Multiple sequence alignment - TraesCS2A01G080900

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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 TraesCS2A01G080900 chr2A 100.000 2458 0 0 1 2458 36673811 36671354 0.000000e+00 4540.0
1 TraesCS2A01G080900 chr2A 88.525 1342 107 19 777 2107 36742591 36743896 0.000000e+00 1581.0
2 TraesCS2A01G080900 chr2A 97.078 753 20 1 1 751 379160359 379159607 0.000000e+00 1267.0
3 TraesCS2A01G080900 chr2A 80.356 1125 117 50 952 2059 27345130 27344093 0.000000e+00 758.0
4 TraesCS2A01G080900 chr2A 83.582 67 4 6 2396 2458 715969626 715969563 3.410000e-04 56.5
5 TraesCS2A01G080900 chr2B 90.335 1252 91 17 876 2115 55913072 55914305 0.000000e+00 1615.0
6 TraesCS2A01G080900 chr2B 94.994 779 38 1 1 778 443792912 443792134 0.000000e+00 1221.0
7 TraesCS2A01G080900 chr2B 90.465 818 70 5 960 1776 55923778 55924588 0.000000e+00 1072.0
8 TraesCS2A01G080900 chr2B 80.773 1139 124 47 1007 2113 40280558 40279483 0.000000e+00 802.0
9 TraesCS2A01G080900 chr2B 91.220 205 18 0 777 981 55916560 55916764 1.860000e-71 279.0
10 TraesCS2A01G080900 chr2B 89.431 123 11 2 2106 2228 465805901 465806021 1.180000e-33 154.0
11 TraesCS2A01G080900 chr2B 85.714 63 6 1 2396 2458 695441864 695441805 2.040000e-06 63.9
12 TraesCS2A01G080900 chr6A 97.686 778 18 0 1 778 407604464 407605241 0.000000e+00 1338.0
13 TraesCS2A01G080900 chr6B 95.379 779 35 1 1 778 193181339 193182117 0.000000e+00 1238.0
14 TraesCS2A01G080900 chr6B 94.595 777 39 1 1 777 459261582 459262355 0.000000e+00 1199.0
15 TraesCS2A01G080900 chr3A 92.555 779 54 4 1 778 456724707 456723932 0.000000e+00 1114.0
16 TraesCS2A01G080900 chr3B 91.271 779 63 5 1 777 791390691 791389916 0.000000e+00 1057.0
17 TraesCS2A01G080900 chr3B 90.141 781 71 5 1 778 242173891 242173114 0.000000e+00 1011.0
18 TraesCS2A01G080900 chr2D 90.162 803 66 8 777 1575 33878035 33878828 0.000000e+00 1033.0
19 TraesCS2A01G080900 chr2D 82.268 1111 105 41 1028 2107 24557098 24558147 0.000000e+00 876.0
20 TraesCS2A01G080900 chr2D 88.603 544 51 7 1573 2107 33878882 33879423 0.000000e+00 651.0
21 TraesCS2A01G080900 chr2D 95.935 246 10 0 777 1022 33729241 33728996 1.370000e-107 399.0
22 TraesCS2A01G080900 chr2D 91.304 115 8 2 2113 2227 78567559 78567671 3.270000e-34 156.0
23 TraesCS2A01G080900 chr5B 89.744 780 74 6 1 778 638299732 638298957 0.000000e+00 992.0
24 TraesCS2A01G080900 chr5B 84.454 476 63 5 971 1445 378816066 378816531 2.230000e-125 459.0
25 TraesCS2A01G080900 chr5B 83.466 502 74 7 964 1461 595659019 595659515 2.230000e-125 459.0
26 TraesCS2A01G080900 chr5D 85.115 477 61 6 971 1445 326369664 326370132 1.710000e-131 479.0
27 TraesCS2A01G080900 chr5A 83.300 503 75 7 964 1461 606159719 606160217 2.880000e-124 455.0
28 TraesCS2A01G080900 chr5A 92.661 109 7 1 2119 2227 605231298 605231191 3.270000e-34 156.0
29 TraesCS2A01G080900 chr6D 90.476 126 6 6 2105 2227 433642534 433642656 7.030000e-36 161.0
30 TraesCS2A01G080900 chr6D 90.244 123 10 2 2106 2227 467802263 467802384 2.530000e-35 159.0
31 TraesCS2A01G080900 chr6D 90.678 118 9 2 2110 2227 431160665 431160780 3.270000e-34 156.0
32 TraesCS2A01G080900 chr1A 91.379 116 10 0 2112 2227 62961098 62960983 2.530000e-35 159.0
33 TraesCS2A01G080900 chr3D 91.743 109 8 1 2119 2227 375693984 375693877 1.520000e-32 150.0
34 TraesCS2A01G080900 chr7A 86.014 143 15 5 2109 2247 134162212 134162353 5.480000e-32 148.0


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 TraesCS2A01G080900 chr2A 36671354 36673811 2457 True 4540 4540 100.0000 1 2458 1 chr2A.!!$R2 2457
1 TraesCS2A01G080900 chr2A 36742591 36743896 1305 False 1581 1581 88.5250 777 2107 1 chr2A.!!$F1 1330
2 TraesCS2A01G080900 chr2A 379159607 379160359 752 True 1267 1267 97.0780 1 751 1 chr2A.!!$R3 750
3 TraesCS2A01G080900 chr2A 27344093 27345130 1037 True 758 758 80.3560 952 2059 1 chr2A.!!$R1 1107
4 TraesCS2A01G080900 chr2B 443792134 443792912 778 True 1221 1221 94.9940 1 778 1 chr2B.!!$R2 777
5 TraesCS2A01G080900 chr2B 55923778 55924588 810 False 1072 1072 90.4650 960 1776 1 chr2B.!!$F1 816
6 TraesCS2A01G080900 chr2B 55913072 55916764 3692 False 947 1615 90.7775 777 2115 2 chr2B.!!$F3 1338
7 TraesCS2A01G080900 chr2B 40279483 40280558 1075 True 802 802 80.7730 1007 2113 1 chr2B.!!$R1 1106
8 TraesCS2A01G080900 chr6A 407604464 407605241 777 False 1338 1338 97.6860 1 778 1 chr6A.!!$F1 777
9 TraesCS2A01G080900 chr6B 193181339 193182117 778 False 1238 1238 95.3790 1 778 1 chr6B.!!$F1 777
10 TraesCS2A01G080900 chr6B 459261582 459262355 773 False 1199 1199 94.5950 1 777 1 chr6B.!!$F2 776
11 TraesCS2A01G080900 chr3A 456723932 456724707 775 True 1114 1114 92.5550 1 778 1 chr3A.!!$R1 777
12 TraesCS2A01G080900 chr3B 791389916 791390691 775 True 1057 1057 91.2710 1 777 1 chr3B.!!$R2 776
13 TraesCS2A01G080900 chr3B 242173114 242173891 777 True 1011 1011 90.1410 1 778 1 chr3B.!!$R1 777
14 TraesCS2A01G080900 chr2D 24557098 24558147 1049 False 876 876 82.2680 1028 2107 1 chr2D.!!$F1 1079
15 TraesCS2A01G080900 chr2D 33878035 33879423 1388 False 842 1033 89.3825 777 2107 2 chr2D.!!$F3 1330
16 TraesCS2A01G080900 chr5B 638298957 638299732 775 True 992 992 89.7440 1 778 1 chr5B.!!$R1 777

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
936 941 0.118346 TGTCACCATCCCTACCCAGT 59.882 55.0 0.0 0.0 0.0 4.0 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2376 4431 0.107459 GGCAATCCGCTCTCTTTCCT 60.107 55.0 0.0 0.0 41.91 3.36 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
200 201 4.620332 CGCCCCTCAAATGCAAAATCTTTA 60.620 41.667 0.00 0.00 0.00 1.85
235 236 5.198207 TCTCAGTATCGGTTATGGACTTCA 58.802 41.667 0.00 0.00 0.00 3.02
480 481 3.077359 AGAGAGGTTTTGATTCGCTTGG 58.923 45.455 0.00 0.00 0.00 3.61
503 504 1.666553 CTGACCGCGTGGCACTTAA 60.667 57.895 16.69 0.00 39.70 1.85
794 799 3.575965 AAAATTCAGTGCCGGCTTTAG 57.424 42.857 29.70 14.90 0.00 1.85
798 803 2.843401 TCAGTGCCGGCTTTAGTTTA 57.157 45.000 29.70 0.07 0.00 2.01
834 839 9.967451 TGTTTGGTAAGATAATCCAATGAAGTA 57.033 29.630 0.00 0.00 40.28 2.24
865 870 8.502738 TCCATAATTAATGCTAGAGGAAAACCT 58.497 33.333 0.00 0.00 33.92 3.50
936 941 0.118346 TGTCACCATCCCTACCCAGT 59.882 55.000 0.00 0.00 0.00 4.00
1087 1095 8.598041 AGATATTGTTATCCTGATGGTTAGGTC 58.402 37.037 0.00 0.00 35.74 3.85
1095 1103 6.696931 TCCTGATGGTTAGGTCGCAGACTA 62.697 50.000 8.26 0.00 45.57 2.59
1134 1142 9.303537 CTAAACAACTATACTTCCTGCTCTAAC 57.696 37.037 0.00 0.00 0.00 2.34
1160 1168 5.912892 TGTCACTGAGAACTTGTATGTCAA 58.087 37.500 0.00 0.00 34.61 3.18
1208 1220 4.462508 TTTGCAGGTGAAAAATGTGACA 57.537 36.364 0.00 0.00 0.00 3.58
1276 1290 5.222631 CCAGAAGGTTTGTGTCTAATTTGC 58.777 41.667 0.00 0.00 0.00 3.68
1393 1421 4.640771 AAGACATAAAGGGTCTGAAGCA 57.359 40.909 0.00 0.00 44.50 3.91
1399 1427 1.130054 AAGGGTCTGAAGCAGGAGCA 61.130 55.000 0.00 0.00 45.49 4.26
1461 1489 5.520748 AAAGGTCAACCCTGAGTGAATAT 57.479 39.130 0.00 0.00 45.47 1.28
1462 1490 4.494091 AGGTCAACCCTGAGTGAATATG 57.506 45.455 0.00 0.00 44.08 1.78
1469 1497 3.131223 ACCCTGAGTGAATATGACAGTCG 59.869 47.826 11.05 7.55 39.64 4.18
1531 1560 8.814235 CAATTTCATTAATGCTTGTTCCAGATC 58.186 33.333 10.76 0.00 0.00 2.75
1532 1561 5.739752 TCATTAATGCTTGTTCCAGATCG 57.260 39.130 10.76 0.00 0.00 3.69
1533 1562 5.427378 TCATTAATGCTTGTTCCAGATCGA 58.573 37.500 10.76 0.00 0.00 3.59
1543 1572 6.525578 TTGTTCCAGATCGAGTTACTGTAT 57.474 37.500 0.00 0.00 0.00 2.29
1554 1583 4.864806 CGAGTTACTGTATGTCTGCATTGT 59.135 41.667 0.00 0.00 36.58 2.71
1558 1587 3.754965 ACTGTATGTCTGCATTGTGGTT 58.245 40.909 0.00 0.00 36.58 3.67
1616 1715 1.271379 ACAATGGAGCTTACGGTGCTT 60.271 47.619 0.00 0.00 41.30 3.91
1624 1723 3.000727 AGCTTACGGTGCTTTATGTCAC 58.999 45.455 0.00 0.00 37.52 3.67
1647 1751 0.179004 TCGTGTTCATGGCCTTGGTT 60.179 50.000 17.95 0.00 0.00 3.67
1652 1772 1.544246 GTTCATGGCCTTGGTTACCAC 59.456 52.381 17.95 0.00 35.99 4.16
1661 1781 4.951094 GGCCTTGGTTACCACAATATTGTA 59.049 41.667 20.39 3.07 39.91 2.41
1687 1807 3.678056 TCTTTGGCTTCACTCACGTAT 57.322 42.857 0.00 0.00 0.00 3.06
1881 2012 5.858581 GTGTTCCACATTTGCTGAGATAAAC 59.141 40.000 0.00 0.00 34.08 2.01
1885 2016 6.422333 TCCACATTTGCTGAGATAAACCATA 58.578 36.000 0.00 0.00 0.00 2.74
1932 2068 4.097551 TGAAATCAGTCAACATCCCACA 57.902 40.909 0.00 0.00 0.00 4.17
1940 2076 3.327757 AGTCAACATCCCACACAGTACAT 59.672 43.478 0.00 0.00 0.00 2.29
1973 2111 0.997196 CTGCCGCTAACGTTAACTCC 59.003 55.000 9.68 0.00 37.70 3.85
2002 2140 5.192327 ACATTTTGTTTTCAGCTGAGGAG 57.808 39.130 17.43 3.65 0.00 3.69
2003 2141 4.038402 ACATTTTGTTTTCAGCTGAGGAGG 59.962 41.667 17.43 3.75 0.00 4.30
2004 2142 3.576078 TTTGTTTTCAGCTGAGGAGGA 57.424 42.857 17.43 0.00 0.00 3.71
2005 2143 2.847327 TGTTTTCAGCTGAGGAGGAG 57.153 50.000 17.43 0.00 0.00 3.69
2006 2144 1.349026 TGTTTTCAGCTGAGGAGGAGG 59.651 52.381 17.43 0.00 0.00 4.30
2007 2145 1.625818 GTTTTCAGCTGAGGAGGAGGA 59.374 52.381 17.43 0.00 0.00 3.71
2022 2169 1.066502 GGAGGAAGAAGAAGCTCGCTT 60.067 52.381 3.43 3.43 39.23 4.68
2110 2259 7.349412 ACTGTCTCCTTAGCGTCTTAATATT 57.651 36.000 0.00 0.00 0.00 1.28
2115 2264 9.786105 GTCTCCTTAGCGTCTTAATATTATACC 57.214 37.037 0.00 0.00 0.00 2.73
2116 2265 8.964772 TCTCCTTAGCGTCTTAATATTATACCC 58.035 37.037 0.00 0.00 0.00 3.69
2117 2266 8.890410 TCCTTAGCGTCTTAATATTATACCCT 57.110 34.615 0.00 0.00 0.00 4.34
2118 2267 8.964772 TCCTTAGCGTCTTAATATTATACCCTC 58.035 37.037 0.00 0.00 0.00 4.30
2119 2268 8.968969 CCTTAGCGTCTTAATATTATACCCTCT 58.031 37.037 0.00 0.00 0.00 3.69
2121 2270 7.407393 AGCGTCTTAATATTATACCCTCTCC 57.593 40.000 0.00 0.00 0.00 3.71
2122 2271 6.095160 AGCGTCTTAATATTATACCCTCTCCG 59.905 42.308 0.00 0.00 0.00 4.63
2124 2273 7.576477 GCGTCTTAATATTATACCCTCTCCGTT 60.576 40.741 0.00 0.00 0.00 4.44
2125 2274 7.967303 CGTCTTAATATTATACCCTCTCCGTTC 59.033 40.741 0.00 0.00 0.00 3.95
2126 2275 8.249638 GTCTTAATATTATACCCTCTCCGTTCC 58.750 40.741 0.00 0.00 0.00 3.62
2127 2276 8.175431 TCTTAATATTATACCCTCTCCGTTCCT 58.825 37.037 0.00 0.00 0.00 3.36
2128 2277 9.471702 CTTAATATTATACCCTCTCCGTTCCTA 57.528 37.037 0.00 0.00 0.00 2.94
2129 2278 9.827198 TTAATATTATACCCTCTCCGTTCCTAA 57.173 33.333 0.00 0.00 0.00 2.69
2130 2279 8.731591 AATATTATACCCTCTCCGTTCCTAAA 57.268 34.615 0.00 0.00 0.00 1.85
2131 2280 8.912614 ATATTATACCCTCTCCGTTCCTAAAT 57.087 34.615 0.00 0.00 0.00 1.40
2132 2281 4.957684 ATACCCTCTCCGTTCCTAAATG 57.042 45.455 0.00 0.00 0.00 2.32
2133 2282 2.547990 ACCCTCTCCGTTCCTAAATGT 58.452 47.619 0.00 0.00 0.00 2.71
2134 2283 3.716431 ACCCTCTCCGTTCCTAAATGTA 58.284 45.455 0.00 0.00 0.00 2.29
2135 2284 4.098894 ACCCTCTCCGTTCCTAAATGTAA 58.901 43.478 0.00 0.00 0.00 2.41
2137 2286 4.161754 CCCTCTCCGTTCCTAAATGTAAGT 59.838 45.833 0.00 0.00 0.00 2.24
2140 2289 6.351117 CCTCTCCGTTCCTAAATGTAAGTCTT 60.351 42.308 0.00 0.00 0.00 3.01
2141 2290 7.001099 TCTCCGTTCCTAAATGTAAGTCTTT 57.999 36.000 0.00 0.00 0.00 2.52
2142 2291 7.447594 TCTCCGTTCCTAAATGTAAGTCTTTT 58.552 34.615 0.00 0.00 0.00 2.27
2175 2536 8.710835 TTTGAATATGAACTACATACGAAGCA 57.289 30.769 0.00 0.00 43.12 3.91
2180 2541 9.935682 AATATGAACTACATACGAAGCAAAATG 57.064 29.630 0.00 0.00 43.12 2.32
2181 2542 7.609760 ATGAACTACATACGAAGCAAAATGA 57.390 32.000 0.00 0.00 37.46 2.57
2183 2544 6.649141 TGAACTACATACGAAGCAAAATGAGT 59.351 34.615 0.00 0.00 0.00 3.41
2185 2546 6.163476 ACTACATACGAAGCAAAATGAGTGA 58.837 36.000 0.00 0.00 0.00 3.41
2188 2549 6.546395 ACATACGAAGCAAAATGAGTGAATC 58.454 36.000 0.00 0.00 0.00 2.52
2190 2551 7.549134 ACATACGAAGCAAAATGAGTGAATCTA 59.451 33.333 0.00 0.00 0.00 1.98
2191 2552 6.170675 ACGAAGCAAAATGAGTGAATCTAC 57.829 37.500 0.00 0.00 0.00 2.59
2208 2569 9.778993 GTGAATCTACACTGTAAAATACGTCTA 57.221 33.333 0.00 0.00 37.73 2.59
2218 2579 9.622004 ACTGTAAAATACGTCTATATTCATCCG 57.378 33.333 0.00 0.00 0.00 4.18
2219 2580 9.622004 CTGTAAAATACGTCTATATTCATCCGT 57.378 33.333 0.00 0.00 0.00 4.69
2226 2587 7.918536 ACGTCTATATTCATCCGTATGTAGT 57.081 36.000 0.00 0.00 34.50 2.73
2229 2590 7.148289 CGTCTATATTCATCCGTATGTAGTGGT 60.148 40.741 0.00 0.00 34.50 4.16
2230 2591 8.521176 GTCTATATTCATCCGTATGTAGTGGTT 58.479 37.037 0.00 0.00 34.50 3.67
2231 2592 9.743581 TCTATATTCATCCGTATGTAGTGGTTA 57.256 33.333 0.00 0.00 34.50 2.85
2234 2595 6.718522 TTCATCCGTATGTAGTGGTTATGA 57.281 37.500 0.00 0.00 34.50 2.15
2235 2596 6.718522 TCATCCGTATGTAGTGGTTATGAA 57.281 37.500 0.00 0.00 34.50 2.57
2236 2597 6.509656 TCATCCGTATGTAGTGGTTATGAAC 58.490 40.000 0.00 0.00 34.50 3.18
2237 2598 5.918426 TCCGTATGTAGTGGTTATGAACA 57.082 39.130 0.00 0.00 0.00 3.18
2239 2600 5.185442 TCCGTATGTAGTGGTTATGAACACA 59.815 40.000 8.54 0.00 39.99 3.72
2240 2601 5.870433 CCGTATGTAGTGGTTATGAACACAA 59.130 40.000 8.54 0.00 39.99 3.33
2241 2602 6.369340 CCGTATGTAGTGGTTATGAACACAAA 59.631 38.462 8.54 0.00 39.99 2.83
2242 2603 7.095144 CCGTATGTAGTGGTTATGAACACAAAA 60.095 37.037 8.54 0.00 39.99 2.44
2243 2604 8.283992 CGTATGTAGTGGTTATGAACACAAAAA 58.716 33.333 8.54 0.00 39.99 1.94
2244 2605 9.607285 GTATGTAGTGGTTATGAACACAAAAAG 57.393 33.333 8.54 0.00 39.99 2.27
2245 2606 7.033530 TGTAGTGGTTATGAACACAAAAAGG 57.966 36.000 8.54 0.00 39.99 3.11
2246 2607 6.829298 TGTAGTGGTTATGAACACAAAAAGGA 59.171 34.615 8.54 0.00 39.99 3.36
2248 2609 6.126409 AGTGGTTATGAACACAAAAAGGAGA 58.874 36.000 8.54 0.00 39.99 3.71
2249 2610 6.039382 AGTGGTTATGAACACAAAAAGGAGAC 59.961 38.462 8.54 0.00 39.99 3.36
2251 2612 6.183360 TGGTTATGAACACAAAAAGGAGACAC 60.183 38.462 0.00 0.00 0.00 3.67
2252 2613 6.183360 GGTTATGAACACAAAAAGGAGACACA 60.183 38.462 0.00 0.00 0.00 3.72
2253 2614 7.425606 GTTATGAACACAAAAAGGAGACACAT 58.574 34.615 0.00 0.00 0.00 3.21
2254 2615 5.499139 TGAACACAAAAAGGAGACACATC 57.501 39.130 0.00 0.00 0.00 3.06
2255 2616 5.192927 TGAACACAAAAAGGAGACACATCT 58.807 37.500 0.00 0.00 38.15 2.90
2256 2617 6.353323 TGAACACAAAAAGGAGACACATCTA 58.647 36.000 0.00 0.00 34.34 1.98
2257 2618 6.998074 TGAACACAAAAAGGAGACACATCTAT 59.002 34.615 0.00 0.00 34.34 1.98
2260 2621 9.520515 AACACAAAAAGGAGACACATCTATTAT 57.479 29.630 0.00 0.00 34.34 1.28
2261 2622 8.950210 ACACAAAAAGGAGACACATCTATTATG 58.050 33.333 0.00 0.00 34.34 1.90
2262 2623 9.166173 CACAAAAAGGAGACACATCTATTATGA 57.834 33.333 0.00 0.00 34.34 2.15
2263 2624 9.388506 ACAAAAAGGAGACACATCTATTATGAG 57.611 33.333 0.00 0.00 34.34 2.90
2264 2625 8.834465 CAAAAAGGAGACACATCTATTATGAGG 58.166 37.037 0.00 0.00 34.34 3.86
2266 2627 8.503428 AAAGGAGACACATCTATTATGAGGAT 57.497 34.615 0.00 0.00 34.34 3.24
2267 2628 9.607333 AAAGGAGACACATCTATTATGAGGATA 57.393 33.333 0.00 0.00 34.34 2.59
2268 2629 8.821686 AGGAGACACATCTATTATGAGGATAG 57.178 38.462 0.00 0.00 34.34 2.08
2269 2630 8.619281 AGGAGACACATCTATTATGAGGATAGA 58.381 37.037 0.00 0.00 39.64 1.98
2270 2631 9.249053 GGAGACACATCTATTATGAGGATAGAA 57.751 37.037 0.00 0.00 39.01 2.10
2272 2633 9.593565 AGACACATCTATTATGAGGATAGAACA 57.406 33.333 0.00 0.00 39.01 3.18
2279 2640 9.868160 TCTATTATGAGGATAGAACAACTCAGA 57.132 33.333 0.00 0.00 42.55 3.27
2282 2643 6.865834 ATGAGGATAGAACAACTCAGAAGT 57.134 37.500 0.00 0.00 42.55 3.01
2283 2644 7.962995 ATGAGGATAGAACAACTCAGAAGTA 57.037 36.000 0.00 0.00 42.55 2.24
2284 2645 7.159322 TGAGGATAGAACAACTCAGAAGTAC 57.841 40.000 0.00 0.00 35.24 2.73
2285 2646 6.153000 TGAGGATAGAACAACTCAGAAGTACC 59.847 42.308 0.00 0.00 35.24 3.34
2286 2647 6.257586 AGGATAGAACAACTCAGAAGTACCT 58.742 40.000 0.00 0.00 33.48 3.08
2287 2648 6.153680 AGGATAGAACAACTCAGAAGTACCTG 59.846 42.308 0.00 0.00 33.48 4.00
2288 2649 6.071278 GGATAGAACAACTCAGAAGTACCTGT 60.071 42.308 0.00 0.00 33.48 4.00
2290 2651 4.649674 AGAACAACTCAGAAGTACCTGTGA 59.350 41.667 7.81 0.46 33.48 3.58
2291 2652 5.128827 AGAACAACTCAGAAGTACCTGTGAA 59.871 40.000 7.81 0.00 33.48 3.18
2292 2653 5.353394 ACAACTCAGAAGTACCTGTGAAA 57.647 39.130 7.81 0.00 33.48 2.69
2293 2654 5.741011 ACAACTCAGAAGTACCTGTGAAAA 58.259 37.500 7.81 0.00 33.48 2.29
2295 2656 5.615925 ACTCAGAAGTACCTGTGAAAACT 57.384 39.130 7.81 0.00 35.71 2.66
2296 2657 6.726490 ACTCAGAAGTACCTGTGAAAACTA 57.274 37.500 7.81 0.00 35.71 2.24
2297 2658 6.750148 ACTCAGAAGTACCTGTGAAAACTAG 58.250 40.000 7.81 0.00 35.71 2.57
2298 2659 6.324254 ACTCAGAAGTACCTGTGAAAACTAGT 59.676 38.462 7.81 0.00 35.71 2.57
2299 2660 6.513180 TCAGAAGTACCTGTGAAAACTAGTG 58.487 40.000 0.00 0.00 35.71 2.74
2300 2661 6.097839 TCAGAAGTACCTGTGAAAACTAGTGT 59.902 38.462 0.00 0.00 35.71 3.55
2301 2662 6.761714 CAGAAGTACCTGTGAAAACTAGTGTT 59.238 38.462 0.00 0.00 38.16 3.32
2302 2663 6.761714 AGAAGTACCTGTGAAAACTAGTGTTG 59.238 38.462 2.08 0.00 36.39 3.33
2305 2666 2.884639 CCTGTGAAAACTAGTGTTGGGG 59.115 50.000 2.08 0.00 36.39 4.96
2306 2667 3.551846 CTGTGAAAACTAGTGTTGGGGT 58.448 45.455 2.08 0.00 36.39 4.95
2309 2670 4.164604 TGTGAAAACTAGTGTTGGGGTAGT 59.835 41.667 2.08 0.00 36.39 2.73
2310 2671 4.514066 GTGAAAACTAGTGTTGGGGTAGTG 59.486 45.833 2.08 0.00 36.39 2.74
2311 2672 2.853235 AACTAGTGTTGGGGTAGTGC 57.147 50.000 0.00 0.00 34.71 4.40
2313 2674 0.108329 CTAGTGTTGGGGTAGTGCCG 60.108 60.000 0.00 0.00 38.44 5.69
2314 2675 0.832983 TAGTGTTGGGGTAGTGCCGT 60.833 55.000 0.00 0.00 38.44 5.68
2315 2676 1.228033 GTGTTGGGGTAGTGCCGTT 60.228 57.895 0.00 0.00 38.44 4.44
2316 2677 1.071814 TGTTGGGGTAGTGCCGTTC 59.928 57.895 0.00 0.00 38.44 3.95
2318 2679 2.148052 TTGGGGTAGTGCCGTTCCA 61.148 57.895 0.00 0.00 38.44 3.53
2319 2680 1.706995 TTGGGGTAGTGCCGTTCCAA 61.707 55.000 2.94 2.94 38.44 3.53
2320 2681 1.073548 GGGGTAGTGCCGTTCCAAA 59.926 57.895 0.00 0.00 38.44 3.28
2321 2682 1.239296 GGGGTAGTGCCGTTCCAAAC 61.239 60.000 0.00 0.00 38.44 2.93
2322 2683 0.535553 GGGTAGTGCCGTTCCAAACA 60.536 55.000 0.00 0.00 38.44 2.83
2323 2684 0.872388 GGTAGTGCCGTTCCAAACAG 59.128 55.000 0.00 0.00 0.00 3.16
2325 2686 1.798813 GTAGTGCCGTTCCAAACAGAG 59.201 52.381 0.00 0.00 0.00 3.35
2328 2689 1.165907 TGCCGTTCCAAACAGAGCAG 61.166 55.000 0.00 0.00 0.00 4.24
2329 2690 1.166531 GCCGTTCCAAACAGAGCAGT 61.167 55.000 0.00 0.00 0.00 4.40
2330 2691 1.308998 CCGTTCCAAACAGAGCAGTT 58.691 50.000 0.00 0.00 0.00 3.16
2332 2693 1.939934 CGTTCCAAACAGAGCAGTTCA 59.060 47.619 0.00 0.00 0.00 3.18
2335 4390 4.143030 CGTTCCAAACAGAGCAGTTCATAG 60.143 45.833 0.00 0.00 0.00 2.23
2343 4398 8.506437 CAAACAGAGCAGTTCATAGAATTTACA 58.494 33.333 0.00 0.00 0.00 2.41
2349 4404 9.346725 GAGCAGTTCATAGAATTTACAAAAAGG 57.653 33.333 0.00 0.00 0.00 3.11
2350 4405 8.860088 AGCAGTTCATAGAATTTACAAAAAGGT 58.140 29.630 0.00 0.00 0.00 3.50
2351 4406 8.915654 GCAGTTCATAGAATTTACAAAAAGGTG 58.084 33.333 0.00 0.00 0.00 4.00
2352 4407 8.915654 CAGTTCATAGAATTTACAAAAAGGTGC 58.084 33.333 0.00 0.00 0.00 5.01
2353 4408 8.637986 AGTTCATAGAATTTACAAAAAGGTGCA 58.362 29.630 0.00 0.00 0.00 4.57
2354 4409 9.255304 GTTCATAGAATTTACAAAAAGGTGCAA 57.745 29.630 0.00 0.00 0.00 4.08
2355 4410 9.823647 TTCATAGAATTTACAAAAAGGTGCAAA 57.176 25.926 0.00 0.00 0.00 3.68
2356 4411 9.474920 TCATAGAATTTACAAAAAGGTGCAAAG 57.525 29.630 0.00 0.00 0.00 2.77
2357 4412 6.603237 AGAATTTACAAAAAGGTGCAAAGC 57.397 33.333 0.00 0.00 0.00 3.51
2358 4413 5.527214 AGAATTTACAAAAAGGTGCAAAGCC 59.473 36.000 0.00 0.00 0.00 4.35
2359 4414 3.895232 TTACAAAAAGGTGCAAAGCCA 57.105 38.095 0.00 0.00 0.00 4.75
2360 4415 4.414337 TTACAAAAAGGTGCAAAGCCAT 57.586 36.364 0.00 0.00 0.00 4.40
2361 4416 5.537300 TTACAAAAAGGTGCAAAGCCATA 57.463 34.783 0.00 0.00 0.00 2.74
2362 4417 4.414337 ACAAAAAGGTGCAAAGCCATAA 57.586 36.364 0.00 0.00 0.00 1.90
2363 4418 4.126437 ACAAAAAGGTGCAAAGCCATAAC 58.874 39.130 0.00 0.00 0.00 1.89
2364 4419 4.141733 ACAAAAAGGTGCAAAGCCATAACT 60.142 37.500 0.00 0.00 0.00 2.24
2365 4420 3.942130 AAAGGTGCAAAGCCATAACTC 57.058 42.857 0.00 0.00 0.00 3.01
2366 4421 2.584835 AGGTGCAAAGCCATAACTCA 57.415 45.000 0.00 0.00 0.00 3.41
2367 4422 2.875296 AGGTGCAAAGCCATAACTCAA 58.125 42.857 0.00 0.00 0.00 3.02
2369 4424 3.640967 AGGTGCAAAGCCATAACTCAAAA 59.359 39.130 0.00 0.00 0.00 2.44
2370 4425 3.989817 GGTGCAAAGCCATAACTCAAAAG 59.010 43.478 0.00 0.00 0.00 2.27
2371 4426 4.501400 GGTGCAAAGCCATAACTCAAAAGT 60.501 41.667 0.00 0.00 37.32 2.66
2372 4427 4.445385 GTGCAAAGCCATAACTCAAAAGTG 59.555 41.667 0.00 0.00 35.36 3.16
2373 4428 3.429881 GCAAAGCCATAACTCAAAAGTGC 59.570 43.478 0.00 0.00 35.36 4.40
2375 4430 1.812571 AGCCATAACTCAAAAGTGCCG 59.187 47.619 0.00 0.00 35.36 5.69
2376 4431 1.810151 GCCATAACTCAAAAGTGCCGA 59.190 47.619 0.00 0.00 35.36 5.54
2377 4432 2.159517 GCCATAACTCAAAAGTGCCGAG 60.160 50.000 0.00 0.00 35.36 4.63
2378 4433 2.420022 CCATAACTCAAAAGTGCCGAGG 59.580 50.000 0.00 0.00 35.36 4.63
2381 4592 2.341846 ACTCAAAAGTGCCGAGGAAA 57.658 45.000 0.00 0.00 33.32 3.13
2383 4594 2.158813 ACTCAAAAGTGCCGAGGAAAGA 60.159 45.455 0.00 0.00 33.32 2.52
2384 4595 2.481952 CTCAAAAGTGCCGAGGAAAGAG 59.518 50.000 0.00 0.00 0.00 2.85
2387 4598 0.036858 AAGTGCCGAGGAAAGAGAGC 60.037 55.000 0.00 0.00 0.00 4.09
2391 4602 2.022240 GCCGAGGAAAGAGAGCGGAT 62.022 60.000 0.00 0.00 44.43 4.18
2392 4603 0.461961 CCGAGGAAAGAGAGCGGATT 59.538 55.000 0.00 0.00 44.43 3.01
2393 4604 1.565305 CGAGGAAAGAGAGCGGATTG 58.435 55.000 0.00 0.00 0.00 2.67
2403 4614 4.147701 GCGGATTGCCATGCTACT 57.852 55.556 0.00 0.00 37.76 2.57
2405 4616 0.740737 GCGGATTGCCATGCTACTTT 59.259 50.000 0.00 0.00 37.76 2.66
2411 4622 5.334879 CGGATTGCCATGCTACTTTTATACC 60.335 44.000 0.00 0.00 0.00 2.73
2413 4624 6.209391 GGATTGCCATGCTACTTTTATACCAT 59.791 38.462 0.00 0.00 0.00 3.55
2415 4626 8.704849 ATTGCCATGCTACTTTTATACCATTA 57.295 30.769 0.00 0.00 0.00 1.90
2416 4627 8.704849 TTGCCATGCTACTTTTATACCATTAT 57.295 30.769 0.00 0.00 0.00 1.28
2417 4628 8.704849 TGCCATGCTACTTTTATACCATTATT 57.295 30.769 0.00 0.00 0.00 1.40
2418 4629 9.800572 TGCCATGCTACTTTTATACCATTATTA 57.199 29.630 0.00 0.00 0.00 0.98
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
152 153 4.209538 CAACTTCTCCATATGCATTGGGA 58.790 43.478 20.70 18.38 34.85 4.37
200 201 1.279496 TACTGAGAGGCAAGCCATGT 58.721 50.000 14.40 6.75 38.92 3.21
294 295 0.321996 GTCTGTTGTGTCCTCCTCCC 59.678 60.000 0.00 0.00 0.00 4.30
295 296 0.321996 GGTCTGTTGTGTCCTCCTCC 59.678 60.000 0.00 0.00 0.00 4.30
503 504 1.594310 GAGCGTTCCTCTGCTTCCT 59.406 57.895 0.00 0.00 42.60 3.36
779 784 2.038033 ACTAAACTAAAGCCGGCACTGA 59.962 45.455 31.54 7.40 0.00 3.41
783 788 4.922471 AAAAACTAAACTAAAGCCGGCA 57.078 36.364 31.54 7.07 0.00 5.69
1087 1095 1.565305 GCCAATGAGACTAGTCTGCG 58.435 55.000 29.84 13.97 40.61 5.18
1095 1103 3.074538 AGTTGTTTAGGGCCAATGAGACT 59.925 43.478 6.18 0.00 0.00 3.24
1098 1106 6.357367 AGTATAGTTGTTTAGGGCCAATGAG 58.643 40.000 6.18 0.00 0.00 2.90
1134 1142 6.479990 TGACATACAAGTTCTCAGTGACAAAG 59.520 38.462 0.00 0.00 0.00 2.77
1172 1180 6.943146 TCACCTGCAAAAATGGTAATGTAGTA 59.057 34.615 0.00 0.00 32.13 1.82
1208 1220 4.423732 GCTTGCCGTCAATTACATCATTT 58.576 39.130 0.00 0.00 0.00 2.32
1309 1328 6.317140 ACATGAAGCAGATTAGTACACCAATG 59.683 38.462 0.00 0.00 0.00 2.82
1393 1421 2.809861 CTTGGCATCACGGTGCTCCT 62.810 60.000 2.51 0.00 44.45 3.69
1399 1427 2.028130 TGTTTTTCTTGGCATCACGGT 58.972 42.857 0.00 0.00 0.00 4.83
1462 1490 5.807520 AGTTCATCACAATATGACGACTGTC 59.192 40.000 0.00 0.00 41.24 3.51
1476 1504 9.897744 GATGAAAAACAGAATAAGTTCATCACA 57.102 29.630 15.69 0.00 45.41 3.58
1509 1538 5.879777 TCGATCTGGAACAAGCATTAATGAA 59.120 36.000 19.73 0.00 38.70 2.57
1531 1560 4.864806 ACAATGCAGACATACAGTAACTCG 59.135 41.667 0.00 0.00 34.62 4.18
1532 1561 5.063944 CCACAATGCAGACATACAGTAACTC 59.936 44.000 0.00 0.00 34.62 3.01
1533 1562 4.937620 CCACAATGCAGACATACAGTAACT 59.062 41.667 0.00 0.00 34.62 2.24
1543 1572 3.023119 ACTCAAAACCACAATGCAGACA 58.977 40.909 0.00 0.00 0.00 3.41
1554 1583 6.429521 AACTACCTAGCTAACTCAAAACCA 57.570 37.500 0.00 0.00 0.00 3.67
1558 1587 9.649167 GATACAAAACTACCTAGCTAACTCAAA 57.351 33.333 0.00 0.00 0.00 2.69
1624 1723 1.234615 AAGGCCATGAACACGAACCG 61.235 55.000 5.01 0.00 0.00 4.44
1636 1740 2.621556 ATTGTGGTAACCAAGGCCAT 57.378 45.000 5.01 0.00 34.18 4.40
1661 1781 4.393062 CGTGAGTGAAGCCAAAGAATATGT 59.607 41.667 0.00 0.00 0.00 2.29
1679 1799 7.323895 CGATGATAAAGACCTACAATACGTGAG 59.676 40.741 0.00 0.00 0.00 3.51
1687 1807 9.613428 ATTTTGATCGATGATAAAGACCTACAA 57.387 29.630 0.54 0.00 0.00 2.41
1932 2068 3.885297 GGCAGCAATGGAATATGTACTGT 59.115 43.478 0.00 0.00 0.00 3.55
1973 2111 5.953205 CAGCTGAAAACAAAATGTTGAAACG 59.047 36.000 8.42 0.00 40.14 3.60
2002 2140 0.534873 AGCGAGCTTCTTCTTCCTCC 59.465 55.000 0.00 0.00 0.00 4.30
2003 2141 2.267426 GAAGCGAGCTTCTTCTTCCTC 58.733 52.381 25.46 1.76 46.38 3.71
2004 2142 2.378445 GAAGCGAGCTTCTTCTTCCT 57.622 50.000 25.46 0.00 46.38 3.36
2022 2169 2.297033 GCCTTCATTTTGCACTCTTGGA 59.703 45.455 0.00 0.00 0.00 3.53
2110 2259 5.461327 ACATTTAGGAACGGAGAGGGTATA 58.539 41.667 0.00 0.00 0.00 1.47
2115 2264 5.127356 AGACTTACATTTAGGAACGGAGAGG 59.873 44.000 0.00 0.00 0.00 3.69
2116 2265 6.210287 AGACTTACATTTAGGAACGGAGAG 57.790 41.667 0.00 0.00 0.00 3.20
2117 2266 6.600882 AAGACTTACATTTAGGAACGGAGA 57.399 37.500 0.00 0.00 0.00 3.71
2118 2267 7.668525 AAAAGACTTACATTTAGGAACGGAG 57.331 36.000 0.00 0.00 0.00 4.63
2149 2298 9.325198 TGCTTCGTATGTAGTTCATATTCAAAT 57.675 29.630 0.00 0.00 40.54 2.32
2151 2300 8.710835 TTGCTTCGTATGTAGTTCATATTCAA 57.289 30.769 0.00 0.00 40.54 2.69
2152 2301 8.710835 TTTGCTTCGTATGTAGTTCATATTCA 57.289 30.769 0.00 0.00 40.54 2.57
2154 2303 9.935682 CATTTTGCTTCGTATGTAGTTCATATT 57.064 29.630 0.00 0.00 40.54 1.28
2155 2304 9.325198 TCATTTTGCTTCGTATGTAGTTCATAT 57.675 29.630 0.00 0.00 40.54 1.78
2157 2306 7.334421 ACTCATTTTGCTTCGTATGTAGTTCAT 59.666 33.333 0.00 0.00 40.25 2.57
2158 2307 6.649141 ACTCATTTTGCTTCGTATGTAGTTCA 59.351 34.615 0.00 0.00 0.00 3.18
2160 2309 6.649141 TCACTCATTTTGCTTCGTATGTAGTT 59.351 34.615 0.00 0.00 0.00 2.24
2161 2310 6.163476 TCACTCATTTTGCTTCGTATGTAGT 58.837 36.000 0.00 0.00 0.00 2.73
2162 2311 6.647212 TCACTCATTTTGCTTCGTATGTAG 57.353 37.500 0.00 0.00 0.00 2.74
2163 2312 7.549134 AGATTCACTCATTTTGCTTCGTATGTA 59.451 33.333 0.00 0.00 0.00 2.29
2165 2314 6.779117 AGATTCACTCATTTTGCTTCGTATG 58.221 36.000 0.00 0.00 0.00 2.39
2166 2315 6.992063 AGATTCACTCATTTTGCTTCGTAT 57.008 33.333 0.00 0.00 0.00 3.06
2167 2316 6.871492 TGTAGATTCACTCATTTTGCTTCGTA 59.129 34.615 0.00 0.00 0.00 3.43
2168 2317 5.700832 TGTAGATTCACTCATTTTGCTTCGT 59.299 36.000 0.00 0.00 0.00 3.85
2170 2319 7.020010 CAGTGTAGATTCACTCATTTTGCTTC 58.980 38.462 0.00 0.00 45.37 3.86
2171 2320 6.488006 ACAGTGTAGATTCACTCATTTTGCTT 59.512 34.615 0.00 0.00 45.37 3.91
2179 2540 8.301720 ACGTATTTTACAGTGTAGATTCACTCA 58.698 33.333 2.68 0.00 45.37 3.41
2180 2541 8.684973 ACGTATTTTACAGTGTAGATTCACTC 57.315 34.615 2.68 0.00 45.37 3.51
2200 2561 9.610705 ACTACATACGGATGAATATAGACGTAT 57.389 33.333 16.36 0.00 45.07 3.06
2201 2562 8.876790 CACTACATACGGATGAATATAGACGTA 58.123 37.037 16.36 0.00 40.43 3.57
2203 2564 7.148289 ACCACTACATACGGATGAATATAGACG 60.148 40.741 16.36 4.03 36.48 4.18
2205 2566 8.645814 AACCACTACATACGGATGAATATAGA 57.354 34.615 16.36 0.00 36.48 1.98
2208 2569 9.031537 TCATAACCACTACATACGGATGAATAT 57.968 33.333 16.36 0.00 36.48 1.28
2213 2574 6.200286 GTGTTCATAACCACTACATACGGATG 59.800 42.308 5.94 5.94 39.16 3.51
2214 2575 6.127281 TGTGTTCATAACCACTACATACGGAT 60.127 38.462 0.00 0.00 0.00 4.18
2216 2577 5.412640 TGTGTTCATAACCACTACATACGG 58.587 41.667 0.00 0.00 0.00 4.02
2217 2578 6.954616 TTGTGTTCATAACCACTACATACG 57.045 37.500 0.00 0.00 0.00 3.06
2218 2579 9.607285 CTTTTTGTGTTCATAACCACTACATAC 57.393 33.333 0.00 0.00 0.00 2.39
2219 2580 8.788806 CCTTTTTGTGTTCATAACCACTACATA 58.211 33.333 0.00 0.00 0.00 2.29
2222 2583 7.227910 TCTCCTTTTTGTGTTCATAACCACTAC 59.772 37.037 0.00 0.00 0.00 2.73
2223 2584 7.227910 GTCTCCTTTTTGTGTTCATAACCACTA 59.772 37.037 0.00 0.00 0.00 2.74
2224 2585 6.039382 GTCTCCTTTTTGTGTTCATAACCACT 59.961 38.462 0.00 0.00 0.00 4.00
2225 2586 6.183360 TGTCTCCTTTTTGTGTTCATAACCAC 60.183 38.462 0.00 0.00 0.00 4.16
2226 2587 5.888724 TGTCTCCTTTTTGTGTTCATAACCA 59.111 36.000 0.00 0.00 0.00 3.67
2229 2590 7.502226 AGATGTGTCTCCTTTTTGTGTTCATAA 59.498 33.333 0.00 0.00 0.00 1.90
2230 2591 6.998074 AGATGTGTCTCCTTTTTGTGTTCATA 59.002 34.615 0.00 0.00 0.00 2.15
2231 2592 5.829924 AGATGTGTCTCCTTTTTGTGTTCAT 59.170 36.000 0.00 0.00 0.00 2.57
2233 2594 5.757850 AGATGTGTCTCCTTTTTGTGTTC 57.242 39.130 0.00 0.00 0.00 3.18
2234 2595 7.823745 AATAGATGTGTCTCCTTTTTGTGTT 57.176 32.000 0.00 0.00 35.87 3.32
2235 2596 8.950210 CATAATAGATGTGTCTCCTTTTTGTGT 58.050 33.333 0.00 0.00 35.87 3.72
2236 2597 9.166173 TCATAATAGATGTGTCTCCTTTTTGTG 57.834 33.333 0.00 0.00 35.87 3.33
2237 2598 9.388506 CTCATAATAGATGTGTCTCCTTTTTGT 57.611 33.333 0.00 0.00 35.87 2.83
2239 2600 8.772250 TCCTCATAATAGATGTGTCTCCTTTTT 58.228 33.333 0.00 0.00 35.87 1.94
2240 2601 8.324191 TCCTCATAATAGATGTGTCTCCTTTT 57.676 34.615 0.00 0.00 35.87 2.27
2241 2602 7.921041 TCCTCATAATAGATGTGTCTCCTTT 57.079 36.000 0.00 0.00 35.87 3.11
2242 2603 9.253832 CTATCCTCATAATAGATGTGTCTCCTT 57.746 37.037 0.00 0.00 35.87 3.36
2243 2604 8.619281 TCTATCCTCATAATAGATGTGTCTCCT 58.381 37.037 0.00 0.00 35.87 3.69
2244 2605 8.815565 TCTATCCTCATAATAGATGTGTCTCC 57.184 38.462 0.00 0.00 35.87 3.71
2246 2607 9.593565 TGTTCTATCCTCATAATAGATGTGTCT 57.406 33.333 0.00 0.00 36.03 3.41
2248 2609 9.988815 GTTGTTCTATCCTCATAATAGATGTGT 57.011 33.333 0.00 0.00 36.03 3.72
2253 2614 9.868160 TCTGAGTTGTTCTATCCTCATAATAGA 57.132 33.333 0.00 0.00 34.66 1.98
2256 2617 8.986991 ACTTCTGAGTTGTTCTATCCTCATAAT 58.013 33.333 0.00 0.00 33.77 1.28
2257 2618 8.367660 ACTTCTGAGTTGTTCTATCCTCATAA 57.632 34.615 0.00 0.00 33.77 1.90
2260 2621 6.153000 GGTACTTCTGAGTTGTTCTATCCTCA 59.847 42.308 0.00 0.00 37.33 3.86
2261 2622 6.378848 AGGTACTTCTGAGTTGTTCTATCCTC 59.621 42.308 0.00 0.00 37.33 3.71
2262 2623 6.153680 CAGGTACTTCTGAGTTGTTCTATCCT 59.846 42.308 0.00 0.00 34.60 3.24
2263 2624 6.071278 ACAGGTACTTCTGAGTTGTTCTATCC 60.071 42.308 6.18 0.00 34.60 2.59
2264 2625 6.809196 CACAGGTACTTCTGAGTTGTTCTATC 59.191 42.308 6.18 0.00 34.60 2.08
2266 2627 5.831525 TCACAGGTACTTCTGAGTTGTTCTA 59.168 40.000 6.18 0.00 34.60 2.10
2267 2628 4.649674 TCACAGGTACTTCTGAGTTGTTCT 59.350 41.667 6.18 0.00 34.60 3.01
2268 2629 4.945246 TCACAGGTACTTCTGAGTTGTTC 58.055 43.478 6.18 0.00 34.60 3.18
2269 2630 5.353394 TTCACAGGTACTTCTGAGTTGTT 57.647 39.130 6.18 0.00 34.60 2.83
2270 2631 5.353394 TTTCACAGGTACTTCTGAGTTGT 57.647 39.130 6.18 0.00 34.60 3.32
2272 2633 5.990668 AGTTTTCACAGGTACTTCTGAGTT 58.009 37.500 6.18 0.00 34.60 3.01
2273 2634 5.615925 AGTTTTCACAGGTACTTCTGAGT 57.384 39.130 6.18 0.00 34.60 3.41
2275 2636 6.097839 ACACTAGTTTTCACAGGTACTTCTGA 59.902 38.462 6.18 0.00 34.60 3.27
2276 2637 6.281405 ACACTAGTTTTCACAGGTACTTCTG 58.719 40.000 0.00 0.00 34.60 3.02
2277 2638 6.481434 ACACTAGTTTTCACAGGTACTTCT 57.519 37.500 0.00 0.00 34.60 2.85
2278 2639 6.018180 CCAACACTAGTTTTCACAGGTACTTC 60.018 42.308 0.00 0.00 32.56 3.01
2279 2640 5.820947 CCAACACTAGTTTTCACAGGTACTT 59.179 40.000 0.00 0.00 32.56 2.24
2280 2641 5.365619 CCAACACTAGTTTTCACAGGTACT 58.634 41.667 0.00 0.00 35.09 2.73
2281 2642 4.514066 CCCAACACTAGTTTTCACAGGTAC 59.486 45.833 0.00 0.00 35.28 3.34
2282 2643 4.445162 CCCCAACACTAGTTTTCACAGGTA 60.445 45.833 0.00 0.00 35.28 3.08
2283 2644 3.551846 CCCAACACTAGTTTTCACAGGT 58.448 45.455 0.00 0.00 35.28 4.00
2284 2645 2.884639 CCCCAACACTAGTTTTCACAGG 59.115 50.000 0.00 0.00 35.28 4.00
2285 2646 3.551846 ACCCCAACACTAGTTTTCACAG 58.448 45.455 0.00 0.00 35.28 3.66
2286 2647 3.655615 ACCCCAACACTAGTTTTCACA 57.344 42.857 0.00 0.00 35.28 3.58
2287 2648 4.514066 CACTACCCCAACACTAGTTTTCAC 59.486 45.833 0.00 0.00 35.28 3.18
2288 2649 4.710324 CACTACCCCAACACTAGTTTTCA 58.290 43.478 0.00 0.00 35.28 2.69
2290 2651 3.483421 GCACTACCCCAACACTAGTTTT 58.517 45.455 0.00 0.00 35.28 2.43
2291 2652 2.224695 GGCACTACCCCAACACTAGTTT 60.225 50.000 0.00 0.00 35.28 2.66
2292 2653 1.350019 GGCACTACCCCAACACTAGTT 59.650 52.381 0.00 0.00 38.88 2.24
2293 2654 0.981943 GGCACTACCCCAACACTAGT 59.018 55.000 0.00 0.00 0.00 2.57
2295 2656 0.832983 ACGGCACTACCCCAACACTA 60.833 55.000 0.00 0.00 33.26 2.74
2296 2657 1.702022 AACGGCACTACCCCAACACT 61.702 55.000 0.00 0.00 33.26 3.55
2297 2658 1.228033 AACGGCACTACCCCAACAC 60.228 57.895 0.00 0.00 33.26 3.32
2298 2659 1.071814 GAACGGCACTACCCCAACA 59.928 57.895 0.00 0.00 33.26 3.33
2299 2660 1.673337 GGAACGGCACTACCCCAAC 60.673 63.158 0.00 0.00 33.26 3.77
2300 2661 1.706995 TTGGAACGGCACTACCCCAA 61.707 55.000 0.00 0.00 35.56 4.12
2301 2662 1.706995 TTTGGAACGGCACTACCCCA 61.707 55.000 0.00 0.00 33.26 4.96
2302 2663 1.073548 TTTGGAACGGCACTACCCC 59.926 57.895 0.00 0.00 33.26 4.95
2305 2666 1.798813 CTCTGTTTGGAACGGCACTAC 59.201 52.381 0.00 0.00 37.69 2.73
2306 2667 1.876416 GCTCTGTTTGGAACGGCACTA 60.876 52.381 0.00 0.00 37.69 2.74
2309 2670 1.153066 TGCTCTGTTTGGAACGGCA 60.153 52.632 0.00 0.00 37.69 5.69
2310 2671 1.166531 ACTGCTCTGTTTGGAACGGC 61.167 55.000 0.00 0.00 37.69 5.68
2311 2672 1.264288 GAACTGCTCTGTTTGGAACGG 59.736 52.381 0.00 0.00 39.17 4.44
2313 2674 4.997395 TCTATGAACTGCTCTGTTTGGAAC 59.003 41.667 0.00 0.00 0.00 3.62
2314 2675 5.227569 TCTATGAACTGCTCTGTTTGGAA 57.772 39.130 0.00 0.00 0.00 3.53
2315 2676 4.890158 TCTATGAACTGCTCTGTTTGGA 57.110 40.909 0.00 0.00 0.00 3.53
2316 2677 6.506500 AATTCTATGAACTGCTCTGTTTGG 57.493 37.500 0.00 0.00 0.00 3.28
2318 2679 8.621532 TGTAAATTCTATGAACTGCTCTGTTT 57.378 30.769 0.00 0.00 0.00 2.83
2319 2680 8.621532 TTGTAAATTCTATGAACTGCTCTGTT 57.378 30.769 0.00 0.00 0.00 3.16
2320 2681 8.621532 TTTGTAAATTCTATGAACTGCTCTGT 57.378 30.769 0.00 0.00 0.00 3.41
2321 2682 9.897744 TTTTTGTAAATTCTATGAACTGCTCTG 57.102 29.630 0.00 0.00 0.00 3.35
2323 2684 9.346725 CCTTTTTGTAAATTCTATGAACTGCTC 57.653 33.333 0.00 0.00 0.00 4.26
2325 2686 8.915654 CACCTTTTTGTAAATTCTATGAACTGC 58.084 33.333 0.00 0.00 0.00 4.40
2328 2689 8.810652 TGCACCTTTTTGTAAATTCTATGAAC 57.189 30.769 0.00 0.00 0.00 3.18
2329 2690 9.823647 TTTGCACCTTTTTGTAAATTCTATGAA 57.176 25.926 0.00 0.00 0.00 2.57
2330 2691 9.474920 CTTTGCACCTTTTTGTAAATTCTATGA 57.525 29.630 0.00 0.00 31.70 2.15
2332 2693 7.387673 GGCTTTGCACCTTTTTGTAAATTCTAT 59.612 33.333 0.00 0.00 31.70 1.98
2335 4390 5.295540 TGGCTTTGCACCTTTTTGTAAATTC 59.704 36.000 0.00 0.00 31.70 2.17
2343 4398 4.100808 TGAGTTATGGCTTTGCACCTTTTT 59.899 37.500 0.00 0.00 0.00 1.94
2348 4403 3.658757 TTTGAGTTATGGCTTTGCACC 57.341 42.857 0.00 0.00 0.00 5.01
2349 4404 4.445385 CACTTTTGAGTTATGGCTTTGCAC 59.555 41.667 0.00 0.00 0.00 4.57
2350 4405 4.619973 CACTTTTGAGTTATGGCTTTGCA 58.380 39.130 0.00 0.00 0.00 4.08
2351 4406 3.429881 GCACTTTTGAGTTATGGCTTTGC 59.570 43.478 0.00 0.00 0.00 3.68
2352 4407 3.989817 GGCACTTTTGAGTTATGGCTTTG 59.010 43.478 0.00 0.00 33.35 2.77
2353 4408 3.305335 CGGCACTTTTGAGTTATGGCTTT 60.305 43.478 0.00 0.00 33.92 3.51
2354 4409 2.228822 CGGCACTTTTGAGTTATGGCTT 59.771 45.455 0.00 0.00 33.92 4.35
2355 4410 1.812571 CGGCACTTTTGAGTTATGGCT 59.187 47.619 0.00 0.00 33.92 4.75
2356 4411 1.810151 TCGGCACTTTTGAGTTATGGC 59.190 47.619 0.00 0.00 0.00 4.40
2357 4412 2.420022 CCTCGGCACTTTTGAGTTATGG 59.580 50.000 0.00 0.00 0.00 2.74
2358 4413 3.334691 TCCTCGGCACTTTTGAGTTATG 58.665 45.455 0.00 0.00 0.00 1.90
2359 4414 3.695830 TCCTCGGCACTTTTGAGTTAT 57.304 42.857 0.00 0.00 0.00 1.89
2360 4415 3.478857 TTCCTCGGCACTTTTGAGTTA 57.521 42.857 0.00 0.00 0.00 2.24
2361 4416 2.341846 TTCCTCGGCACTTTTGAGTT 57.658 45.000 0.00 0.00 0.00 3.01
2362 4417 2.158813 TCTTTCCTCGGCACTTTTGAGT 60.159 45.455 0.00 0.00 0.00 3.41
2363 4418 2.481952 CTCTTTCCTCGGCACTTTTGAG 59.518 50.000 0.00 0.00 0.00 3.02
2364 4419 2.104111 TCTCTTTCCTCGGCACTTTTGA 59.896 45.455 0.00 0.00 0.00 2.69
2365 4420 2.481952 CTCTCTTTCCTCGGCACTTTTG 59.518 50.000 0.00 0.00 0.00 2.44
2366 4421 2.772287 CTCTCTTTCCTCGGCACTTTT 58.228 47.619 0.00 0.00 0.00 2.27
2367 4422 1.609320 GCTCTCTTTCCTCGGCACTTT 60.609 52.381 0.00 0.00 0.00 2.66
2369 4424 1.594310 GCTCTCTTTCCTCGGCACT 59.406 57.895 0.00 0.00 0.00 4.40
2370 4425 1.807573 CGCTCTCTTTCCTCGGCAC 60.808 63.158 0.00 0.00 0.00 5.01
2371 4426 2.573869 CGCTCTCTTTCCTCGGCA 59.426 61.111 0.00 0.00 0.00 5.69
2372 4427 2.022240 ATCCGCTCTCTTTCCTCGGC 62.022 60.000 0.00 0.00 39.90 5.54
2373 4428 0.461961 AATCCGCTCTCTTTCCTCGG 59.538 55.000 0.00 0.00 41.30 4.63
2375 4430 1.294857 GCAATCCGCTCTCTTTCCTC 58.705 55.000 0.00 0.00 37.77 3.71
2376 4431 0.107459 GGCAATCCGCTCTCTTTCCT 60.107 55.000 0.00 0.00 41.91 3.36
2377 4432 0.392998 TGGCAATCCGCTCTCTTTCC 60.393 55.000 0.00 0.00 41.91 3.13
2378 4433 1.332997 CATGGCAATCCGCTCTCTTTC 59.667 52.381 0.00 0.00 41.91 2.62
2381 4592 1.525535 GCATGGCAATCCGCTCTCT 60.526 57.895 0.00 0.00 41.91 3.10
2383 4594 0.533755 GTAGCATGGCAATCCGCTCT 60.534 55.000 7.25 0.00 41.91 4.09
2384 4595 0.533755 AGTAGCATGGCAATCCGCTC 60.534 55.000 7.25 1.81 41.91 5.03
2387 4598 4.836125 ATAAAAGTAGCATGGCAATCCG 57.164 40.909 0.00 0.00 34.14 4.18
2391 4602 8.704849 ATAATGGTATAAAAGTAGCATGGCAA 57.295 30.769 0.00 0.00 40.74 4.52
2392 4603 8.704849 AATAATGGTATAAAAGTAGCATGGCA 57.295 30.769 0.00 0.00 40.74 4.92


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

AutoCloner maintained by Alex Coulton.