Multiple sequence alignment - TraesCS3A01G167700

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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 TraesCS3A01G167700 chr3A 100.000 6765 0 0 522 7286 174283019 174289783 0.000000e+00 12493.0
1 TraesCS3A01G167700 chr3A 100.000 310 0 0 1 310 174282498 174282807 2.280000e-159 573.0
2 TraesCS3A01G167700 chr3A 98.780 164 1 1 2068 2230 119691779 119691942 2.570000e-74 291.0
3 TraesCS3A01G167700 chr3A 97.561 164 2 2 2068 2230 538841711 538841873 5.570000e-71 279.0
4 TraesCS3A01G167700 chr3D 97.904 3913 61 6 2551 6451 155556996 155560899 0.000000e+00 6752.0
5 TraesCS3A01G167700 chr3D 95.667 1200 30 8 880 2067 155555534 155556723 0.000000e+00 1908.0
6 TraesCS3A01G167700 chr3D 85.119 504 47 17 6778 7260 155561661 155562157 2.360000e-134 490.0
7 TraesCS3A01G167700 chr3D 96.043 278 6 3 2232 2504 155556718 155556995 1.440000e-121 448.0
8 TraesCS3A01G167700 chr3D 93.878 49 3 0 6439 6487 155560923 155560971 2.820000e-09 75.0
9 TraesCS3A01G167700 chr3D 89.091 55 6 0 1515 1569 155556216 155556270 1.310000e-07 69.4
10 TraesCS3A01G167700 chr3B 87.930 1251 111 12 2232 3454 226089767 226088529 0.000000e+00 1437.0
11 TraesCS3A01G167700 chr3B 92.134 928 34 18 3603 4496 226088409 226087487 0.000000e+00 1273.0
12 TraesCS3A01G167700 chr3B 96.438 758 20 2 5701 6451 226085683 226084926 0.000000e+00 1243.0
13 TraesCS3A01G167700 chr3B 91.436 759 30 9 880 1634 226090984 226090257 0.000000e+00 1009.0
14 TraesCS3A01G167700 chr3B 94.077 439 14 3 4864 5301 226086913 226086486 0.000000e+00 656.0
15 TraesCS3A01G167700 chr3B 95.169 414 19 1 5296 5708 226086282 226085869 0.000000e+00 652.0
16 TraesCS3A01G167700 chr3B 96.936 359 11 0 523 881 52929727 52930085 2.910000e-168 603.0
17 TraesCS3A01G167700 chr3B 95.822 359 10 2 522 880 160145984 160146337 6.340000e-160 575.0
18 TraesCS3A01G167700 chr3B 98.387 310 5 0 1 310 52929402 52929711 4.970000e-151 545.0
19 TraesCS3A01G167700 chr3B 98.387 310 5 0 1 310 160145657 160145966 4.970000e-151 545.0
20 TraesCS3A01G167700 chr3B 93.123 349 22 2 1721 2067 226090110 226089762 1.810000e-140 510.0
21 TraesCS3A01G167700 chr3B 92.188 256 15 2 4483 4738 226087437 226087187 2.500000e-94 357.0
22 TraesCS3A01G167700 chr3B 88.189 254 8 8 7024 7256 226084315 226084063 4.300000e-72 283.0
23 TraesCS3A01G167700 chr3B 90.455 220 14 3 6742 6954 226084560 226084341 4.300000e-72 283.0
24 TraesCS3A01G167700 chr3B 89.933 149 14 1 2300 2448 246144713 246144860 2.680000e-44 191.0
25 TraesCS3A01G167700 chr3B 94.231 104 3 3 6626 6729 226084749 226084649 9.790000e-34 156.0
26 TraesCS3A01G167700 chr3B 95.833 48 2 0 3268 3315 650366157 650366110 2.180000e-10 78.7
27 TraesCS3A01G167700 chr3B 90.566 53 5 0 1515 1567 226090324 226090272 3.650000e-08 71.3
28 TraesCS3A01G167700 chr2A 93.269 312 15 3 2 308 762294416 762294106 8.620000e-124 455.0
29 TraesCS3A01G167700 chr2A 93.676 253 16 0 629 881 762294060 762293808 5.330000e-101 379.0
30 TraesCS3A01G167700 chr2A 91.837 98 4 1 522 619 762294137 762294044 4.590000e-27 134.0
31 TraesCS3A01G167700 chr2A 97.917 48 1 0 3268 3315 216527924 216527877 4.680000e-12 84.2
32 TraesCS3A01G167700 chr7A 99.387 163 0 1 2068 2229 641434428 641434266 1.990000e-75 294.0
33 TraesCS3A01G167700 chr7A 98.788 165 1 1 2066 2229 685912170 685912334 7.150000e-75 292.0
34 TraesCS3A01G167700 chr7A 97.576 165 1 2 2068 2229 668098255 668098091 5.570000e-71 279.0
35 TraesCS3A01G167700 chr7A 90.541 148 13 1 2301 2448 83784831 83784977 2.070000e-45 195.0
36 TraesCS3A01G167700 chr6A 98.171 164 2 1 2068 2230 465615429 465615266 1.200000e-72 285.0
37 TraesCS3A01G167700 chr1A 98.758 161 1 1 2068 2227 95858867 95859027 1.200000e-72 285.0
38 TraesCS3A01G167700 chr5A 97.561 164 2 2 2068 2229 91122747 91122584 5.570000e-71 279.0
39 TraesCS3A01G167700 chr4A 97.546 163 3 1 2068 2229 620192493 620192655 2.000000e-70 278.0
40 TraesCS3A01G167700 chr4A 93.220 59 3 1 3268 3326 80843761 80843704 1.300000e-12 86.1
41 TraesCS3A01G167700 chr2B 93.431 137 9 0 2312 2448 426480569 426480433 3.450000e-48 204.0
42 TraesCS3A01G167700 chr6B 91.034 145 12 1 2304 2448 500227034 500227177 2.070000e-45 195.0
43 TraesCS3A01G167700 chr6B 95.833 48 2 0 3268 3315 503546962 503546915 2.180000e-10 78.7
44 TraesCS3A01G167700 chr4D 89.103 156 15 2 2295 2448 65536304 65536149 7.460000e-45 193.0
45 TraesCS3A01G167700 chr5B 88.608 158 16 2 2293 2448 574956431 574956588 2.680000e-44 191.0
46 TraesCS3A01G167700 chr5B 97.917 48 1 0 3268 3315 574956578 574956625 4.680000e-12 84.2
47 TraesCS3A01G167700 chr7B 89.474 152 13 3 2297 2448 411048503 411048355 9.650000e-44 189.0
48 TraesCS3A01G167700 chr1B 97.826 46 1 0 3270 3315 139663142 139663097 6.060000e-11 80.5
49 TraesCS3A01G167700 chr1B 97.826 46 1 0 3270 3315 271899658 271899703 6.060000e-11 80.5


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 TraesCS3A01G167700 chr3A 174282498 174289783 7285 False 6533.000000 12493 100.000000 1 7286 2 chr3A.!!$F3 7285
1 TraesCS3A01G167700 chr3D 155555534 155562157 6623 False 1623.733333 6752 92.950333 880 7260 6 chr3D.!!$F1 6380
2 TraesCS3A01G167700 chr3B 226084063 226090984 6921 True 660.858333 1437 92.161333 880 7256 12 chr3B.!!$R2 6376
3 TraesCS3A01G167700 chr3B 52929402 52930085 683 False 574.000000 603 97.661500 1 881 2 chr3B.!!$F2 880
4 TraesCS3A01G167700 chr3B 160145657 160146337 680 False 560.000000 575 97.104500 1 880 2 chr3B.!!$F3 879
5 TraesCS3A01G167700 chr2A 762293808 762294416 608 True 322.666667 455 92.927333 2 881 3 chr2A.!!$R2 879

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
609 621 0.037447 GTTCCCCTGCTGAAGCTCTT 59.963 55.000 3.61 0.0 42.66 2.85 F
736 748 0.176680 CCTAGCCACGTCAGCAATCT 59.823 55.000 9.59 0.0 0.00 2.40 F
2095 2210 0.174162 TAAAGCGTCCCTAAGGCGAC 59.826 55.000 0.00 0.0 43.57 5.19 F
2920 3060 0.250513 GACCACAGCCTAGACCCTTG 59.749 60.000 0.00 0.0 0.00 3.61 F
3880 4033 4.065088 TCAGCTGAATAACTCACACCAAC 58.935 43.478 15.67 0.0 0.00 3.77 F
5472 6075 0.037512 CTGCCCATATGCTCTCGGAG 60.038 60.000 0.00 0.0 0.00 4.63 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2076 2191 0.174162 GTCGCCTTAGGGACGCTTTA 59.826 55.000 0.0 0.0 44.82 1.85 R
2123 2238 0.521735 AAGCGGTCGATTTCCAAAGC 59.478 50.000 0.0 0.0 0.00 3.51 R
3232 3372 1.377333 CCGAAACAAGAGAGGGGGC 60.377 63.158 0.0 0.0 0.00 5.80 R
4453 4635 1.133790 GACAGTCAAATGCATGAGCCC 59.866 52.381 0.0 0.0 41.13 5.19 R
5474 6077 0.106819 ACTGCTCCCATCATCCAAGC 60.107 55.000 0.0 0.0 0.00 4.01 R
6582 7462 0.043652 GTTCGTTGTTGTCGTGGACG 60.044 55.000 0.0 0.0 41.45 4.79 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
284 287 0.537188 AGGAAGACATCGCCGATTGT 59.463 50.000 0.00 0.00 0.00 2.71
609 621 0.037447 GTTCCCCTGCTGAAGCTCTT 59.963 55.000 3.61 0.00 42.66 2.85
694 706 1.675641 GGCCCGCAGTCAGTTCATT 60.676 57.895 0.00 0.00 0.00 2.57
704 716 1.006825 TCAGTTCATTGTCGCGTCCG 61.007 55.000 5.77 0.00 0.00 4.79
736 748 0.176680 CCTAGCCACGTCAGCAATCT 59.823 55.000 9.59 0.00 0.00 2.40
827 839 6.306199 TGATTTCAGGGATTCTCAGTTCAAA 58.694 36.000 0.00 0.00 0.00 2.69
995 1007 4.699522 ACTCCCGCCCGCTTCAAC 62.700 66.667 0.00 0.00 0.00 3.18
1333 1348 3.426568 GCACCAGCGTCCTCAAGC 61.427 66.667 0.00 0.00 0.00 4.01
1421 1438 3.555518 GCTGGTTCGTGAAATCAGTTTC 58.444 45.455 12.61 0.00 43.22 2.78
1483 1500 3.340928 CTTAAGTGTACCTTTTCCCCCG 58.659 50.000 0.00 0.00 34.46 5.73
1497 1514 1.445942 CCCCGGCTACATGTACCTG 59.554 63.158 17.11 10.29 0.00 4.00
1498 1515 1.335132 CCCCGGCTACATGTACCTGT 61.335 60.000 17.11 8.87 0.00 4.00
1499 1516 0.179084 CCCGGCTACATGTACCTGTG 60.179 60.000 13.39 5.47 0.00 3.66
1500 1517 0.821517 CCGGCTACATGTACCTGTGA 59.178 55.000 13.39 0.00 0.00 3.58
1501 1518 1.202417 CCGGCTACATGTACCTGTGAG 60.202 57.143 13.39 8.20 0.00 3.51
1502 1519 1.749063 CGGCTACATGTACCTGTGAGA 59.251 52.381 13.39 0.00 0.00 3.27
1503 1520 2.479730 CGGCTACATGTACCTGTGAGAC 60.480 54.545 13.39 8.28 0.00 3.36
1504 1521 2.496070 GGCTACATGTACCTGTGAGACA 59.504 50.000 13.39 0.00 0.00 3.41
1544 1561 3.072211 GCTGTAAACACAGGGACTAACC 58.928 50.000 6.89 0.00 36.02 2.85
1547 1564 2.538512 AAACACAGGGACTAACCGAC 57.461 50.000 0.00 0.00 36.02 4.79
1549 1566 0.966920 ACACAGGGACTAACCGACTG 59.033 55.000 0.00 0.00 36.02 3.51
1589 1606 2.340210 TGCTTGCTGTAAACACAGGA 57.660 45.000 6.89 0.93 38.14 3.86
1596 1613 3.071023 TGCTGTAAACACAGGAACTAGCT 59.929 43.478 6.89 0.00 36.02 3.32
1626 1643 6.049790 GGGAGATGTCTTTTGGTGACTATAC 58.950 44.000 0.00 0.00 35.63 1.47
1831 1945 6.591834 AGAAAAATACTTCTGTGGAGTGATCG 59.408 38.462 0.00 0.00 34.31 3.69
1833 1947 4.909696 ATACTTCTGTGGAGTGATCGAG 57.090 45.455 0.00 0.00 0.00 4.04
1840 1954 0.684535 TGGAGTGATCGAGCCAAACA 59.315 50.000 0.00 0.00 0.00 2.83
1867 1981 9.244799 TCATATGTTTAGTGTAAGCTGAATACG 57.755 33.333 1.90 0.00 0.00 3.06
1905 2019 6.375455 TCTTGAACAGATTGGAAATTCTAGCC 59.625 38.462 0.00 0.00 0.00 3.93
2060 2175 9.862371 CTTATCTGGTATATAGGTAGCAACAAG 57.138 37.037 0.00 0.00 32.30 3.16
2061 2176 7.857404 ATCTGGTATATAGGTAGCAACAAGT 57.143 36.000 0.00 0.00 32.30 3.16
2062 2177 7.050970 TCTGGTATATAGGTAGCAACAAGTG 57.949 40.000 0.00 0.00 32.30 3.16
2063 2178 6.837048 TCTGGTATATAGGTAGCAACAAGTGA 59.163 38.462 0.00 0.00 32.30 3.41
2064 2179 7.509318 TCTGGTATATAGGTAGCAACAAGTGAT 59.491 37.037 0.00 0.00 32.30 3.06
2065 2180 8.715190 TGGTATATAGGTAGCAACAAGTGATA 57.285 34.615 0.00 0.00 0.00 2.15
2066 2181 8.582437 TGGTATATAGGTAGCAACAAGTGATAC 58.418 37.037 0.00 0.00 46.40 2.24
2074 2189 7.611213 GTAGCAACAAGTGATACCTATGTTT 57.389 36.000 0.00 0.00 42.24 2.83
2075 2190 8.040716 GTAGCAACAAGTGATACCTATGTTTT 57.959 34.615 0.00 0.00 42.24 2.43
2076 2191 7.524717 AGCAACAAGTGATACCTATGTTTTT 57.475 32.000 0.00 0.00 32.25 1.94
2077 2192 8.630054 AGCAACAAGTGATACCTATGTTTTTA 57.370 30.769 0.00 0.00 32.25 1.52
2078 2193 9.073475 AGCAACAAGTGATACCTATGTTTTTAA 57.927 29.630 0.00 0.00 32.25 1.52
2079 2194 9.685828 GCAACAAGTGATACCTATGTTTTTAAA 57.314 29.630 0.00 0.00 32.25 1.52
2081 2196 9.908152 AACAAGTGATACCTATGTTTTTAAAGC 57.092 29.630 0.00 0.00 30.50 3.51
2082 2197 8.234546 ACAAGTGATACCTATGTTTTTAAAGCG 58.765 33.333 0.00 0.00 0.00 4.68
2083 2198 7.916914 AGTGATACCTATGTTTTTAAAGCGT 57.083 32.000 0.00 0.00 0.00 5.07
2084 2199 7.971455 AGTGATACCTATGTTTTTAAAGCGTC 58.029 34.615 0.00 0.00 0.00 5.19
2085 2200 7.065443 AGTGATACCTATGTTTTTAAAGCGTCC 59.935 37.037 0.00 0.00 0.00 4.79
2086 2201 6.316890 TGATACCTATGTTTTTAAAGCGTCCC 59.683 38.462 0.00 0.00 0.00 4.46
2087 2202 4.659115 ACCTATGTTTTTAAAGCGTCCCT 58.341 39.130 0.00 0.00 0.00 4.20
2088 2203 5.807909 ACCTATGTTTTTAAAGCGTCCCTA 58.192 37.500 0.00 0.00 0.00 3.53
2089 2204 6.240145 ACCTATGTTTTTAAAGCGTCCCTAA 58.760 36.000 0.00 0.00 0.00 2.69
2090 2205 6.373495 ACCTATGTTTTTAAAGCGTCCCTAAG 59.627 38.462 0.00 0.00 0.00 2.18
2091 2206 5.638596 ATGTTTTTAAAGCGTCCCTAAGG 57.361 39.130 0.00 0.00 0.00 2.69
2092 2207 3.253921 TGTTTTTAAAGCGTCCCTAAGGC 59.746 43.478 0.00 0.00 39.09 4.35
2093 2208 1.729284 TTTAAAGCGTCCCTAAGGCG 58.271 50.000 0.00 0.00 43.57 5.52
2094 2209 0.896923 TTAAAGCGTCCCTAAGGCGA 59.103 50.000 0.00 0.00 43.57 5.54
2095 2210 0.174162 TAAAGCGTCCCTAAGGCGAC 59.826 55.000 0.00 0.00 43.57 5.19
2121 2236 4.516195 GTCGAAGCGCTCCCCCTC 62.516 72.222 12.06 2.47 0.00 4.30
2129 2244 4.803908 GCTCCCCCTCCGCTTTGG 62.804 72.222 0.00 0.00 40.09 3.28
2138 2253 2.849081 TCCGCTTTGGAAATCGACC 58.151 52.632 0.00 0.00 46.38 4.79
2139 2254 1.017177 TCCGCTTTGGAAATCGACCG 61.017 55.000 0.00 0.00 46.38 4.79
2140 2255 1.226018 CGCTTTGGAAATCGACCGC 60.226 57.895 0.00 0.00 0.00 5.68
2141 2256 1.635663 CGCTTTGGAAATCGACCGCT 61.636 55.000 0.00 0.00 0.00 5.52
2142 2257 0.521735 GCTTTGGAAATCGACCGCTT 59.478 50.000 0.00 0.00 0.00 4.68
2143 2258 1.068541 GCTTTGGAAATCGACCGCTTT 60.069 47.619 0.00 0.00 0.00 3.51
2144 2259 2.584791 CTTTGGAAATCGACCGCTTTG 58.415 47.619 0.00 0.00 0.00 2.77
2145 2260 0.878416 TTGGAAATCGACCGCTTTGG 59.122 50.000 0.00 0.00 46.41 3.28
2146 2261 0.958382 TGGAAATCGACCGCTTTGGG 60.958 55.000 0.00 0.00 44.64 4.12
2147 2262 1.136774 GAAATCGACCGCTTTGGGC 59.863 57.895 0.00 0.00 45.45 5.36
2165 2280 3.195698 GCCTAGGCGTCCAAAGCG 61.196 66.667 20.16 0.00 35.00 4.68
2173 2288 4.770874 GTCCAAAGCGCCCGCCTA 62.771 66.667 2.29 0.00 43.17 3.93
2174 2289 4.467084 TCCAAAGCGCCCGCCTAG 62.467 66.667 2.29 0.00 43.17 3.02
2205 2320 4.817909 CCCCCTCCCTAAGGCGGT 62.818 72.222 0.00 0.00 44.71 5.68
2206 2321 2.284493 CCCCTCCCTAAGGCGGTA 59.716 66.667 0.00 0.00 44.71 4.02
2207 2322 1.383525 CCCCTCCCTAAGGCGGTAA 60.384 63.158 0.00 0.00 44.71 2.85
2208 2323 1.408453 CCCCTCCCTAAGGCGGTAAG 61.408 65.000 0.00 0.00 44.71 2.34
2209 2324 1.408453 CCCTCCCTAAGGCGGTAAGG 61.408 65.000 0.00 0.00 44.71 2.69
2228 2343 3.047613 GGCGTCGCCTTAAAAACATAG 57.952 47.619 28.98 0.00 46.69 2.23
2229 2344 2.674357 GGCGTCGCCTTAAAAACATAGA 59.326 45.455 28.98 0.00 46.69 1.98
2230 2345 3.242316 GGCGTCGCCTTAAAAACATAGAG 60.242 47.826 28.98 0.00 46.69 2.43
2255 2370 7.504238 AGTGATACTTGGTGATGTGGTTTTAAA 59.496 33.333 0.00 0.00 0.00 1.52
2335 2450 2.815647 GTGCACGTAGCTCCTGCC 60.816 66.667 0.00 0.00 45.94 4.85
2452 2572 1.001641 GCCCTCATGGTCACTTGCT 60.002 57.895 0.00 0.00 36.04 3.91
2543 2668 2.846950 AGGTATACTTTGGCCCAGTCT 58.153 47.619 7.96 2.04 0.00 3.24
2544 2669 2.505819 AGGTATACTTTGGCCCAGTCTG 59.494 50.000 7.96 0.00 0.00 3.51
2686 2811 1.214673 AGTCCATAGTGAGGCGACCTA 59.785 52.381 0.00 0.00 31.76 3.08
2836 2968 2.489073 GGGGTTTCTTCTTGGCTTCTCA 60.489 50.000 0.00 0.00 0.00 3.27
2920 3060 0.250513 GACCACAGCCTAGACCCTTG 59.749 60.000 0.00 0.00 0.00 3.61
3232 3372 4.280677 ACCATATTGTGTGTTGGAGTTTGG 59.719 41.667 0.00 0.00 33.36 3.28
3423 3571 4.884164 AGATTGCCCATTAGTTCTTAGCAC 59.116 41.667 0.00 0.00 0.00 4.40
3880 4033 4.065088 TCAGCTGAATAACTCACACCAAC 58.935 43.478 15.67 0.00 0.00 3.77
3973 4126 6.644592 TGCTTCATACAACCTTTGCAAATAAC 59.355 34.615 13.23 0.00 0.00 1.89
3991 4144 7.548780 GCAAATAACCTTCTCCAAATTTATGCA 59.451 33.333 0.00 0.00 0.00 3.96
4453 4635 5.583495 CAGTAAATCTCTCTCAAGGTACCG 58.417 45.833 6.18 0.00 0.00 4.02
4866 5259 2.503331 TGTCCTGCCAACAGTACAATG 58.497 47.619 0.00 0.00 39.53 2.82
5466 6069 1.678101 GGTTTGACTGCCCATATGCTC 59.322 52.381 0.00 0.00 0.00 4.26
5467 6070 2.648059 GTTTGACTGCCCATATGCTCT 58.352 47.619 0.00 0.00 0.00 4.09
5468 6071 2.615912 GTTTGACTGCCCATATGCTCTC 59.384 50.000 0.00 0.00 0.00 3.20
5469 6072 0.390492 TGACTGCCCATATGCTCTCG 59.610 55.000 0.00 0.00 0.00 4.04
5470 6073 0.320247 GACTGCCCATATGCTCTCGG 60.320 60.000 0.00 0.00 0.00 4.63
5471 6074 0.760567 ACTGCCCATATGCTCTCGGA 60.761 55.000 0.00 0.00 0.00 4.55
5472 6075 0.037512 CTGCCCATATGCTCTCGGAG 60.038 60.000 0.00 0.00 0.00 4.63
5473 6076 1.294780 GCCCATATGCTCTCGGAGG 59.705 63.158 4.96 0.00 0.00 4.30
5474 6077 1.978473 CCCATATGCTCTCGGAGGG 59.022 63.158 4.96 2.09 0.00 4.30
5582 6195 0.610232 AAAGGCCAGAGCGCTTCATT 60.610 50.000 13.26 2.52 41.24 2.57
5976 6782 0.320247 CTGACAGCCACACAGAGACC 60.320 60.000 0.00 0.00 34.07 3.85
6036 6842 2.094675 ACAAATGAGGCATCGAAAGGG 58.905 47.619 0.00 0.00 0.00 3.95
6038 6844 2.044123 AATGAGGCATCGAAAGGGAC 57.956 50.000 0.00 0.00 0.00 4.46
6039 6845 0.911769 ATGAGGCATCGAAAGGGACA 59.088 50.000 0.00 0.00 0.00 4.02
6132 6941 4.173924 GCCCAGCTCTGCTCCCTC 62.174 72.222 0.00 0.00 36.40 4.30
6325 7139 6.032956 TGTTGTACCATGTGTAACTCTAGG 57.967 41.667 0.00 0.00 38.04 3.02
6404 7218 6.581712 TGATGAAGAATGATGGATCGTTGTA 58.418 36.000 0.00 0.00 36.24 2.41
6440 7254 3.428045 GGATGGAAATGCACCTTTTCTCG 60.428 47.826 10.28 0.00 34.29 4.04
6444 7258 3.120165 GGAAATGCACCTTTTCTCGTCTC 60.120 47.826 10.28 0.00 34.29 3.36
6481 7331 7.029563 CCTTTCATTAGGCTTGATTGTACAAC 58.970 38.462 11.22 5.88 0.00 3.32
6487 7337 7.987750 TTAGGCTTGATTGTACAACATGTTA 57.012 32.000 11.22 0.00 0.00 2.41
6489 7339 6.855836 AGGCTTGATTGTACAACATGTTATG 58.144 36.000 11.22 3.05 0.00 1.90
6491 7341 6.527722 GGCTTGATTGTACAACATGTTATGTG 59.472 38.462 11.22 1.82 44.07 3.21
6493 7343 7.271223 GCTTGATTGTACAACATGTTATGTGTC 59.729 37.037 11.22 6.46 44.07 3.67
6494 7344 7.139896 TGATTGTACAACATGTTATGTGTCC 57.860 36.000 11.22 0.00 44.07 4.02
6495 7345 5.950758 TTGTACAACATGTTATGTGTCCC 57.049 39.130 11.53 1.45 44.07 4.46
6496 7346 4.328536 TGTACAACATGTTATGTGTCCCC 58.671 43.478 11.53 0.00 44.07 4.81
6497 7347 2.432444 ACAACATGTTATGTGTCCCCG 58.568 47.619 11.53 0.00 44.07 5.73
6498 7348 1.132262 CAACATGTTATGTGTCCCCGC 59.868 52.381 11.53 0.00 44.07 6.13
6499 7349 0.326595 ACATGTTATGTGTCCCCGCA 59.673 50.000 0.00 0.00 43.01 5.69
6500 7350 1.271652 ACATGTTATGTGTCCCCGCAA 60.272 47.619 0.00 0.00 43.01 4.85
6501 7351 1.815613 CATGTTATGTGTCCCCGCAAA 59.184 47.619 0.00 0.00 34.15 3.68
6502 7352 1.982660 TGTTATGTGTCCCCGCAAAA 58.017 45.000 0.00 0.00 34.15 2.44
6503 7353 2.307768 TGTTATGTGTCCCCGCAAAAA 58.692 42.857 0.00 0.00 34.15 1.94
6550 7430 1.826487 ACAACTGGACGGCCCAAAC 60.826 57.895 3.83 0.00 46.07 2.93
6553 7433 3.047877 CTGGACGGCCCAAACGAC 61.048 66.667 3.83 0.00 46.07 4.34
6561 7441 2.664436 GCCCAAACGACGACCGAAG 61.664 63.158 0.00 0.00 41.76 3.79
6578 7458 2.921754 CGAAGGACTAAAAGGCACTACG 59.078 50.000 0.00 0.00 38.49 3.51
6580 7460 4.677250 CGAAGGACTAAAAGGCACTACGAT 60.677 45.833 0.00 0.00 38.49 3.73
6581 7461 4.388378 AGGACTAAAAGGCACTACGATC 57.612 45.455 0.00 0.00 38.49 3.69
6582 7462 3.132467 AGGACTAAAAGGCACTACGATCC 59.868 47.826 0.00 0.00 38.49 3.36
6583 7463 3.114065 GACTAAAAGGCACTACGATCCG 58.886 50.000 0.00 0.00 38.49 4.18
6584 7464 2.494870 ACTAAAAGGCACTACGATCCGT 59.505 45.455 0.00 0.00 38.49 4.69
6585 7465 2.005971 AAAAGGCACTACGATCCGTC 57.994 50.000 0.00 0.00 38.49 4.79
6586 7466 0.175073 AAAGGCACTACGATCCGTCC 59.825 55.000 0.00 0.00 38.49 4.79
6587 7467 0.968901 AAGGCACTACGATCCGTCCA 60.969 55.000 0.00 0.00 38.49 4.02
6588 7468 1.226888 GGCACTACGATCCGTCCAC 60.227 63.158 0.00 0.00 41.54 4.02
6589 7469 1.585521 GCACTACGATCCGTCCACG 60.586 63.158 0.00 0.00 41.54 4.94
6590 7470 1.985447 GCACTACGATCCGTCCACGA 61.985 60.000 0.00 0.00 41.54 4.35
6591 7471 0.247974 CACTACGATCCGTCCACGAC 60.248 60.000 0.00 0.00 41.54 4.34
6592 7472 0.674581 ACTACGATCCGTCCACGACA 60.675 55.000 0.00 0.00 41.54 4.35
6593 7473 0.448990 CTACGATCCGTCCACGACAA 59.551 55.000 0.00 0.00 41.54 3.18
6594 7474 0.168788 TACGATCCGTCCACGACAAC 59.831 55.000 0.00 0.00 41.54 3.32
6595 7475 1.081041 CGATCCGTCCACGACAACA 60.081 57.895 0.00 0.00 43.02 3.33
6596 7476 0.665068 CGATCCGTCCACGACAACAA 60.665 55.000 0.00 0.00 43.02 2.83
6597 7477 0.788391 GATCCGTCCACGACAACAAC 59.212 55.000 0.00 0.00 43.02 3.32
6598 7478 0.942410 ATCCGTCCACGACAACAACG 60.942 55.000 0.00 0.00 43.02 4.10
6599 7479 1.589461 CCGTCCACGACAACAACGA 60.589 57.895 0.00 0.00 43.02 3.85
6600 7480 1.146957 CCGTCCACGACAACAACGAA 61.147 55.000 0.00 0.00 43.02 3.85
6608 7488 0.385473 GACAACAACGAACATGCCGG 60.385 55.000 11.89 0.00 0.00 6.13
6609 7489 1.081509 CAACAACGAACATGCCGGG 60.082 57.895 2.18 0.00 0.00 5.73
6664 7544 3.442625 GCACAGATACAAACCCTTAACCC 59.557 47.826 0.00 0.00 0.00 4.11
6666 7546 3.010920 ACAGATACAAACCCTTAACCCCC 59.989 47.826 0.00 0.00 0.00 5.40
6667 7547 3.010808 CAGATACAAACCCTTAACCCCCA 59.989 47.826 0.00 0.00 0.00 4.96
6707 7587 3.473367 CTTTTGTTGCTCGATTCTCGTG 58.527 45.455 0.00 0.00 41.35 4.35
6709 7589 1.698165 TGTTGCTCGATTCTCGTGTC 58.302 50.000 0.00 0.00 41.35 3.67
6729 7609 1.301293 CTCTTTCACAGCCCCTCCC 59.699 63.158 0.00 0.00 0.00 4.30
6730 7610 1.151810 TCTTTCACAGCCCCTCCCT 60.152 57.895 0.00 0.00 0.00 4.20
6731 7611 0.118346 TCTTTCACAGCCCCTCCCTA 59.882 55.000 0.00 0.00 0.00 3.53
6733 7613 2.022428 TCTTTCACAGCCCCTCCCTATA 60.022 50.000 0.00 0.00 0.00 1.31
6734 7614 1.802553 TTCACAGCCCCTCCCTATAC 58.197 55.000 0.00 0.00 0.00 1.47
6735 7615 0.941963 TCACAGCCCCTCCCTATACT 59.058 55.000 0.00 0.00 0.00 2.12
6736 7616 2.149556 TCACAGCCCCTCCCTATACTA 58.850 52.381 0.00 0.00 0.00 1.82
6767 7723 1.999071 CTCTCGACCTTCCCGCTGAG 61.999 65.000 0.00 0.00 0.00 3.35
6768 7724 2.035155 TCGACCTTCCCGCTGAGA 59.965 61.111 0.00 0.00 0.00 3.27
6774 7730 2.203938 TTCCCGCTGAGACCCCTT 60.204 61.111 0.00 0.00 0.00 3.95
6775 7731 0.976073 CTTCCCGCTGAGACCCCTTA 60.976 60.000 0.00 0.00 0.00 2.69
6776 7732 1.262640 TTCCCGCTGAGACCCCTTAC 61.263 60.000 0.00 0.00 0.00 2.34
6780 8112 2.040178 CCGCTGAGACCCCTTACTAAT 58.960 52.381 0.00 0.00 0.00 1.73
6787 8119 6.183361 GCTGAGACCCCTTACTAATTGGATAA 60.183 42.308 0.00 0.00 0.00 1.75
6801 8133 0.539986 GGATAAACCTCCGGAGCACA 59.460 55.000 26.87 10.67 35.41 4.57
6851 8183 4.194720 ACGCCGTCGCTGATCTCC 62.195 66.667 0.00 0.00 39.84 3.71
6921 8253 3.701205 TTAGCTGTGGATTCTTGCTCA 57.299 42.857 0.00 0.00 35.47 4.26
6933 8265 1.144565 CTTGCTCAGCGAGATGACCG 61.145 60.000 8.42 0.00 42.27 4.79
6957 8291 7.492669 CCGCTCTTATCTTTTTCTGTCTAATCA 59.507 37.037 0.00 0.00 0.00 2.57
6958 8292 8.873830 CGCTCTTATCTTTTTCTGTCTAATCAA 58.126 33.333 0.00 0.00 0.00 2.57
6964 8308 8.924511 ATCTTTTTCTGTCTAATCAAGTCCAA 57.075 30.769 0.00 0.00 0.00 3.53
6979 8323 3.209410 AGTCCAAATGATCCGCTGAATC 58.791 45.455 0.00 0.00 0.00 2.52
6999 8363 9.154847 CTGAATCTGTCATCTAACATTACAACA 57.845 33.333 0.00 0.00 35.07 3.33
7015 8379 7.117812 ACATTACAACATAGACTCAGAAAACCG 59.882 37.037 0.00 0.00 0.00 4.44
7016 8380 4.957296 ACAACATAGACTCAGAAAACCGT 58.043 39.130 0.00 0.00 0.00 4.83
7017 8381 4.989168 ACAACATAGACTCAGAAAACCGTC 59.011 41.667 0.00 0.00 0.00 4.79
7018 8382 5.221461 ACAACATAGACTCAGAAAACCGTCT 60.221 40.000 0.00 0.00 39.76 4.18
7019 8383 6.015688 ACAACATAGACTCAGAAAACCGTCTA 60.016 38.462 0.00 0.00 41.56 2.59
7020 8384 6.585695 ACATAGACTCAGAAAACCGTCTAA 57.414 37.500 0.00 0.00 40.93 2.10
7021 8385 6.989659 ACATAGACTCAGAAAACCGTCTAAA 58.010 36.000 0.00 0.00 40.93 1.85
7022 8386 6.867293 ACATAGACTCAGAAAACCGTCTAAAC 59.133 38.462 0.00 0.00 40.93 2.01
7028 8392 4.590222 TCAGAAAACCGTCTAAACTACCCT 59.410 41.667 0.00 0.00 0.00 4.34
7091 8455 8.980832 ATCCTTCTTTCCTACCATATCATACT 57.019 34.615 0.00 0.00 0.00 2.12
7100 8464 6.206829 TCCTACCATATCATACTGACTTGTCG 59.793 42.308 0.00 0.00 0.00 4.35
7172 8536 6.183360 ACAAATGTTAGACGTTTTGGCAGTTA 60.183 34.615 11.59 0.00 35.31 2.24
7173 8537 4.799419 TGTTAGACGTTTTGGCAGTTAC 57.201 40.909 0.00 0.00 0.00 2.50
7174 8538 4.444536 TGTTAGACGTTTTGGCAGTTACT 58.555 39.130 0.00 0.00 0.00 2.24
7175 8539 4.508861 TGTTAGACGTTTTGGCAGTTACTC 59.491 41.667 0.00 0.00 0.00 2.59
7176 8540 2.490991 AGACGTTTTGGCAGTTACTCC 58.509 47.619 0.00 0.00 0.00 3.85
7177 8541 1.534163 GACGTTTTGGCAGTTACTCCC 59.466 52.381 0.00 0.00 0.00 4.30
7256 8641 4.202264 CCCTGTGATACCAGATACAAGGAC 60.202 50.000 0.00 0.00 34.23 3.85
7257 8642 4.405680 CCTGTGATACCAGATACAAGGACA 59.594 45.833 0.00 0.00 34.23 4.02
7258 8643 5.452496 CCTGTGATACCAGATACAAGGACAG 60.452 48.000 0.00 0.00 34.23 3.51
7259 8644 5.023452 TGTGATACCAGATACAAGGACAGT 58.977 41.667 0.00 0.00 0.00 3.55
7260 8645 5.105351 TGTGATACCAGATACAAGGACAGTG 60.105 44.000 0.00 0.00 0.00 3.66
7261 8646 5.023452 TGATACCAGATACAAGGACAGTGT 58.977 41.667 0.00 0.00 0.00 3.55
7262 8647 6.096423 GTGATACCAGATACAAGGACAGTGTA 59.904 42.308 0.00 0.00 35.98 2.90
7263 8648 6.666113 TGATACCAGATACAAGGACAGTGTAA 59.334 38.462 0.00 0.00 35.21 2.41
7264 8649 5.148651 ACCAGATACAAGGACAGTGTAAC 57.851 43.478 0.00 0.00 35.21 2.50
7284 8669 9.733219 GTGTAACTTCAACCATCTATACTACTC 57.267 37.037 0.00 0.00 0.00 2.59
7285 8670 9.470399 TGTAACTTCAACCATCTATACTACTCA 57.530 33.333 0.00 0.00 0.00 3.41
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
619 631 7.310052 GGGGAAAGAACAGAGCTTTTTATTGAT 60.310 37.037 0.00 0.00 35.83 2.57
694 706 2.049248 GGTTAACCGGACGCGACA 60.049 61.111 15.93 0.00 0.00 4.35
704 716 3.493873 CGTGGCTAGGATTAGGGTTAACC 60.494 52.174 16.85 16.85 40.67 2.85
736 748 0.037590 ATAGCTGGTTTGGGCGTTGA 59.962 50.000 0.00 0.00 0.00 3.18
827 839 7.630242 TTGTTCTTCAAGTCTGAATCAAACT 57.370 32.000 0.00 0.00 40.78 2.66
888 900 2.507854 GGATCGGATCGGCAAGGGA 61.508 63.158 11.62 0.00 0.00 4.20
995 1007 2.280186 GGGGCGCGGACATAAGAG 60.280 66.667 8.83 0.00 0.00 2.85
1140 1155 2.166821 TCTCCTCGTAGGATAGCGAC 57.833 55.000 4.39 0.00 44.81 5.19
1226 1241 2.747686 GGCAACGTCAGGGGAGAA 59.252 61.111 0.00 0.00 0.00 2.87
1295 1310 0.333993 AACCCCTGCAGATCAAGCAT 59.666 50.000 17.39 0.00 41.82 3.79
1299 1314 2.657297 GCAAACCCCTGCAGATCAA 58.343 52.632 17.39 0.00 42.17 2.57
1311 1326 2.594592 AGGACGCTGGTGCAAACC 60.595 61.111 0.00 0.00 39.64 3.27
1483 1500 2.496070 TGTCTCACAGGTACATGTAGCC 59.504 50.000 27.07 19.80 34.31 3.93
1497 1514 4.142945 GCATTCATGTTCTCACTGTCTCAC 60.143 45.833 0.00 0.00 0.00 3.51
1498 1515 3.999001 GCATTCATGTTCTCACTGTCTCA 59.001 43.478 0.00 0.00 0.00 3.27
1499 1516 4.252073 AGCATTCATGTTCTCACTGTCTC 58.748 43.478 0.00 0.00 0.00 3.36
1500 1517 4.283363 AGCATTCATGTTCTCACTGTCT 57.717 40.909 0.00 0.00 0.00 3.41
1501 1518 4.720090 CAAGCATTCATGTTCTCACTGTC 58.280 43.478 0.00 0.00 0.00 3.51
1502 1519 3.057736 GCAAGCATTCATGTTCTCACTGT 60.058 43.478 0.00 0.00 0.00 3.55
1503 1520 3.190744 AGCAAGCATTCATGTTCTCACTG 59.809 43.478 0.00 0.00 0.00 3.66
1504 1521 3.190744 CAGCAAGCATTCATGTTCTCACT 59.809 43.478 0.00 0.00 0.00 3.41
1544 1561 4.568359 CACCAAAAGATATCTGTCCAGTCG 59.432 45.833 5.86 0.00 0.00 4.18
1547 1564 6.459298 GCATTCACCAAAAGATATCTGTCCAG 60.459 42.308 5.86 0.00 0.00 3.86
1549 1566 5.591877 AGCATTCACCAAAAGATATCTGTCC 59.408 40.000 5.86 0.00 0.00 4.02
1589 1606 3.034635 ACATCTCCCGATTCAGCTAGTT 58.965 45.455 0.00 0.00 0.00 2.24
1596 1613 3.009033 ACCAAAAGACATCTCCCGATTCA 59.991 43.478 0.00 0.00 0.00 2.57
1626 1643 4.584029 AAGCAATGTGAGTTCGTATTCG 57.416 40.909 0.00 0.00 38.55 3.34
1809 1918 6.037786 TCGATCACTCCACAGAAGTATTTT 57.962 37.500 0.00 0.00 0.00 1.82
1867 1981 3.674997 TGTTCAAGAACATGGTAGAGGC 58.325 45.455 11.34 0.00 45.42 4.70
1951 2066 2.747855 CTGGTTCAAGCTCCGCCC 60.748 66.667 0.00 0.00 0.00 6.13
2060 2175 7.184779 GGACGCTTTAAAAACATAGGTATCAC 58.815 38.462 0.00 0.00 0.00 3.06
2061 2176 6.316890 GGGACGCTTTAAAAACATAGGTATCA 59.683 38.462 0.00 0.00 0.00 2.15
2062 2177 6.541278 AGGGACGCTTTAAAAACATAGGTATC 59.459 38.462 0.00 0.00 0.00 2.24
2063 2178 6.420638 AGGGACGCTTTAAAAACATAGGTAT 58.579 36.000 0.00 0.00 0.00 2.73
2064 2179 5.807909 AGGGACGCTTTAAAAACATAGGTA 58.192 37.500 0.00 0.00 0.00 3.08
2065 2180 4.659115 AGGGACGCTTTAAAAACATAGGT 58.341 39.130 0.00 0.00 0.00 3.08
2066 2181 6.183360 CCTTAGGGACGCTTTAAAAACATAGG 60.183 42.308 0.00 0.00 33.58 2.57
2067 2182 6.677187 GCCTTAGGGACGCTTTAAAAACATAG 60.677 42.308 0.00 0.00 33.58 2.23
2068 2183 5.124297 GCCTTAGGGACGCTTTAAAAACATA 59.876 40.000 0.00 0.00 33.58 2.29
2069 2184 4.082408 GCCTTAGGGACGCTTTAAAAACAT 60.082 41.667 0.00 0.00 33.58 2.71
2070 2185 3.253921 GCCTTAGGGACGCTTTAAAAACA 59.746 43.478 0.00 0.00 33.58 2.83
2071 2186 3.668757 CGCCTTAGGGACGCTTTAAAAAC 60.669 47.826 0.00 0.00 33.58 2.43
2072 2187 2.485038 CGCCTTAGGGACGCTTTAAAAA 59.515 45.455 0.00 0.00 33.58 1.94
2073 2188 2.078392 CGCCTTAGGGACGCTTTAAAA 58.922 47.619 0.00 0.00 33.58 1.52
2074 2189 1.275856 TCGCCTTAGGGACGCTTTAAA 59.724 47.619 0.00 0.00 34.09 1.52
2075 2190 0.896923 TCGCCTTAGGGACGCTTTAA 59.103 50.000 0.00 0.00 34.09 1.52
2076 2191 0.174162 GTCGCCTTAGGGACGCTTTA 59.826 55.000 0.00 0.00 44.82 1.85
2077 2192 1.079336 GTCGCCTTAGGGACGCTTT 60.079 57.895 0.00 0.00 44.82 3.51
2078 2193 2.577593 GTCGCCTTAGGGACGCTT 59.422 61.111 0.00 0.00 44.82 4.68
2104 2219 4.516195 GAGGGGGAGCGCTTCGAC 62.516 72.222 13.26 5.82 0.00 4.20
2112 2227 4.803908 CCAAAGCGGAGGGGGAGC 62.804 72.222 0.00 0.00 36.56 4.70
2113 2228 3.009115 TCCAAAGCGGAGGGGGAG 61.009 66.667 0.00 0.00 39.64 4.30
2120 2235 1.017177 CGGTCGATTTCCAAAGCGGA 61.017 55.000 9.60 0.00 46.63 5.54
2121 2236 1.423845 CGGTCGATTTCCAAAGCGG 59.576 57.895 9.60 0.00 46.63 5.52
2123 2238 0.521735 AAGCGGTCGATTTCCAAAGC 59.478 50.000 0.00 0.00 0.00 3.51
2124 2239 2.584791 CAAAGCGGTCGATTTCCAAAG 58.415 47.619 3.55 0.00 30.80 2.77
2125 2240 1.268352 CCAAAGCGGTCGATTTCCAAA 59.732 47.619 3.55 0.00 30.80 3.28
2126 2241 0.878416 CCAAAGCGGTCGATTTCCAA 59.122 50.000 3.55 0.00 30.80 3.53
2127 2242 0.958382 CCCAAAGCGGTCGATTTCCA 60.958 55.000 3.55 0.00 30.80 3.53
2128 2243 1.800681 CCCAAAGCGGTCGATTTCC 59.199 57.895 3.55 0.00 30.80 3.13
2129 2244 1.136774 GCCCAAAGCGGTCGATTTC 59.863 57.895 3.55 0.00 30.80 2.17
2130 2245 3.274067 GCCCAAAGCGGTCGATTT 58.726 55.556 0.55 0.55 33.72 2.17
2148 2263 3.195698 CGCTTTGGACGCCTAGGC 61.196 66.667 24.75 24.75 37.85 3.93
2156 2271 4.770874 TAGGCGGGCGCTTTGGAC 62.771 66.667 7.64 0.00 41.60 4.02
2157 2272 4.467084 CTAGGCGGGCGCTTTGGA 62.467 66.667 7.64 0.00 41.60 3.53
2192 2307 1.446366 GCCTTACCGCCTTAGGGAG 59.554 63.158 0.00 0.00 35.02 4.30
2193 2308 2.428925 CGCCTTACCGCCTTAGGGA 61.429 63.158 0.00 0.00 35.02 4.20
2194 2309 2.108362 CGCCTTACCGCCTTAGGG 59.892 66.667 0.00 0.00 35.02 3.53
2195 2310 1.227176 GACGCCTTACCGCCTTAGG 60.227 63.158 0.00 0.00 37.30 2.69
2196 2311 1.588139 CGACGCCTTACCGCCTTAG 60.588 63.158 0.00 0.00 0.00 2.18
2197 2312 2.491152 CGACGCCTTACCGCCTTA 59.509 61.111 0.00 0.00 0.00 2.69
2209 2324 3.370061 ACTCTATGTTTTTAAGGCGACGC 59.630 43.478 12.43 12.43 0.00 5.19
2210 2325 4.624024 TCACTCTATGTTTTTAAGGCGACG 59.376 41.667 0.00 0.00 0.00 5.12
2211 2326 6.663944 ATCACTCTATGTTTTTAAGGCGAC 57.336 37.500 0.00 0.00 0.00 5.19
2212 2327 7.553334 AGTATCACTCTATGTTTTTAAGGCGA 58.447 34.615 0.00 0.00 0.00 5.54
2213 2328 7.772332 AGTATCACTCTATGTTTTTAAGGCG 57.228 36.000 0.00 0.00 0.00 5.52
2214 2329 8.398665 CCAAGTATCACTCTATGTTTTTAAGGC 58.601 37.037 0.00 0.00 0.00 4.35
2215 2330 9.449719 ACCAAGTATCACTCTATGTTTTTAAGG 57.550 33.333 0.00 0.00 0.00 2.69
2219 2334 8.950210 CATCACCAAGTATCACTCTATGTTTTT 58.050 33.333 0.00 0.00 0.00 1.94
2220 2335 8.103305 ACATCACCAAGTATCACTCTATGTTTT 58.897 33.333 0.00 0.00 0.00 2.43
2221 2336 7.550551 CACATCACCAAGTATCACTCTATGTTT 59.449 37.037 0.00 0.00 0.00 2.83
2222 2337 7.044181 CACATCACCAAGTATCACTCTATGTT 58.956 38.462 0.00 0.00 0.00 2.71
2223 2338 6.407412 CCACATCACCAAGTATCACTCTATGT 60.407 42.308 0.00 0.00 0.00 2.29
2224 2339 5.987953 CCACATCACCAAGTATCACTCTATG 59.012 44.000 0.00 0.00 0.00 2.23
2225 2340 5.663106 ACCACATCACCAAGTATCACTCTAT 59.337 40.000 0.00 0.00 0.00 1.98
2226 2341 5.023452 ACCACATCACCAAGTATCACTCTA 58.977 41.667 0.00 0.00 0.00 2.43
2227 2342 3.840666 ACCACATCACCAAGTATCACTCT 59.159 43.478 0.00 0.00 0.00 3.24
2228 2343 4.207891 ACCACATCACCAAGTATCACTC 57.792 45.455 0.00 0.00 0.00 3.51
2229 2344 4.640771 AACCACATCACCAAGTATCACT 57.359 40.909 0.00 0.00 0.00 3.41
2230 2345 5.705609 AAAACCACATCACCAAGTATCAC 57.294 39.130 0.00 0.00 0.00 3.06
2255 2370 3.011595 TGTCAACAATTCCCCATCCTGAT 59.988 43.478 0.00 0.00 0.00 2.90
2310 2425 2.656646 CTACGTGCACCAGGCTGA 59.343 61.111 17.94 0.00 45.15 4.26
2335 2450 3.190738 TTCCACGGGCCCTGAACAG 62.191 63.158 22.43 5.20 0.00 3.16
2452 2572 2.102109 TTTGGCCTCCACGACGCTTA 62.102 55.000 3.32 0.00 30.78 3.09
2543 2668 0.607620 GTGGGCTTTAATTGCTGCCA 59.392 50.000 15.75 1.36 46.53 4.92
2544 2669 0.897621 AGTGGGCTTTAATTGCTGCC 59.102 50.000 0.00 8.35 44.22 4.85
2686 2811 4.290722 AGGATGAAGACAACCAAGGAGATT 59.709 41.667 0.00 0.00 40.71 2.40
2836 2968 4.102113 GCTGTGGCTCCAACCAAT 57.898 55.556 0.00 0.00 42.70 3.16
2920 3060 8.403236 GTGTATTGGACATACCTAATCAAAACC 58.597 37.037 0.00 0.00 41.14 3.27
3232 3372 1.377333 CCGAAACAAGAGAGGGGGC 60.377 63.158 0.00 0.00 0.00 5.80
3423 3571 3.877559 TGTGAATTGCTGACCTGATAGG 58.122 45.455 0.00 0.00 42.49 2.57
3553 3701 1.423161 GGCTTTCATGAGGGCCTATCT 59.577 52.381 24.62 0.00 41.20 1.98
3779 3927 7.843686 GGTGTGAAAATGAACAAATAAAACACG 59.156 33.333 0.00 0.00 35.14 4.49
3880 4033 6.255844 CATCCAGATGTAAACGGAAAGCCG 62.256 50.000 2.34 2.34 46.83 5.52
3973 4126 4.100498 AGCCATGCATAAATTTGGAGAAGG 59.900 41.667 5.94 0.00 0.00 3.46
4110 4263 1.556911 CCAGCTGGGAAGAGTACACAT 59.443 52.381 26.14 0.00 40.01 3.21
4453 4635 1.133790 GACAGTCAAATGCATGAGCCC 59.866 52.381 0.00 0.00 41.13 5.19
4616 4861 6.687081 AATTGGACTTGTCGTGTCTTAAAA 57.313 33.333 0.00 0.00 35.04 1.52
4866 5259 5.840940 AAAGTAGTGTGCGACAAATAGAC 57.159 39.130 0.00 0.00 0.00 2.59
5466 6069 0.250209 CATCATCCAAGCCCTCCGAG 60.250 60.000 0.00 0.00 0.00 4.63
5467 6070 1.699054 CCATCATCCAAGCCCTCCGA 61.699 60.000 0.00 0.00 0.00 4.55
5468 6071 1.228063 CCATCATCCAAGCCCTCCG 60.228 63.158 0.00 0.00 0.00 4.63
5469 6072 1.152368 CCCATCATCCAAGCCCTCC 59.848 63.158 0.00 0.00 0.00 4.30
5470 6073 0.110104 CTCCCATCATCCAAGCCCTC 59.890 60.000 0.00 0.00 0.00 4.30
5471 6074 2.004408 GCTCCCATCATCCAAGCCCT 62.004 60.000 0.00 0.00 0.00 5.19
5472 6075 1.530183 GCTCCCATCATCCAAGCCC 60.530 63.158 0.00 0.00 0.00 5.19
5473 6076 0.822532 CTGCTCCCATCATCCAAGCC 60.823 60.000 0.00 0.00 31.96 4.35
5474 6077 0.106819 ACTGCTCCCATCATCCAAGC 60.107 55.000 0.00 0.00 0.00 4.01
5524 6137 4.151867 GGATCGTTTAAACAGAGTGGTCAC 59.848 45.833 18.07 0.00 0.00 3.67
5527 6140 3.326880 AGGGATCGTTTAAACAGAGTGGT 59.673 43.478 18.07 0.00 0.00 4.16
5582 6195 9.868277 AACAAACTCAGAAATGAACAACAATAA 57.132 25.926 0.00 0.00 0.00 1.40
5627 6240 7.181569 ATTGTACCATAAACTGGGAAAATGG 57.818 36.000 0.00 0.00 43.37 3.16
5653 6266 5.005107 GGTTAAGAGTAATTGTAAGACGCCG 59.995 44.000 0.00 0.00 0.00 6.46
5684 6297 7.546358 TCATTACAACAATCATCATTTGGTCC 58.454 34.615 0.00 0.00 0.00 4.46
6036 6842 2.159680 CCAGTCTAACTCGTCGTCTGTC 60.160 54.545 0.00 0.00 0.00 3.51
6038 6844 1.130749 CCCAGTCTAACTCGTCGTCTG 59.869 57.143 0.00 0.00 0.00 3.51
6039 6845 1.451067 CCCAGTCTAACTCGTCGTCT 58.549 55.000 0.00 0.00 0.00 4.18
6117 6926 2.733669 CCTGAGGGAGCAGAGCTGG 61.734 68.421 0.00 0.00 39.88 4.85
6159 6968 2.031012 TCACCGTTCAGCAGCCTG 59.969 61.111 0.00 0.00 40.54 4.85
6265 7074 2.107953 GGCTAGCTTGCTCCTCCG 59.892 66.667 19.45 0.00 0.00 4.63
6325 7139 1.670811 CCACATCGGTTGCTACAATCC 59.329 52.381 0.00 0.00 0.00 3.01
6421 7235 2.552315 GACGAGAAAAGGTGCATTTCCA 59.448 45.455 7.49 0.00 37.47 3.53
6440 7254 7.674471 AATGAAAGGCTACTTAAACAGAGAC 57.326 36.000 0.00 0.00 35.41 3.36
6481 7331 1.458398 TTGCGGGGACACATAACATG 58.542 50.000 0.00 0.00 0.00 3.21
6508 7363 3.450457 CCAGATAGAAGCCTCACAGAACT 59.550 47.826 0.00 0.00 0.00 3.01
6524 7404 0.249120 CCGTCCAGTTGTGCCAGATA 59.751 55.000 0.00 0.00 0.00 1.98
6550 7430 2.248487 CTTTTAGTCCTTCGGTCGTCG 58.752 52.381 0.00 0.00 40.90 5.12
6553 7433 1.337447 TGCCTTTTAGTCCTTCGGTCG 60.337 52.381 0.00 0.00 0.00 4.79
6561 7441 3.455327 GGATCGTAGTGCCTTTTAGTCC 58.545 50.000 0.00 0.00 0.00 3.85
6569 7449 1.379443 TGGACGGATCGTAGTGCCT 60.379 57.895 0.00 0.00 41.37 4.75
6571 7451 1.585521 CGTGGACGGATCGTAGTGC 60.586 63.158 0.00 0.48 41.37 4.40
6572 7452 0.247974 GTCGTGGACGGATCGTAGTG 60.248 60.000 0.00 0.00 41.37 2.74
6573 7453 0.674581 TGTCGTGGACGGATCGTAGT 60.675 55.000 0.00 0.00 41.37 2.73
6574 7454 0.448990 TTGTCGTGGACGGATCGTAG 59.551 55.000 0.00 0.00 41.37 3.51
6575 7455 0.168788 GTTGTCGTGGACGGATCGTA 59.831 55.000 0.00 0.00 41.37 3.43
6576 7456 1.080974 GTTGTCGTGGACGGATCGT 60.081 57.895 0.00 0.00 45.10 3.73
6577 7457 0.665068 TTGTTGTCGTGGACGGATCG 60.665 55.000 0.00 0.00 40.29 3.69
6578 7458 0.788391 GTTGTTGTCGTGGACGGATC 59.212 55.000 0.00 0.00 40.29 3.36
6580 7460 1.589461 CGTTGTTGTCGTGGACGGA 60.589 57.895 0.00 0.00 40.29 4.69
6581 7461 1.146957 TTCGTTGTTGTCGTGGACGG 61.147 55.000 0.00 0.00 40.29 4.79
6582 7462 0.043652 GTTCGTTGTTGTCGTGGACG 60.044 55.000 0.00 0.00 41.45 4.79
6583 7463 1.000884 TGTTCGTTGTTGTCGTGGAC 58.999 50.000 0.00 0.00 0.00 4.02
6584 7464 1.595328 CATGTTCGTTGTTGTCGTGGA 59.405 47.619 0.00 0.00 0.00 4.02
6585 7465 1.919839 GCATGTTCGTTGTTGTCGTGG 60.920 52.381 0.00 0.00 0.00 4.94
6586 7466 1.385038 GCATGTTCGTTGTTGTCGTG 58.615 50.000 0.00 0.00 0.00 4.35
6587 7467 0.306533 GGCATGTTCGTTGTTGTCGT 59.693 50.000 0.00 0.00 0.00 4.34
6588 7468 0.721155 CGGCATGTTCGTTGTTGTCG 60.721 55.000 0.00 0.00 0.00 4.35
6589 7469 0.385473 CCGGCATGTTCGTTGTTGTC 60.385 55.000 0.00 0.00 0.00 3.18
6590 7470 1.652012 CCGGCATGTTCGTTGTTGT 59.348 52.632 0.00 0.00 0.00 3.32
6591 7471 1.081509 CCCGGCATGTTCGTTGTTG 60.082 57.895 0.00 0.00 0.00 3.33
6592 7472 2.914908 GCCCGGCATGTTCGTTGTT 61.915 57.895 3.91 0.00 0.00 2.83
6593 7473 3.361977 GCCCGGCATGTTCGTTGT 61.362 61.111 3.91 0.00 0.00 3.32
6594 7474 4.114997 GGCCCGGCATGTTCGTTG 62.115 66.667 12.58 2.79 0.00 4.10
6608 7488 0.519077 CAACTTCTGAGAAAGCGGCC 59.481 55.000 0.00 0.00 0.00 6.13
6609 7489 1.195674 GTCAACTTCTGAGAAAGCGGC 59.804 52.381 0.00 0.00 33.60 6.53
6616 7496 0.603569 GGGCTCGTCAACTTCTGAGA 59.396 55.000 0.00 0.00 33.60 3.27
6618 7498 0.318441 CTGGGCTCGTCAACTTCTGA 59.682 55.000 0.00 0.00 0.00 3.27
6664 7544 1.878522 CGAGCCGAGTTCGATTGGG 60.879 63.158 2.59 0.00 38.48 4.12
6666 7546 2.517450 GCCGAGCCGAGTTCGATTG 61.517 63.158 10.69 0.00 38.48 2.67
6667 7547 2.202756 GCCGAGCCGAGTTCGATT 60.203 61.111 10.69 0.00 38.48 3.34
6707 7587 1.002011 GGGGCTGTGAAAGAGGGAC 60.002 63.158 0.00 0.00 0.00 4.46
6709 7589 1.301293 GAGGGGCTGTGAAAGAGGG 59.699 63.158 0.00 0.00 0.00 4.30
6729 7609 8.810427 GTCGAGAGGATTCGTCTATTAGTATAG 58.190 40.741 8.78 0.00 41.22 1.31
6730 7610 7.763528 GGTCGAGAGGATTCGTCTATTAGTATA 59.236 40.741 8.78 0.00 41.22 1.47
6731 7611 6.594937 GGTCGAGAGGATTCGTCTATTAGTAT 59.405 42.308 8.78 0.00 41.22 2.12
6733 7613 4.756135 GGTCGAGAGGATTCGTCTATTAGT 59.244 45.833 8.78 0.00 41.22 2.24
6734 7614 4.998672 AGGTCGAGAGGATTCGTCTATTAG 59.001 45.833 8.78 2.59 41.22 1.73
6735 7615 4.970711 AGGTCGAGAGGATTCGTCTATTA 58.029 43.478 8.78 0.00 41.22 0.98
6736 7616 3.822940 AGGTCGAGAGGATTCGTCTATT 58.177 45.455 8.78 0.00 41.22 1.73
6767 7723 6.907961 AGGTTTATCCAATTAGTAAGGGGTC 58.092 40.000 4.12 0.00 39.02 4.46
6768 7724 6.126273 GGAGGTTTATCCAATTAGTAAGGGGT 60.126 42.308 4.12 0.19 39.34 4.95
6871 8203 2.317371 AGCTTGAGAGAGAGGGACAA 57.683 50.000 0.00 0.00 0.00 3.18
6872 8204 3.678965 ATAGCTTGAGAGAGAGGGACA 57.321 47.619 0.00 0.00 0.00 4.02
6957 8291 2.787473 TCAGCGGATCATTTGGACTT 57.213 45.000 0.00 0.00 0.00 3.01
6958 8292 2.787473 TTCAGCGGATCATTTGGACT 57.213 45.000 0.00 0.00 0.00 3.85
6964 8308 3.548745 TGACAGATTCAGCGGATCATT 57.451 42.857 0.00 0.00 0.00 2.57
6979 8323 9.809096 AGTCTATGTTGTAATGTTAGATGACAG 57.191 33.333 0.00 0.00 32.19 3.51
6999 8363 7.229581 AGTTTAGACGGTTTTCTGAGTCTAT 57.770 36.000 5.21 0.00 43.19 1.98
7015 8379 5.752036 AGGGTAAACAGGGTAGTTTAGAC 57.248 43.478 0.00 0.00 42.68 2.59
7016 8380 6.438425 CACTAGGGTAAACAGGGTAGTTTAGA 59.562 42.308 0.00 0.00 42.68 2.10
7017 8381 6.212187 ACACTAGGGTAAACAGGGTAGTTTAG 59.788 42.308 0.00 0.00 42.68 1.85
7018 8382 6.014327 CACACTAGGGTAAACAGGGTAGTTTA 60.014 42.308 0.00 0.00 41.58 2.01
7019 8383 4.909695 ACACTAGGGTAAACAGGGTAGTTT 59.090 41.667 0.00 0.00 43.58 2.66
7020 8384 4.285260 CACACTAGGGTAAACAGGGTAGTT 59.715 45.833 0.00 0.00 0.00 2.24
7021 8385 3.836562 CACACTAGGGTAAACAGGGTAGT 59.163 47.826 0.00 0.00 0.00 2.73
7022 8386 3.836562 ACACACTAGGGTAAACAGGGTAG 59.163 47.826 0.00 0.00 0.00 3.18
7028 8392 7.970102 AGATCTTTAACACACTAGGGTAAACA 58.030 34.615 0.00 0.00 0.00 2.83
7091 8455 3.804786 TTACTGTGGAACGACAAGTCA 57.195 42.857 0.72 0.00 42.39 3.41
7100 8464 3.460103 TCGTCCTTGTTTACTGTGGAAC 58.540 45.455 0.00 0.00 37.35 3.62
7172 8536 6.295916 CCTCTGTAAACAAATGTAGAGGGAGT 60.296 42.308 17.04 0.00 44.71 3.85
7173 8537 6.109359 CCTCTGTAAACAAATGTAGAGGGAG 58.891 44.000 17.04 9.18 44.71 4.30
7174 8538 6.049955 CCTCTGTAAACAAATGTAGAGGGA 57.950 41.667 17.04 2.03 44.71 4.20
7176 8540 6.049955 TCCCTCTGTAAACAAATGTAGAGG 57.950 41.667 17.57 17.57 46.84 3.69
7177 8541 6.702329 ACTCCCTCTGTAAACAAATGTAGAG 58.298 40.000 4.72 4.72 33.29 2.43
7256 8641 9.517609 GTAGTATAGATGGTTGAAGTTACACTG 57.482 37.037 0.00 0.00 0.00 3.66
7257 8642 9.476928 AGTAGTATAGATGGTTGAAGTTACACT 57.523 33.333 0.00 0.00 0.00 3.55
7258 8643 9.733219 GAGTAGTATAGATGGTTGAAGTTACAC 57.267 37.037 0.00 0.00 0.00 2.90
7259 8644 9.470399 TGAGTAGTATAGATGGTTGAAGTTACA 57.530 33.333 0.00 0.00 0.00 2.41


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

AutoCloner maintained by Alex Coulton.