTTGGATCAAATGA 57.985 40.909 0.00 0.00 0.00 2.57
2401 2709 3.751175 TCGTTGGAGTTGGATCAAATGAC 59.249 43.478 0.00 0.00 0.00 3.06
2402 2710 3.424829 CGTTGGAGTTGGATCAAATGACG 60.425 47.826 0.00 0.00 0.00 4.35
2411 2719 6.536582 AGTTGGATCAAATGACGTCAAGATAG 59.463 38.462 24.13 11.02 0.00 2.08
2412 2720 5.977635 TGGATCAAATGACGTCAAGATAGT 58.022 37.500 24.13 7.37 0.00 2.12
2418 2726 4.909696 ATGACGTCAAGATAGTGAGAGG 57.090 45.455 24.13 0.00 0.00 3.69
2449 2757 6.299141 AGACCTTATTTCAGTGTGTCATTGT 58.701 36.000 0.00 0.00 0.00 2.71
2461 2769 2.297033 GTGTCATTGTTGCCACCATCTT 59.703 45.455 0.00 0.00 0.00 2.40
2470 2778 0.745845 GCCACCATCTTGTCGATGCT 60.746 55.000 0.00 0.00 46.61 3.79
2489 2797 1.996191 CTGCAAGACGGCTAGAGAAAC 59.004 52.381 0.00 0.00 34.07 2.78
2499 2808 6.708949 AGACGGCTAGAGAAACAAAATGTAAA 59.291 34.615 0.00 0.00 0.00 2.01
2503 2812 7.746475 CGGCTAGAGAAACAAAATGTAAAGAAG 59.254 37.037 0.00 0.00 0.00 2.85
2534 2843 5.589192 CCTATAAGGTCACCACTTAAGACG 58.411 45.833 10.09 0.61 34.42 4.18
2535 2844 2.833631 AAGGTCACCACTTAAGACGG 57.166 50.000 10.09 11.49 33.18 4.79
2536 2845 0.320697 AGGTCACCACTTAAGACGGC 59.679 55.000 10.09 0.00 33.18 5.68
2537 2846 0.320697 GGTCACCACTTAAGACGGCT 59.679 55.000 10.09 0.00 33.18 5.52
2538 2847 1.672145 GGTCACCACTTAAGACGGCTC 60.672 57.143 10.09 3.78 33.18 4.70
2539 2848 0.242825 TCACCACTTAAGACGGCTCG 59.757 55.000 10.09 2.41 0.00 5.03
2540 2849 1.080025 ACCACTTAAGACGGCTCGC 60.080 57.895 10.09 0.00 0.00 5.03
2541 2850 1.215647 CCACTTAAGACGGCTCGCT 59.784 57.895 10.09 0.00 0.00 4.93
2542 2851 0.389948 CCACTTAAGACGGCTCGCTT 60.390 55.000 10.09 0.00 0.00 4.68
2543 2852 0.992802 CACTTAAGACGGCTCGCTTC 59.007 55.000 10.09 0.00 0.00 3.86
2544 2853 0.601558 ACTTAAGACGGCTCGCTTCA 59.398 50.000 10.09 0.00 0.00 3.02
2545 2854 1.272781 CTTAAGACGGCTCGCTTCAG 58.727 55.000 0.00 4.36 0.00 3.02
2546 2855 0.601558 TTAAGACGGCTCGCTTCAGT 59.398 50.000 0.00 0.00 0.00 3.41
2547 2856 0.109272 TAAGACGGCTCGCTTCAGTG 60.109 55.000 0.00 0.00 0.00 3.66
2548 2857 3.482783 GACGGCTCGCTTCAGTGC 61.483 66.667 0.00 0.00 0.00 4.40
2549 2858 3.923563 GACGGCTCGCTTCAGTGCT 62.924 63.158 0.00 0.00 0.00 4.40
2550 2859 2.740055 CGGCTCGCTTCAGTGCTT 60.740 61.111 0.00 0.00 0.00 3.91
2551 2860 2.866028 GGCTCGCTTCAGTGCTTG 59.134 61.111 0.00 0.00 0.00 4.01
2552 2861 1.963338 GGCTCGCTTCAGTGCTTGT 60.963 57.895 0.00 0.00 0.00 3.16
2553 2862 0.670546 GGCTCGCTTCAGTGCTTGTA 60.671 55.000 0.00 0.00 0.00 2.41
2554 2863 0.718343 GCTCGCTTCAGTGCTTGTAG 59.282 55.000 0.00 0.00 0.00 2.74
2555 2864 1.937108 GCTCGCTTCAGTGCTTGTAGT 60.937 52.381 0.00 0.00 0.00 2.73
2556 2865 1.989165 CTCGCTTCAGTGCTTGTAGTC 59.011 52.381 0.00 0.00 0.00 2.59
2557 2866 0.710567 CGCTTCAGTGCTTGTAGTCG 59.289 55.000 0.00 0.00 0.00 4.18
2558 2867 1.784525 GCTTCAGTGCTTGTAGTCGT 58.215 50.000 0.00 0.00 0.00 4.34
2559 2868 1.721926 GCTTCAGTGCTTGTAGTCGTC 59.278 52.381 0.00 0.00 0.00 4.20
2560 2869 1.979469 CTTCAGTGCTTGTAGTCGTCG 59.021 52.381 0.00 0.00 0.00 5.12
2561 2870 0.386858 TCAGTGCTTGTAGTCGTCGC 60.387 55.000 0.00 0.00 0.00 5.19
2562 2871 0.387367 CAGTGCTTGTAGTCGTCGCT 60.387 55.000 0.00 0.00 0.00 4.93
2563 2872 0.314302 AGTGCTTGTAGTCGTCGCTT 59.686 50.000 0.00 0.00 0.00 4.68
2564 2873 0.435008 GTGCTTGTAGTCGTCGCTTG 59.565 55.000 0.00 0.00 0.00 4.01
2565 2874 0.666274 TGCTTGTAGTCGTCGCTTGG 60.666 55.000 0.00 0.00 0.00 3.61
2566 2875 0.666577 GCTTGTAGTCGTCGCTTGGT 60.667 55.000 0.00 0.00 0.00 3.67
2567 2876 1.060713 CTTGTAGTCGTCGCTTGGTG 58.939 55.000 0.00 0.00 0.00 4.17
2568 2877 0.319211 TTGTAGTCGTCGCTTGGTGG 60.319 55.000 0.00 0.00 0.00 4.61
2569 2878 1.288127 GTAGTCGTCGCTTGGTGGT 59.712 57.895 0.00 0.00 0.00 4.16
2570 2879 0.731855 GTAGTCGTCGCTTGGTGGTC 60.732 60.000 0.00 0.00 0.00 4.02
2571 2880 0.892358 TAGTCGTCGCTTGGTGGTCT 60.892 55.000 0.00 0.00 0.00 3.85
2572 2881 0.892358 AGTCGTCGCTTGGTGGTCTA 60.892 55.000 0.00 0.00 0.00 2.59
2573 2882 0.731855 GTCGTCGCTTGGTGGTCTAC 60.732 60.000 0.00 0.00 0.00 2.59
2574 2883 1.800315 CGTCGCTTGGTGGTCTACG 60.800 63.158 0.00 0.00 0.00 3.51
2575 2884 1.445582 GTCGCTTGGTGGTCTACGG 60.446 63.158 0.00 0.00 0.00 4.02
2576 2885 1.604308 TCGCTTGGTGGTCTACGGA 60.604 57.895 0.00 0.00 0.00 4.69
2577 2886 0.968901 TCGCTTGGTGGTCTACGGAT 60.969 55.000 0.00 0.00 0.00 4.18
2578 2887 0.527817 CGCTTGGTGGTCTACGGATC 60.528 60.000 0.00 0.00 0.00 3.36
2579 2888 0.824759 GCTTGGTGGTCTACGGATCT 59.175 55.000 0.00 0.00 0.00 2.75
2580 2889 1.471676 GCTTGGTGGTCTACGGATCTG 60.472 57.143 0.00 0.00 0.00 2.90
2581 2890 1.137086 CTTGGTGGTCTACGGATCTGG 59.863 57.143 6.47 0.00 0.00 3.86
2582 2891 0.333652 TGGTGGTCTACGGATCTGGA 59.666 55.000 6.47 0.00 0.00 3.86
2583 2892 1.063190 TGGTGGTCTACGGATCTGGAT 60.063 52.381 6.47 0.00 0.00 3.41
2584 2893 1.341531 GGTGGTCTACGGATCTGGATG 59.658 57.143 6.47 0.00 0.00 3.51
2585 2894 2.032620 GTGGTCTACGGATCTGGATGT 58.967 52.381 6.47 0.00 0.00 3.06
2586 2895 3.220110 GTGGTCTACGGATCTGGATGTA 58.780 50.000 6.47 0.00 0.00 2.29
2587 2896 3.635373 GTGGTCTACGGATCTGGATGTAA 59.365 47.826 6.47 0.00 0.00 2.41
2588 2897 4.281182 GTGGTCTACGGATCTGGATGTAAT 59.719 45.833 6.47 0.00 0.00 1.89
2589 2898 4.899457 TGGTCTACGGATCTGGATGTAATT 59.101 41.667 6.47 0.00 0.00 1.40
2590 2899 5.365605 TGGTCTACGGATCTGGATGTAATTT 59.634 40.000 6.47 0.00 0.00 1.82
2591 2900 6.126883 TGGTCTACGGATCTGGATGTAATTTT 60.127 38.462 6.47 0.00 0.00 1.82
2592 2901 6.766467 GGTCTACGGATCTGGATGTAATTTTT 59.234 38.462 6.47 0.00 0.00 1.94
2593 2902 7.929785 GGTCTACGGATCTGGATGTAATTTTTA 59.070 37.037 6.47 0.00 0.00 1.52
2594 2903 9.490379 GTCTACGGATCTGGATGTAATTTTTAT 57.510 33.333 6.47 0.00 0.00 1.40
2623 2932 9.952030 TTTCTAATGTTTGATGTACTACCATGA 57.048 29.630 0.00 0.00 0.00 3.07
2627 2936 8.806429 AATGTTTGATGTACTACCATGATTGA 57.194 30.769 0.00 0.00 0.00 2.57
2628 2937 8.806429 ATGTTTGATGTACTACCATGATTGAA 57.194 30.769 0.00 0.00 0.00 2.69
2629 2938 8.267620 TGTTTGATGTACTACCATGATTGAAG 57.732 34.615 0.00 0.00 0.00 3.02
2630 2939 8.100164 TGTTTGATGTACTACCATGATTGAAGA 58.900 33.333 0.00 0.00 0.00 2.87
2631 2940 9.113838 GTTTGATGTACTACCATGATTGAAGAT 57.886 33.333 0.00 0.00 0.00 2.40
2632 2941 8.667076 TTGATGTACTACCATGATTGAAGATG 57.333 34.615 0.00 0.00 0.00 2.90
2633 2942 8.021898 TGATGTACTACCATGATTGAAGATGA 57.978 34.615 0.00 0.00 0.00 2.92
2634 2943 8.485392 TGATGTACTACCATGATTGAAGATGAA 58.515 33.333 0.00 0.00 0.00 2.57
2635 2944 9.499479 GATGTACTACCATGATTGAAGATGAAT 57.501 33.333 0.00 0.00 0.00 2.57
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
46 47 4.154347 CTGCCGCTCTGGGGACTC 62.154 72.222 4.81 0.00 37.91 3.36
52 53 4.154347 GGAGACCTGCCGCTCTGG 62.154 72.222 0.00 0.00 42.50 3.86
94 95 1.471501 CCGGCGACAATGATCTCTTCA 60.472 52.381 9.30 0.00 39.12 3.02
143 144 4.142182 GGCTATAGCTGACTGATCATCCTC 60.142 50.000 23.53 0.00 41.70 3.71
145 146 4.122143 GGCTATAGCTGACTGATCATCC 57.878 50.000 23.53 0.00 41.70 3.51
168 169 2.028203 TGAGATTTCAGATGCCGTGACA 60.028 45.455 0.00 0.00 0.00 3.58
173 182 4.447054 GTGACTATGAGATTTCAGATGCCG 59.553 45.833 0.00 0.00 36.61 5.69
177 186 8.995027 AGTAGAGTGACTATGAGATTTCAGAT 57.005 34.615 0.00 0.00 36.61 2.90
262 305 3.813443 CTGGAAAGGATATGTGACCAGG 58.187 50.000 0.00 0.00 39.47 4.45
350 393 2.494059 CAGACGTTGACCTCCATGTTT 58.506 47.619 0.00 0.00 0.00 2.83
352 395 0.320771 GCAGACGTTGACCTCCATGT 60.321 55.000 0.00 0.00 0.00 3.21
400 443 9.635520 ATGATTGAAATTTGTCATTCTCAGTTC 57.364 29.630 0.00 0.00 31.90 3.01
410 453 8.070034 AGCCTAATGATGATTGAAATTTGTCA 57.930 30.769 0.00 0.00 0.00 3.58
412 455 9.193806 ACTAGCCTAATGATGATTGAAATTTGT 57.806 29.630 0.00 0.00 0.00 2.83
423 466 6.150641 GTGGATACGTACTAGCCTAATGATGA 59.849 42.308 0.00 0.00 42.51 2.92
426 469 5.628130 AGTGGATACGTACTAGCCTAATGA 58.372 41.667 0.00 0.00 42.51 2.57
427 470 5.961396 AGTGGATACGTACTAGCCTAATG 57.039 43.478 0.00 0.00 42.51 1.90
428 471 7.230027 ACTAAGTGGATACGTACTAGCCTAAT 58.770 38.462 0.00 0.00 42.51 1.73
429 472 6.595682 ACTAAGTGGATACGTACTAGCCTAA 58.404 40.000 0.00 0.00 42.51 2.69
520 563 5.048921 TCTCGTACTGGTGAAAGACTACAAG 60.049 44.000 0.00 0.00 0.00 3.16
558 601 1.732259 CAGGGACGAAAGAAATGGTCG 59.268 52.381 0.00 0.00 40.56 4.79
613 656 1.497991 GCGTGTTGTGAGCTCACTTA 58.502 50.000 38.81 27.02 46.55 2.24
614 657 1.490693 CGCGTGTTGTGAGCTCACTT 61.491 55.000 38.81 0.00 46.55 3.16
739 782 9.892130 AGTACGAAATTTTTCTAAGATCCTGAT 57.108 29.630 0.00 0.00 35.07 2.90
765 808 1.153449 CCAGCCGCGAAGTCCATAA 60.153 57.895 8.23 0.00 0.00 1.90
816 859 7.707464 TGATGGTGATCAAATTGAATTACATGC 59.293 33.333 0.00 0.16 35.55 4.06
833 876 6.283544 TGTAAATTGCAATGTGATGGTGAT 57.716 33.333 13.82 0.00 0.00 3.06
838 881 6.645827 TCTTGGTTGTAAATTGCAATGTGATG 59.354 34.615 13.82 0.00 0.00 3.07
872 915 7.013083 CGGTTGCTTACTCTAGGAGAAATAGTA 59.987 40.741 1.31 0.00 33.32 1.82
884 927 3.958798 AGCTAATCCGGTTGCTTACTCTA 59.041 43.478 0.00 0.00 30.96 2.43
955 998 5.256474 TGGCCTCCTTTCTTCTCTAATTTG 58.744 41.667 3.32 0.00 0.00 2.32
976 1019 2.856222 CTGATTTAAGCTAGCCCCTGG 58.144 52.381 12.13 0.00 0.00 4.45
1038 1081 2.508887 CTCTCGACTGCTGCTGCC 60.509 66.667 13.47 0.00 38.71 4.85
1049 1092 0.249280 TTTTGTCGCTGTGCTCTCGA 60.249 50.000 0.00 0.00 0.00 4.04
1065 1114 3.694538 GCCATGGCGCCCACTTTT 61.695 61.111 26.77 0.00 35.80 2.27
1087 1136 3.255379 GATGCTCCCGAACGTCGC 61.255 66.667 0.00 0.00 38.82 5.19
1194 1243 2.515901 GTGACCACCCTGTTGGCT 59.484 61.111 0.00 0.00 40.77 4.75
1655 1704 1.363807 CGGGAGAGCGCATACATCA 59.636 57.895 11.47 0.00 0.00 3.07
1747 1796 4.966965 TGAACGCACACCTAAAGAAAAA 57.033 36.364 0.00 0.00 0.00 1.94
1748 1797 4.336993 ACATGAACGCACACCTAAAGAAAA 59.663 37.500 0.00 0.00 0.00 2.29
1749 1798 3.880490 ACATGAACGCACACCTAAAGAAA 59.120 39.130 0.00 0.00 0.00 2.52
1750 1799 3.249799 CACATGAACGCACACCTAAAGAA 59.750 43.478 0.00 0.00 0.00 2.52
1751 1800 2.805671 CACATGAACGCACACCTAAAGA 59.194 45.455 0.00 0.00 0.00 2.52
1752 1801 2.665519 GCACATGAACGCACACCTAAAG 60.666 50.000 0.00 0.00 0.00 1.85
1753 1802 1.265635 GCACATGAACGCACACCTAAA 59.734 47.619 0.00 0.00 0.00 1.85
1754 1803 0.871722 GCACATGAACGCACACCTAA 59.128 50.000 0.00 0.00 0.00 2.69
1755 1804 0.953471 GGCACATGAACGCACACCTA 60.953 55.000 0.00 0.00 0.00 3.08
1756 1805 2.260869 GGCACATGAACGCACACCT 61.261 57.895 0.00 0.00 0.00 4.00
1757 1806 2.255252 GGCACATGAACGCACACC 59.745 61.111 0.00 0.00 0.00 4.16
1787 1845 0.313987 GACGAACCAAAAGCCCAAGG 59.686 55.000 0.00 0.00 0.00 3.61
1788 1846 0.040425 CGACGAACCAAAAGCCCAAG 60.040 55.000 0.00 0.00 0.00 3.61
1789 1847 2.026522 CGACGAACCAAAAGCCCAA 58.973 52.632 0.00 0.00 0.00 4.12
1790 1848 2.548295 GCGACGAACCAAAAGCCCA 61.548 57.895 0.00 0.00 0.00 5.36
1791 1849 2.254350 GCGACGAACCAAAAGCCC 59.746 61.111 0.00 0.00 0.00 5.19
1792 1850 1.082104 CTGCGACGAACCAAAAGCC 60.082 57.895 0.00 0.00 0.00 4.35
1895 2001 1.546029 GCCCTTTAGCTGTCCTTTTGG 59.454 52.381 0.00 0.00 42.21 3.28
1901 2007 3.181500 CGTAAAATGCCCTTTAGCTGTCC 60.181 47.826 0.00 0.00 0.00 4.02
1906 2012 5.806366 TCTTACGTAAAATGCCCTTTAGC 57.194 39.130 9.68 0.00 0.00 3.09
1950 2057 6.158598 GCATCATATTGTGTTTCTTGGTTGT 58.841 36.000 0.00 0.00 0.00 3.32
1951 2058 6.157904 TGCATCATATTGTGTTTCTTGGTTG 58.842 36.000 0.00 0.00 0.00 3.77
1957 2064 6.676950 TCGTTTTGCATCATATTGTGTTTCT 58.323 32.000 0.00 0.00 0.00 2.52
1962 2069 8.124823 AGAATACTCGTTTTGCATCATATTGTG 58.875 33.333 0.00 0.00 0.00 3.33
1967 2074 7.722363 TCCTAGAATACTCGTTTTGCATCATA 58.278 34.615 0.00 0.00 0.00 2.15
1969 2076 5.972935 TCCTAGAATACTCGTTTTGCATCA 58.027 37.500 0.00 0.00 0.00 3.07
1972 2079 7.499321 TTTTTCCTAGAATACTCGTTTTGCA 57.501 32.000 0.00 0.00 0.00 4.08
2012 2120 9.525826 AAGTGAAAGAAGAAGATGGTCAATATT 57.474 29.630 0.00 0.00 0.00 1.28
2020 2128 4.612259 CGTGCAAGTGAAAGAAGAAGATGG 60.612 45.833 0.00 0.00 0.00 3.51
2034 2149 0.371301 CGATGGATGACGTGCAAGTG 59.629 55.000 10.87 0.00 0.00 3.16
2035 2150 0.246360 TCGATGGATGACGTGCAAGT 59.754 50.000 4.50 4.50 0.00 3.16
2036 2151 1.358877 TTCGATGGATGACGTGCAAG 58.641 50.000 0.00 0.00 0.00 4.01
2040 2155 2.993220 TCAAGTTTCGATGGATGACGTG 59.007 45.455 0.00 2.92 0.00 4.49
2046 2161 7.596248 CACTTCAATTTTCAAGTTTCGATGGAT 59.404 33.333 0.00 0.00 30.06 3.41
2050 2165 6.638468 GCTCACTTCAATTTTCAAGTTTCGAT 59.362 34.615 0.00 0.00 30.06 3.59
2068 2183 6.293790 GGTTTTTCGTTACTATTGGCTCACTT 60.294 38.462 0.00 0.00 0.00 3.16
2074 2193 4.163552 GCAGGTTTTTCGTTACTATTGGC 58.836 43.478 0.00 0.00 0.00 4.52
2077 2196 5.910723 CGTTTGCAGGTTTTTCGTTACTATT 59.089 36.000 0.00 0.00 0.00 1.73
2078 2197 5.445845 CGTTTGCAGGTTTTTCGTTACTAT 58.554 37.500 0.00 0.00 0.00 2.12
2079 2198 4.785975 GCGTTTGCAGGTTTTTCGTTACTA 60.786 41.667 0.00 0.00 42.15 1.82
2080 2199 3.687200 CGTTTGCAGGTTTTTCGTTACT 58.313 40.909 0.00 0.00 0.00 2.24
2085 2204 1.212455 GGGCGTTTGCAGGTTTTTCG 61.212 55.000 0.00 0.00 45.35 3.46
2091 2210 2.193536 GTTGAGGGCGTTTGCAGGT 61.194 57.895 0.00 0.00 45.35 4.00
2094 2213 1.225376 CTACGTTGAGGGCGTTTGCA 61.225 55.000 0.00 0.00 45.35 4.08
2101 2220 0.535797 AAGCCTACTACGTTGAGGGC 59.464 55.000 21.46 21.46 39.82 5.19
2102 2221 4.460948 TTAAAGCCTACTACGTTGAGGG 57.539 45.455 3.44 6.35 0.00 4.30
2106 2225 5.119743 GTGGTCTTTAAAGCCTACTACGTTG 59.880 44.000 21.55 0.00 0.00 4.10
2110 2229 6.877322 TCATTGTGGTCTTTAAAGCCTACTAC 59.123 38.462 21.55 17.13 0.00 2.73
2113 2232 6.374333 TGATCATTGTGGTCTTTAAAGCCTAC 59.626 38.462 21.55 15.16 0.00 3.18
2116 2235 5.643379 TGATCATTGTGGTCTTTAAAGCC 57.357 39.130 10.51 14.43 0.00 4.35
2122 2241 6.127810 CGATGAATGATCATTGTGGTCTTT 57.872 37.500 25.37 0.00 46.30 2.52
2153 2443 9.722056 CCCTAATTCAACAATTTTTAGATCTCG 57.278 33.333 0.00 0.00 33.95 4.04
2154 2444 9.521503 GCCCTAATTCAACAATTTTTAGATCTC 57.478 33.333 0.00 0.00 33.95 2.75
2196 2497 9.612066 AATGGTAGTGAAAAACAAAAATCATGT 57.388 25.926 0.00 0.00 0.00 3.21
2204 2505 9.238368 CCCTCTATAATGGTAGTGAAAAACAAA 57.762 33.333 0.00 0.00 0.00 2.83
2205 2506 8.387813 ACCCTCTATAATGGTAGTGAAAAACAA 58.612 33.333 0.00 0.00 0.00 2.83
2207 2508 7.282450 CCACCCTCTATAATGGTAGTGAAAAAC 59.718 40.741 0.00 0.00 0.00 2.43
2209 2510 6.126594 CCCACCCTCTATAATGGTAGTGAAAA 60.127 42.308 0.00 0.00 0.00 2.29
2215 2516 5.011982 TCTCCCACCCTCTATAATGGTAG 57.988 47.826 0.00 0.00 0.00 3.18
2219 2520 5.896073 AGTTTCTCCCACCCTCTATAATG 57.104 43.478 0.00 0.00 0.00 1.90
2222 2523 5.664457 GGTTTAGTTTCTCCCACCCTCTATA 59.336 44.000 0.00 0.00 0.00 1.31
2228 2529 2.963599 TGGTTTAGTTTCTCCCACCC 57.036 50.000 0.00 0.00 0.00 4.61
2232 2533 1.743394 CGGCATGGTTTAGTTTCTCCC 59.257 52.381 0.00 0.00 0.00 4.30
2240 2541 3.773860 TTGTTATGCGGCATGGTTTAG 57.226 42.857 24.99 0.00 0.00 1.85
2241 2542 5.532779 TCATATTGTTATGCGGCATGGTTTA 59.467 36.000 24.99 10.51 36.03 2.01
2242 2543 4.340666 TCATATTGTTATGCGGCATGGTTT 59.659 37.500 24.99 8.74 36.03 3.27
2261 2562 2.115427 TGGGAGGATTTCAGCGTCATA 58.885 47.619 0.00 0.00 0.00 2.15
2262 2563 0.911769 TGGGAGGATTTCAGCGTCAT 59.088 50.000 0.00 0.00 0.00 3.06
2263 2564 0.036388 GTGGGAGGATTTCAGCGTCA 60.036 55.000 0.00 0.00 0.00 4.35
2266 2574 1.452108 GGGTGGGAGGATTTCAGCG 60.452 63.158 0.00 0.00 0.00 5.18
2276 2584 2.608988 ACTGGCTCTGGGTGGGAG 60.609 66.667 0.00 0.00 0.00 4.30
2278 2586 2.930019 TGACTGGCTCTGGGTGGG 60.930 66.667 0.00 0.00 0.00 4.61
2279 2587 2.667418 CTGACTGGCTCTGGGTGG 59.333 66.667 0.00 0.00 0.00 4.61
2284 2592 2.941720 GGAAATTAGCTGACTGGCTCTG 59.058 50.000 0.00 0.00 42.97 3.35
2293 2601 6.489700 TGTGTCAAATCAAGGAAATTAGCTGA 59.510 34.615 0.00 0.00 0.00 4.26
2296 2604 5.863935 GGTGTGTCAAATCAAGGAAATTAGC 59.136 40.000 0.00 0.00 0.00 3.09
2299 2607 5.867903 TGGTGTGTCAAATCAAGGAAATT 57.132 34.783 0.00 0.00 0.00 1.82
2300 2608 5.363580 AGTTGGTGTGTCAAATCAAGGAAAT 59.636 36.000 0.00 0.00 0.00 2.17
2303 2611 3.631686 CAGTTGGTGTGTCAAATCAAGGA 59.368 43.478 0.00 0.00 0.00 3.36
2320 2628 9.185192 CTGGCTTTCTTTAGATTTAAACAGTTG 57.815 33.333 0.00 0.00 0.00 3.16
2323 2631 7.370383 TGCTGGCTTTCTTTAGATTTAAACAG 58.630 34.615 0.00 0.00 0.00 3.16
2344 2652 3.181493 GGTAGATGTTGCCAGATTTGCTG 60.181 47.826 0.00 0.00 44.49 4.41
2355 2663 0.175760 TCTGCGAGGGTAGATGTTGC 59.824 55.000 0.00 0.00 29.27 4.17
2356 2664 1.471676 GGTCTGCGAGGGTAGATGTTG 60.472 57.143 0.00 0.00 37.24 3.33
2357 2665 0.824759 GGTCTGCGAGGGTAGATGTT 59.175 55.000 0.00 0.00 37.24 2.71
2371 2679 1.512926 CAACTCCAACGAAGGGTCTG 58.487 55.000 0.00 0.00 0.00 3.51
2372 2680 0.396811 CCAACTCCAACGAAGGGTCT 59.603 55.000 0.00 0.00 0.00 3.85
2373 2681 0.395312 TCCAACTCCAACGAAGGGTC 59.605 55.000 0.00 0.00 0.00 4.46
2374 2682 1.003233 GATCCAACTCCAACGAAGGGT 59.997 52.381 0.00 0.00 0.00 4.34
2375 2683 1.003118 TGATCCAACTCCAACGAAGGG 59.997 52.381 0.00 0.00 0.00 3.95
2376 2684 2.472695 TGATCCAACTCCAACGAAGG 57.527 50.000 0.00 0.00 0.00 3.46
2377 2685 4.455533 TCATTTGATCCAACTCCAACGAAG 59.544 41.667 0.00 0.00 0.00 3.79
2378 2686 4.215399 GTCATTTGATCCAACTCCAACGAA 59.785 41.667 0.00 0.00 0.00 3.85
2379 2687 3.751175 GTCATTTGATCCAACTCCAACGA 59.249 43.478 0.00 0.00 0.00 3.85
2380 2688 3.424829 CGTCATTTGATCCAACTCCAACG 60.425 47.826 0.00 0.00 0.00 4.10
2381 2689 3.502211 ACGTCATTTGATCCAACTCCAAC 59.498 43.478 0.00 0.00 0.00 3.77
2382 2690 3.750371 ACGTCATTTGATCCAACTCCAA 58.250 40.909 0.00 0.00 0.00 3.53
2383 2691 3.244387 TGACGTCATTTGATCCAACTCCA 60.244 43.478 15.76 0.00 0.00 3.86
2384 2692 3.334691 TGACGTCATTTGATCCAACTCC 58.665 45.455 15.76 0.00 0.00 3.85
2385 2693 4.690748 TCTTGACGTCATTTGATCCAACTC 59.309 41.667 20.80 0.00 0.00 3.01
2386 2694 4.641396 TCTTGACGTCATTTGATCCAACT 58.359 39.130 20.80 0.00 0.00 3.16
2387 2695 5.551760 ATCTTGACGTCATTTGATCCAAC 57.448 39.130 20.80 0.00 0.00 3.77
2388 2696 6.313658 CACTATCTTGACGTCATTTGATCCAA 59.686 38.462 20.80 7.96 0.00 3.53
2389 2697 5.812127 CACTATCTTGACGTCATTTGATCCA 59.188 40.000 20.80 8.58 0.00 3.41
2390 2698 6.042777 TCACTATCTTGACGTCATTTGATCC 58.957 40.000 20.80 0.00 0.00 3.36
2391 2699 6.975197 TCTCACTATCTTGACGTCATTTGATC 59.025 38.462 20.80 0.00 0.00 2.92
2392 2700 6.867550 TCTCACTATCTTGACGTCATTTGAT 58.132 36.000 20.80 22.34 0.00 2.57
2393 2701 6.267496 TCTCACTATCTTGACGTCATTTGA 57.733 37.500 20.80 17.46 0.00 2.69
2394 2702 5.518128 CCTCTCACTATCTTGACGTCATTTG 59.482 44.000 20.80 12.71 0.00 2.32
2395 2703 5.655488 CCTCTCACTATCTTGACGTCATTT 58.345 41.667 20.80 9.70 0.00 2.32
2396 2704 4.440802 GCCTCTCACTATCTTGACGTCATT 60.441 45.833 20.80 10.06 0.00 2.57
2397 2705 3.067461 GCCTCTCACTATCTTGACGTCAT 59.933 47.826 20.80 7.28 0.00 3.06
2398 2706 2.423892 GCCTCTCACTATCTTGACGTCA 59.576 50.000 15.76 15.76 0.00 4.35
2399 2707 2.223618 GGCCTCTCACTATCTTGACGTC 60.224 54.545 9.11 9.11 0.00 4.34
2400 2708 1.751924 GGCCTCTCACTATCTTGACGT 59.248 52.381 0.00 0.00 0.00 4.34
2401 2709 1.751351 TGGCCTCTCACTATCTTGACG 59.249 52.381 3.32 0.00 0.00 4.35
2402 2710 3.895232 TTGGCCTCTCACTATCTTGAC 57.105 47.619 3.32 0.00 0.00 3.18
2411 2719 3.542046 GGTCTCTTTGGCCTCTCAC 57.458 57.895 3.32 0.00 37.49 3.51
2418 2726 4.762251 ACACTGAAATAAGGTCTCTTTGGC 59.238 41.667 0.00 0.00 34.59 4.52
2449 2757 3.955145 ATCGACAAGATGGTGGCAA 57.045 47.368 0.00 0.00 38.36 4.52
2461 2769 1.737735 CCGTCTTGCAGCATCGACA 60.738 57.895 19.62 0.00 0.00 4.35
2470 2778 1.343142 TGTTTCTCTAGCCGTCTTGCA 59.657 47.619 0.00 0.00 0.00 4.08
2524 2833 0.992802 GAAGCGAGCCGTCTTAAGTG 59.007 55.000 1.63 0.00 0.00 3.16
2534 2843 0.670546 TACAAGCACTGAAGCGAGCC 60.671 55.000 0.00 0.00 40.15 4.70
2535 2844 0.718343 CTACAAGCACTGAAGCGAGC 59.282 55.000 0.00 0.00 40.15 5.03
2536 2845 1.989165 GACTACAAGCACTGAAGCGAG 59.011 52.381 0.00 0.00 40.15 5.03
2537 2846 1.666023 CGACTACAAGCACTGAAGCGA 60.666 52.381 0.00 0.00 40.15 4.93
2538 2847 0.710567 CGACTACAAGCACTGAAGCG 59.289 55.000 0.00 0.00 40.15 4.68
2539 2848 1.721926 GACGACTACAAGCACTGAAGC 59.278 52.381 0.00 0.00 0.00 3.86
2540 2849 1.979469 CGACGACTACAAGCACTGAAG 59.021 52.381 0.00 0.00 0.00 3.02
2541 2850 1.929038 GCGACGACTACAAGCACTGAA 60.929 52.381 0.00 0.00 0.00 3.02
2542 2851 0.386858 GCGACGACTACAAGCACTGA 60.387 55.000 0.00 0.00 0.00 3.41
2543 2852 0.387367 AGCGACGACTACAAGCACTG 60.387 55.000 0.00 0.00 0.00 3.66
2544 2853 0.314302 AAGCGACGACTACAAGCACT 59.686 50.000 0.00 0.00 0.00 4.40
2545 2854 0.435008 CAAGCGACGACTACAAGCAC 59.565 55.000 0.00 0.00 0.00 4.40
2546 2855 0.666274 CCAAGCGACGACTACAAGCA 60.666 55.000 0.00 0.00 0.00 3.91
2547 2856 0.666577 ACCAAGCGACGACTACAAGC 60.667 55.000 0.00 0.00 0.00 4.01
2548 2857 1.060713 CACCAAGCGACGACTACAAG 58.939 55.000 0.00 0.00 0.00 3.16
2549 2858 0.319211 CCACCAAGCGACGACTACAA 60.319 55.000 0.00 0.00 0.00 2.41
2550 2859 1.287815 CCACCAAGCGACGACTACA 59.712 57.895 0.00 0.00 0.00 2.74
2551 2860 0.731855 GACCACCAAGCGACGACTAC 60.732 60.000 0.00 0.00 0.00 2.73
2552 2861 0.892358 AGACCACCAAGCGACGACTA 60.892 55.000 0.00 0.00 0.00 2.59
2553 2862 0.892358 TAGACCACCAAGCGACGACT 60.892 55.000 0.00 0.00 0.00 4.18
2554 2863 0.731855 GTAGACCACCAAGCGACGAC 60.732 60.000 0.00 0.00 0.00 4.34
2555 2864 1.582968 GTAGACCACCAAGCGACGA 59.417 57.895 0.00 0.00 0.00 4.20
2556 2865 1.800315 CGTAGACCACCAAGCGACG 60.800 63.158 0.00 0.00 0.00 5.12
2557 2866 1.445582 CCGTAGACCACCAAGCGAC 60.446 63.158 0.00 0.00 0.00 5.19
2558 2867 0.968901 ATCCGTAGACCACCAAGCGA 60.969 55.000 0.00 0.00 0.00 4.93
2559 2868 0.527817 GATCCGTAGACCACCAAGCG 60.528 60.000 0.00 0.00 0.00 4.68
2560 2869 0.824759 AGATCCGTAGACCACCAAGC 59.175 55.000 0.00 0.00 0.00 4.01
2561 2870 1.137086 CCAGATCCGTAGACCACCAAG 59.863 57.143 0.00 0.00 0.00 3.61
2562 2871 1.191535 CCAGATCCGTAGACCACCAA 58.808 55.000 0.00 0.00 0.00 3.67
2563 2872 0.333652 TCCAGATCCGTAGACCACCA 59.666 55.000 0.00 0.00 0.00 4.17
2564 2873 1.341531 CATCCAGATCCGTAGACCACC 59.658 57.143 0.00 0.00 0.00 4.61
2565 2874 2.032620 ACATCCAGATCCGTAGACCAC 58.967 52.381 0.00 0.00 0.00 4.16
2566 2875 2.454336 ACATCCAGATCCGTAGACCA 57.546 50.000 0.00 0.00 0.00 4.02
2567 2876 5.470047 AATTACATCCAGATCCGTAGACC 57.530 43.478 0.00 0.00 0.00 3.85
2568 2877 7.787725 AAAAATTACATCCAGATCCGTAGAC 57.212 36.000 0.00 0.00 0.00 2.59
2597 2906 9.952030 TCATGGTAGTACATCAAACATTAGAAA 57.048 29.630 2.06 0.00 0.00 2.52
2601 2910 9.898152 TCAATCATGGTAGTACATCAAACATTA 57.102 29.630 2.06 0.00 0.00 1.90
2602 2911 8.806429 TCAATCATGGTAGTACATCAAACATT 57.194 30.769 2.06 0.00 0.00 2.71
2603 2912 8.806429 TTCAATCATGGTAGTACATCAAACAT 57.194 30.769 2.06 0.00 0.00 2.71
2604 2913 8.100164 TCTTCAATCATGGTAGTACATCAAACA 58.900 33.333 2.06 0.00 0.00 2.83
2605 2914 8.492673 TCTTCAATCATGGTAGTACATCAAAC 57.507 34.615 2.06 0.00 0.00 2.93
2606 2915 9.112725 CATCTTCAATCATGGTAGTACATCAAA 57.887 33.333 2.06 0.00 0.00 2.69
2607 2916 8.485392 TCATCTTCAATCATGGTAGTACATCAA 58.515 33.333 2.06 0.00 0.00 2.57
2608 2917 8.021898 TCATCTTCAATCATGGTAGTACATCA 57.978 34.615 2.06 0.00 0.00 3.07
2609 2918 8.893219 TTCATCTTCAATCATGGTAGTACATC 57.107 34.615 2.06 0.00 0.00 3.06


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

AutoCloner maintained by Alex Coulton.