Multiple sequence alignment - TraesCS6A01G175600

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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 TraesCS6A01G175600 chr6A 100.000 2272 0 0 1 2272 190747300 190749571 0.000000e+00 4196.0
1 TraesCS6A01G175600 chr6A 98.817 169 2 0 1 169 190670907 190671075 3.670000e-78 302.0
2 TraesCS6A01G175600 chr2B 92.420 1306 91 4 1 1302 119207428 119206127 0.000000e+00 1857.0
3 TraesCS6A01G175600 chr2B 86.250 80 11 0 1311 1390 504196261 504196182 1.120000e-13 87.9
4 TraesCS6A01G175600 chr7B 92.220 1311 95 4 1 1308 716504288 716505594 0.000000e+00 1849.0
5 TraesCS6A01G175600 chr1B 91.794 1304 100 5 1 1302 539834558 539835856 0.000000e+00 1808.0
6 TraesCS6A01G175600 chr1B 95.833 120 5 0 2003 2122 669017052 669017171 6.400000e-46 195.0
7 TraesCS6A01G175600 chr7A 89.674 1317 130 6 1 1313 445629708 445628394 0.000000e+00 1674.0
8 TraesCS6A01G175600 chr7A 79.365 126 19 7 1438 1561 202218729 202218849 5.200000e-12 82.4
9 TraesCS6A01G175600 chr6B 87.450 1259 135 12 50 1305 591574886 591576124 0.000000e+00 1428.0
10 TraesCS6A01G175600 chr6B 87.194 695 73 8 1311 2004 276730704 276730025 0.000000e+00 776.0
11 TraesCS6A01G175600 chr6B 96.667 120 4 0 2003 2122 240304100 240303981 1.380000e-47 200.0
12 TraesCS6A01G175600 chr6D 87.167 1200 125 16 52 1248 395692487 395693660 0.000000e+00 1336.0
13 TraesCS6A01G175600 chr6D 86.804 682 87 3 1323 2004 152188782 152188104 0.000000e+00 758.0
14 TraesCS6A01G175600 chr5B 87.993 1116 128 5 190 1303 271313322 271312211 0.000000e+00 1314.0
15 TraesCS6A01G175600 chr5B 91.304 138 11 1 2000 2136 439951846 439951983 1.070000e-43 187.0
16 TraesCS6A01G175600 chr4A 96.653 478 13 3 834 1310 75219800 75220275 0.000000e+00 791.0
17 TraesCS6A01G175600 chr4A 77.329 1288 282 9 3 1284 634433502 634434785 0.000000e+00 752.0
18 TraesCS6A01G175600 chr4A 80.797 276 45 8 130 401 19527700 19527429 2.290000e-50 209.0
19 TraesCS6A01G175600 chr3D 78.501 1121 233 8 187 1302 533687332 533688449 0.000000e+00 728.0
20 TraesCS6A01G175600 chr3B 76.183 1247 279 17 66 1302 731116937 731118175 1.900000e-180 641.0
21 TraesCS6A01G175600 chr3B 93.233 133 9 0 2002 2134 45520878 45520746 1.780000e-46 196.0
22 TraesCS6A01G175600 chr3A 93.939 396 22 2 916 1310 716108364 716107970 4.180000e-167 597.0
23 TraesCS6A01G175600 chr3A 92.481 133 10 0 2002 2134 569426551 569426419 8.280000e-45 191.0
24 TraesCS6A01G175600 chr1A 93.846 130 8 0 1993 2122 27289560 27289689 1.780000e-46 196.0
25 TraesCS6A01G175600 chr4B 93.077 130 9 0 2002 2131 294107702 294107573 8.280000e-45 191.0
26 TraesCS6A01G175600 chr2A 94.400 125 6 1 1998 2122 767942978 767943101 8.280000e-45 191.0
27 TraesCS6A01G175600 chr2A 89.726 146 11 4 2003 2148 293062987 293062846 1.390000e-42 183.0


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 TraesCS6A01G175600 chr6A 190747300 190749571 2271 False 4196 4196 100.000 1 2272 1 chr6A.!!$F2 2271
1 TraesCS6A01G175600 chr2B 119206127 119207428 1301 True 1857 1857 92.420 1 1302 1 chr2B.!!$R1 1301
2 TraesCS6A01G175600 chr7B 716504288 716505594 1306 False 1849 1849 92.220 1 1308 1 chr7B.!!$F1 1307
3 TraesCS6A01G175600 chr1B 539834558 539835856 1298 False 1808 1808 91.794 1 1302 1 chr1B.!!$F1 1301
4 TraesCS6A01G175600 chr7A 445628394 445629708 1314 True 1674 1674 89.674 1 1313 1 chr7A.!!$R1 1312
5 TraesCS6A01G175600 chr6B 591574886 591576124 1238 False 1428 1428 87.450 50 1305 1 chr6B.!!$F1 1255
6 TraesCS6A01G175600 chr6B 276730025 276730704 679 True 776 776 87.194 1311 2004 1 chr6B.!!$R2 693
7 TraesCS6A01G175600 chr6D 395692487 395693660 1173 False 1336 1336 87.167 52 1248 1 chr6D.!!$F1 1196
8 TraesCS6A01G175600 chr6D 152188104 152188782 678 True 758 758 86.804 1323 2004 1 chr6D.!!$R1 681
9 TraesCS6A01G175600 chr5B 271312211 271313322 1111 True 1314 1314 87.993 190 1303 1 chr5B.!!$R1 1113
10 TraesCS6A01G175600 chr4A 634433502 634434785 1283 False 752 752 77.329 3 1284 1 chr4A.!!$F2 1281
11 TraesCS6A01G175600 chr3D 533687332 533688449 1117 False 728 728 78.501 187 1302 1 chr3D.!!$F1 1115
12 TraesCS6A01G175600 chr3B 731116937 731118175 1238 False 641 641 76.183 66 1302 1 chr3B.!!$F1 1236

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
510 526 0.315706 GCTCGCATGCAAGACGATTC 60.316 55.0 19.57 0.0 34.94 2.52 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2121 2171 0.035439 CCGCTTCCCAACTACCACAT 60.035 55.0 0.0 0.0 0.0 3.21 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
21 22 2.237643 TCCCAGGTACAATACGCATGTT 59.762 45.455 0.00 0.00 32.27 2.71
34 35 4.008074 ACGCATGTTCCCTATGATTAGG 57.992 45.455 0.00 0.00 44.17 2.69
48 49 2.511218 TGATTAGGCCAGCCAATTCTCT 59.489 45.455 12.03 0.00 38.92 3.10
52 53 3.220674 AGGCCAGCCAATTCTCTAATC 57.779 47.619 12.03 0.00 38.92 1.75
158 159 5.467063 GCAGAGGCTATCTTAAACATACCAC 59.533 44.000 0.00 0.00 35.47 4.16
218 219 5.163550 GCTTTTGAAACCTCAGGTGTTTACT 60.164 40.000 0.00 0.00 36.13 2.24
219 220 6.627287 GCTTTTGAAACCTCAGGTGTTTACTT 60.627 38.462 0.00 0.00 36.13 2.24
220 221 6.844097 TTTGAAACCTCAGGTGTTTACTTT 57.156 33.333 0.00 0.00 36.13 2.66
221 222 5.828299 TGAAACCTCAGGTGTTTACTTTG 57.172 39.130 0.00 0.00 36.13 2.77
299 304 4.814294 CGGCTACCGGCACCTCAC 62.814 72.222 0.00 0.00 44.15 3.51
315 320 3.006323 ACCTCACAGACAGATCAACAGAC 59.994 47.826 0.00 0.00 0.00 3.51
394 399 2.102588 AGTAATCCGTGGAATTCTCCCG 59.897 50.000 5.23 5.33 41.64 5.14
510 526 0.315706 GCTCGCATGCAAGACGATTC 60.316 55.000 19.57 0.00 34.94 2.52
632 657 2.785679 ACGCGCAAAGATTATTTCAGC 58.214 42.857 5.73 0.00 0.00 4.26
647 672 9.231297 GATTATTTCAGCTATGTGGGCTATTTA 57.769 33.333 0.00 0.00 38.03 1.40
672 697 2.515057 TGCAACCGGTGGACACAC 60.515 61.111 15.02 0.00 46.97 3.82
757 782 3.397482 GAGATCCCATGTGTAGATGCAC 58.603 50.000 0.00 0.00 39.65 4.57
934 959 0.747644 TATTACCGACCCGCTCGTCA 60.748 55.000 1.60 0.00 41.18 4.35
1099 1144 6.014771 TGGTAGAGATTGGAGAGCTTACTA 57.985 41.667 0.00 0.00 0.00 1.82
1158 1206 0.397816 AGCTAATCTCCCGGCTCACT 60.398 55.000 0.00 0.00 0.00 3.41
1210 1258 2.771943 TGACTGAGAGTTGGTTGGACTT 59.228 45.455 0.00 0.00 0.00 3.01
1290 1338 6.037720 TGTTTGAATAAAGCTCTCACGTTTCA 59.962 34.615 0.00 0.00 0.00 2.69
1347 1395 7.350382 TGTATAATAGGCTGACCCAAAATTCA 58.650 34.615 0.00 0.00 36.11 2.57
1348 1396 7.836685 TGTATAATAGGCTGACCCAAAATTCAA 59.163 33.333 0.00 0.00 36.11 2.69
1349 1397 7.732222 ATAATAGGCTGACCCAAAATTCAAA 57.268 32.000 0.00 0.00 36.11 2.69
1351 1399 2.634453 AGGCTGACCCAAAATTCAAAGG 59.366 45.455 0.00 0.00 36.11 3.11
1358 1406 1.419387 CCAAAATTCAAAGGTGGGCCA 59.581 47.619 0.00 0.00 37.19 5.36
1361 1409 0.178975 AATTCAAAGGTGGGCCACGA 60.179 50.000 29.18 18.23 34.83 4.35
1362 1410 0.039618 ATTCAAAGGTGGGCCACGAT 59.960 50.000 29.18 18.21 34.83 3.73
1363 1411 0.893270 TTCAAAGGTGGGCCACGATG 60.893 55.000 29.18 24.98 34.83 3.84
1377 1425 4.722700 GATGCACCCTGGCCACGT 62.723 66.667 0.00 0.00 0.00 4.49
1381 1429 3.286751 CACCCTGGCCACGTTGTG 61.287 66.667 0.00 2.80 0.00 3.33
1390 1438 3.345808 CACGTTGTGGCTCCACCG 61.346 66.667 15.76 14.52 45.63 4.94
1424 1472 7.068716 GCAGTGGTGGATCTAGGAATTTAAAAT 59.931 37.037 0.00 0.00 0.00 1.82
1428 1476 8.787818 TGGTGGATCTAGGAATTTAAAATAGGT 58.212 33.333 0.00 0.00 0.00 3.08
1429 1477 9.286170 GGTGGATCTAGGAATTTAAAATAGGTC 57.714 37.037 0.00 0.00 0.00 3.85
1432 1480 9.508642 GGATCTAGGAATTTAAAATAGGTCAGG 57.491 37.037 11.97 0.00 0.00 3.86
1445 1494 8.507524 AAAATAGGTCAGGCTATCTACAAAAC 57.492 34.615 0.00 0.00 0.00 2.43
1634 1684 9.200817 ACATTTTAACATCCCTTGCATTAGTAT 57.799 29.630 0.00 0.00 0.00 2.12
1638 1688 8.815565 TTAACATCCCTTGCATTAGTATCAAA 57.184 30.769 0.00 0.00 0.00 2.69
1709 1759 5.047660 CCGAAATTGACAAAATTAGGGACCA 60.048 40.000 0.00 0.00 0.00 4.02
1719 1769 8.442660 ACAAAATTAGGGACCATGGAAATTTA 57.557 30.769 21.47 1.18 0.00 1.40
1724 1774 7.715267 TTAGGGACCATGGAAATTTAGGATA 57.285 36.000 21.47 0.00 0.00 2.59
1739 1789 8.882415 AATTTAGGATAACCGTACATGTGTAG 57.118 34.615 9.11 0.00 41.83 2.74
1740 1790 4.317671 AGGATAACCGTACATGTGTAGC 57.682 45.455 9.11 0.00 41.83 3.58
1774 1824 2.123425 CGGTGGGAGGGCTAGCTA 60.123 66.667 15.72 0.00 0.00 3.32
1786 1836 2.363795 TAGCTAGCAGCCGGTGGT 60.364 61.111 18.83 7.53 43.77 4.16
1787 1837 2.356818 CTAGCTAGCAGCCGGTGGTC 62.357 65.000 18.83 0.00 43.77 4.02
1870 1920 2.280823 GACCGCCGAACAGGACTAGG 62.281 65.000 0.00 0.00 45.00 3.02
1874 1924 1.041437 GCCGAACAGGACTAGGCTAT 58.959 55.000 0.00 0.00 45.00 2.97
1902 1952 4.314440 GCTGGGTGCGGTGAGTGA 62.314 66.667 0.00 0.00 0.00 3.41
1925 1975 3.268603 CGTGGCAGTTGCGTGTGA 61.269 61.111 0.00 0.00 43.26 3.58
1932 1982 1.071471 AGTTGCGTGTGAGGAAGGG 59.929 57.895 0.00 0.00 0.00 3.95
1937 1987 4.373116 GTGTGAGGAAGGGCGCGA 62.373 66.667 12.10 0.00 0.00 5.87
1951 2001 2.892425 GCGACGAGGCAGGGAATG 60.892 66.667 0.00 0.00 0.00 2.67
1962 2012 2.272146 GGGAATGAAGCGGCAGGA 59.728 61.111 1.45 0.00 0.00 3.86
2016 2066 4.781264 AGGTACTCCCTCCGTTCC 57.219 61.111 0.00 0.00 40.71 3.62
2017 2067 1.379576 AGGTACTCCCTCCGTTCCG 60.380 63.158 0.00 0.00 40.71 4.30
2018 2068 1.379044 GGTACTCCCTCCGTTCCGA 60.379 63.158 0.00 0.00 0.00 4.55
2019 2069 0.967380 GGTACTCCCTCCGTTCCGAA 60.967 60.000 0.00 0.00 0.00 4.30
2020 2070 1.109609 GTACTCCCTCCGTTCCGAAT 58.890 55.000 0.00 0.00 0.00 3.34
2021 2071 1.479730 GTACTCCCTCCGTTCCGAATT 59.520 52.381 0.00 0.00 0.00 2.17
2022 2072 1.856629 ACTCCCTCCGTTCCGAATTA 58.143 50.000 0.00 0.00 0.00 1.40
2023 2073 1.479730 ACTCCCTCCGTTCCGAATTAC 59.520 52.381 0.00 0.00 0.00 1.89
2024 2074 1.755380 CTCCCTCCGTTCCGAATTACT 59.245 52.381 0.00 0.00 0.00 2.24
2025 2075 2.167900 CTCCCTCCGTTCCGAATTACTT 59.832 50.000 0.00 0.00 0.00 2.24
2026 2076 2.093869 TCCCTCCGTTCCGAATTACTTG 60.094 50.000 0.00 0.00 0.00 3.16
2027 2077 2.354403 CCCTCCGTTCCGAATTACTTGT 60.354 50.000 0.00 0.00 0.00 3.16
2028 2078 2.928116 CCTCCGTTCCGAATTACTTGTC 59.072 50.000 0.00 0.00 0.00 3.18
2029 2079 3.368116 CCTCCGTTCCGAATTACTTGTCT 60.368 47.826 0.00 0.00 0.00 3.41
2030 2080 4.243270 CTCCGTTCCGAATTACTTGTCTT 58.757 43.478 0.00 0.00 0.00 3.01
2031 2081 3.991773 TCCGTTCCGAATTACTTGTCTTG 59.008 43.478 0.00 0.00 0.00 3.02
2032 2082 3.124636 CCGTTCCGAATTACTTGTCTTGG 59.875 47.826 0.00 0.00 0.00 3.61
2033 2083 3.991773 CGTTCCGAATTACTTGTCTTGGA 59.008 43.478 0.00 0.00 0.00 3.53
2034 2084 4.630069 CGTTCCGAATTACTTGTCTTGGAT 59.370 41.667 0.00 0.00 0.00 3.41
2035 2085 5.121768 CGTTCCGAATTACTTGTCTTGGATT 59.878 40.000 0.00 0.00 0.00 3.01
2036 2086 6.348213 CGTTCCGAATTACTTGTCTTGGATTT 60.348 38.462 0.00 0.00 0.00 2.17
2037 2087 6.494893 TCCGAATTACTTGTCTTGGATTTG 57.505 37.500 0.00 0.00 0.00 2.32
2038 2088 6.001460 TCCGAATTACTTGTCTTGGATTTGT 58.999 36.000 0.00 0.00 0.00 2.83
2039 2089 6.148811 TCCGAATTACTTGTCTTGGATTTGTC 59.851 38.462 0.00 0.00 0.00 3.18
2040 2090 6.149474 CCGAATTACTTGTCTTGGATTTGTCT 59.851 38.462 0.00 0.00 0.00 3.41
2041 2091 7.333423 CCGAATTACTTGTCTTGGATTTGTCTA 59.667 37.037 0.00 0.00 0.00 2.59
2042 2092 8.383619 CGAATTACTTGTCTTGGATTTGTCTAG 58.616 37.037 0.00 0.00 0.00 2.43
2043 2093 9.436957 GAATTACTTGTCTTGGATTTGTCTAGA 57.563 33.333 0.00 0.00 0.00 2.43
2044 2094 9.965902 AATTACTTGTCTTGGATTTGTCTAGAT 57.034 29.630 0.00 0.00 0.00 1.98
2046 2096 9.871238 TTACTTGTCTTGGATTTGTCTAGATAC 57.129 33.333 0.00 0.00 0.00 2.24
2047 2097 7.036220 ACTTGTCTTGGATTTGTCTAGATACG 58.964 38.462 0.00 0.00 0.00 3.06
2048 2098 5.902681 TGTCTTGGATTTGTCTAGATACGG 58.097 41.667 0.00 0.00 0.00 4.02
2049 2099 5.655090 TGTCTTGGATTTGTCTAGATACGGA 59.345 40.000 0.00 0.00 0.00 4.69
2050 2100 6.323996 TGTCTTGGATTTGTCTAGATACGGAT 59.676 38.462 0.00 0.00 0.00 4.18
2051 2101 6.642950 GTCTTGGATTTGTCTAGATACGGATG 59.357 42.308 0.00 0.00 0.00 3.51
2052 2102 6.323996 TCTTGGATTTGTCTAGATACGGATGT 59.676 38.462 0.00 0.00 0.00 3.06
2053 2103 7.504574 TCTTGGATTTGTCTAGATACGGATGTA 59.495 37.037 0.00 0.00 34.45 2.29
2054 2104 7.776618 TGGATTTGTCTAGATACGGATGTAT 57.223 36.000 0.00 0.00 43.97 2.29
2094 2144 8.670490 AGTGTTAGATACCTCCATATCTAGACA 58.330 37.037 0.00 11.32 42.43 3.41
2095 2145 9.298250 GTGTTAGATACCTCCATATCTAGACAA 57.702 37.037 0.00 0.00 42.43 3.18
2096 2146 9.877222 TGTTAGATACCTCCATATCTAGACAAA 57.123 33.333 0.00 0.00 42.43 2.83
2100 2150 9.607333 AGATACCTCCATATCTAGACAAATTCA 57.393 33.333 0.00 0.00 39.63 2.57
2103 2153 8.324191 ACCTCCATATCTAGACAAATTCAAGA 57.676 34.615 0.00 0.00 0.00 3.02
2104 2154 8.207545 ACCTCCATATCTAGACAAATTCAAGAC 58.792 37.037 0.00 0.00 0.00 3.01
2105 2155 8.206867 CCTCCATATCTAGACAAATTCAAGACA 58.793 37.037 0.00 0.00 0.00 3.41
2106 2156 9.605275 CTCCATATCTAGACAAATTCAAGACAA 57.395 33.333 0.00 0.00 0.00 3.18
2107 2157 9.605275 TCCATATCTAGACAAATTCAAGACAAG 57.395 33.333 0.00 0.00 0.00 3.16
2108 2158 9.388506 CCATATCTAGACAAATTCAAGACAAGT 57.611 33.333 0.00 0.00 0.00 3.16
2116 2166 9.342308 AGACAAATTCAAGACAAGTAATTCAGA 57.658 29.630 0.00 0.00 0.00 3.27
2117 2167 9.950680 GACAAATTCAAGACAAGTAATTCAGAA 57.049 29.630 0.00 0.00 0.00 3.02
2118 2168 9.736023 ACAAATTCAAGACAAGTAATTCAGAAC 57.264 29.630 0.00 0.00 0.00 3.01
2119 2169 8.895845 CAAATTCAAGACAAGTAATTCAGAACG 58.104 33.333 0.00 0.00 0.00 3.95
2120 2170 6.539649 TTCAAGACAAGTAATTCAGAACGG 57.460 37.500 0.00 0.00 0.00 4.44
2121 2171 5.849510 TCAAGACAAGTAATTCAGAACGGA 58.150 37.500 0.00 0.00 0.00 4.69
2122 2172 6.464222 TCAAGACAAGTAATTCAGAACGGAT 58.536 36.000 0.00 0.00 0.00 4.18
2123 2173 6.368791 TCAAGACAAGTAATTCAGAACGGATG 59.631 38.462 0.00 0.00 0.00 3.51
2124 2174 5.794894 AGACAAGTAATTCAGAACGGATGT 58.205 37.500 0.00 0.00 0.00 3.06
2125 2175 5.639506 AGACAAGTAATTCAGAACGGATGTG 59.360 40.000 0.00 0.00 0.00 3.21
2126 2176 4.695455 ACAAGTAATTCAGAACGGATGTGG 59.305 41.667 0.00 0.00 0.00 4.17
2127 2177 4.553330 AGTAATTCAGAACGGATGTGGT 57.447 40.909 0.00 0.00 0.00 4.16
2128 2178 5.670792 AGTAATTCAGAACGGATGTGGTA 57.329 39.130 0.00 0.00 0.00 3.25
2129 2179 5.661458 AGTAATTCAGAACGGATGTGGTAG 58.339 41.667 0.00 0.00 0.00 3.18
2130 2180 4.553330 AATTCAGAACGGATGTGGTAGT 57.447 40.909 0.00 0.00 0.00 2.73
2131 2181 4.553330 ATTCAGAACGGATGTGGTAGTT 57.447 40.909 0.00 0.00 0.00 2.24
2132 2182 3.313012 TCAGAACGGATGTGGTAGTTG 57.687 47.619 0.00 0.00 0.00 3.16
2133 2183 2.028476 TCAGAACGGATGTGGTAGTTGG 60.028 50.000 0.00 0.00 0.00 3.77
2134 2184 1.278127 AGAACGGATGTGGTAGTTGGG 59.722 52.381 0.00 0.00 0.00 4.12
2135 2185 1.276989 GAACGGATGTGGTAGTTGGGA 59.723 52.381 0.00 0.00 0.00 4.37
2136 2186 1.354101 ACGGATGTGGTAGTTGGGAA 58.646 50.000 0.00 0.00 0.00 3.97
2137 2187 1.278127 ACGGATGTGGTAGTTGGGAAG 59.722 52.381 0.00 0.00 0.00 3.46
2138 2188 1.751437 GGATGTGGTAGTTGGGAAGC 58.249 55.000 0.00 0.00 0.00 3.86
2139 2189 1.369625 GATGTGGTAGTTGGGAAGCG 58.630 55.000 0.00 0.00 0.00 4.68
2140 2190 0.035439 ATGTGGTAGTTGGGAAGCGG 60.035 55.000 0.00 0.00 0.00 5.52
2141 2191 2.038837 GTGGTAGTTGGGAAGCGGC 61.039 63.158 0.00 0.00 0.00 6.53
2142 2192 2.221299 TGGTAGTTGGGAAGCGGCT 61.221 57.895 0.00 0.00 0.00 5.52
2143 2193 1.745489 GGTAGTTGGGAAGCGGCTG 60.745 63.158 1.81 0.00 0.00 4.85
2144 2194 1.745489 GTAGTTGGGAAGCGGCTGG 60.745 63.158 1.81 0.00 0.00 4.85
2145 2195 3.622060 TAGTTGGGAAGCGGCTGGC 62.622 63.158 1.81 0.00 44.05 4.85
2157 2207 3.353836 GCTGGCGGCGAGTTCAAA 61.354 61.111 12.98 0.00 0.00 2.69
2158 2208 2.690778 GCTGGCGGCGAGTTCAAAT 61.691 57.895 12.98 0.00 0.00 2.32
2159 2209 1.366111 GCTGGCGGCGAGTTCAAATA 61.366 55.000 12.98 0.00 0.00 1.40
2160 2210 1.299541 CTGGCGGCGAGTTCAAATAT 58.700 50.000 12.98 0.00 0.00 1.28
2161 2211 1.003545 CTGGCGGCGAGTTCAAATATG 60.004 52.381 12.98 0.00 0.00 1.78
2162 2212 0.307760 GGCGGCGAGTTCAAATATGG 59.692 55.000 12.98 0.00 0.00 2.74
2163 2213 1.295792 GCGGCGAGTTCAAATATGGA 58.704 50.000 12.98 0.00 0.00 3.41
2164 2214 1.668751 GCGGCGAGTTCAAATATGGAA 59.331 47.619 12.98 0.00 0.00 3.53
2165 2215 2.096819 GCGGCGAGTTCAAATATGGAAA 59.903 45.455 12.98 0.00 0.00 3.13
2166 2216 3.788797 GCGGCGAGTTCAAATATGGAAAG 60.789 47.826 12.98 0.00 0.00 2.62
2167 2217 3.695816 GGCGAGTTCAAATATGGAAAGC 58.304 45.455 0.00 0.00 0.00 3.51
2168 2218 3.489229 GGCGAGTTCAAATATGGAAAGCC 60.489 47.826 12.58 12.58 35.76 4.35
2179 2229 0.179073 TGGAAAGCCATAGAGCGAGC 60.179 55.000 0.00 0.00 39.92 5.03
2180 2230 0.179073 GGAAAGCCATAGAGCGAGCA 60.179 55.000 0.00 0.00 38.01 4.26
2181 2231 1.216122 GAAAGCCATAGAGCGAGCAG 58.784 55.000 0.00 0.00 38.01 4.24
2182 2232 0.826715 AAAGCCATAGAGCGAGCAGA 59.173 50.000 0.00 0.00 38.01 4.26
2183 2233 0.388659 AAGCCATAGAGCGAGCAGAG 59.611 55.000 0.00 0.00 38.01 3.35
2184 2234 0.467106 AGCCATAGAGCGAGCAGAGA 60.467 55.000 0.00 0.00 38.01 3.10
2185 2235 0.039256 GCCATAGAGCGAGCAGAGAG 60.039 60.000 0.00 0.00 0.00 3.20
2186 2236 0.597568 CCATAGAGCGAGCAGAGAGG 59.402 60.000 0.00 0.00 0.00 3.69
2187 2237 1.603456 CATAGAGCGAGCAGAGAGGA 58.397 55.000 0.00 0.00 0.00 3.71
2188 2238 1.952990 CATAGAGCGAGCAGAGAGGAA 59.047 52.381 0.00 0.00 0.00 3.36
2189 2239 2.356665 TAGAGCGAGCAGAGAGGAAT 57.643 50.000 0.00 0.00 0.00 3.01
2190 2240 2.356665 AGAGCGAGCAGAGAGGAATA 57.643 50.000 0.00 0.00 0.00 1.75
2191 2241 2.660572 AGAGCGAGCAGAGAGGAATAA 58.339 47.619 0.00 0.00 0.00 1.40
2192 2242 2.622942 AGAGCGAGCAGAGAGGAATAAG 59.377 50.000 0.00 0.00 0.00 1.73
2193 2243 1.686052 AGCGAGCAGAGAGGAATAAGG 59.314 52.381 0.00 0.00 0.00 2.69
2194 2244 1.270041 GCGAGCAGAGAGGAATAAGGG 60.270 57.143 0.00 0.00 0.00 3.95
2195 2245 2.311463 CGAGCAGAGAGGAATAAGGGA 58.689 52.381 0.00 0.00 0.00 4.20
2196 2246 2.035321 CGAGCAGAGAGGAATAAGGGAC 59.965 54.545 0.00 0.00 0.00 4.46
2198 2248 3.037549 AGCAGAGAGGAATAAGGGACTG 58.962 50.000 0.00 0.00 40.86 3.51
2199 2249 2.103941 GCAGAGAGGAATAAGGGACTGG 59.896 54.545 0.00 0.00 40.86 4.00
2200 2250 2.703007 CAGAGAGGAATAAGGGACTGGG 59.297 54.545 0.00 0.00 40.86 4.45
2201 2251 1.418264 GAGAGGAATAAGGGACTGGGC 59.582 57.143 0.00 0.00 40.86 5.36
2202 2252 0.474614 GAGGAATAAGGGACTGGGCC 59.525 60.000 0.00 0.00 40.86 5.80
2203 2253 0.253630 AGGAATAAGGGACTGGGCCA 60.254 55.000 5.85 5.85 40.86 5.36
2204 2254 0.106669 GGAATAAGGGACTGGGCCAC 60.107 60.000 0.00 0.00 40.86 5.01
2205 2255 0.919710 GAATAAGGGACTGGGCCACT 59.080 55.000 0.00 0.00 40.86 4.00
2206 2256 0.919710 AATAAGGGACTGGGCCACTC 59.080 55.000 0.00 2.77 40.86 3.51
2207 2257 1.338136 ATAAGGGACTGGGCCACTCG 61.338 60.000 0.00 0.00 40.86 4.18
2211 2261 4.394712 GACTGGGCCACTCGGGTG 62.395 72.222 8.97 8.97 42.65 4.61
2212 2262 4.954118 ACTGGGCCACTCGGGTGA 62.954 66.667 19.37 0.00 45.61 4.02
2213 2263 4.087892 CTGGGCCACTCGGGTGAG 62.088 72.222 19.37 8.37 45.61 3.51
2221 2271 4.891566 CTCGGGTGAGTCCTTTCG 57.108 61.111 0.00 0.00 37.46 3.46
2222 2272 1.446272 CTCGGGTGAGTCCTTTCGC 60.446 63.158 0.00 0.00 37.46 4.70
2223 2273 2.154798 CTCGGGTGAGTCCTTTCGCA 62.155 60.000 0.00 0.00 37.46 5.10
2224 2274 2.027625 CGGGTGAGTCCTTTCGCAC 61.028 63.158 0.00 0.00 37.39 5.34
2225 2275 3.967715 GGTGAGTCCTTTCGCACC 58.032 61.111 0.00 0.00 46.92 5.01
2226 2276 4.771127 GTGAGTCCTTTCGCACCA 57.229 55.556 0.00 0.00 33.31 4.17
2227 2277 2.533318 GTGAGTCCTTTCGCACCAG 58.467 57.895 0.00 0.00 33.31 4.00
2228 2278 0.951040 GTGAGTCCTTTCGCACCAGG 60.951 60.000 0.00 0.00 33.31 4.45
2229 2279 1.376037 GAGTCCTTTCGCACCAGGG 60.376 63.158 0.00 0.00 0.00 4.45
2230 2280 1.827399 GAGTCCTTTCGCACCAGGGA 61.827 60.000 0.00 0.00 34.56 4.20
2231 2281 1.671379 GTCCTTTCGCACCAGGGAC 60.671 63.158 0.00 0.00 39.41 4.46
2232 2282 2.742372 CCTTTCGCACCAGGGACG 60.742 66.667 0.00 0.00 36.32 4.79
2233 2283 3.423154 CTTTCGCACCAGGGACGC 61.423 66.667 0.00 0.00 36.32 5.19
2234 2284 3.883744 CTTTCGCACCAGGGACGCT 62.884 63.158 0.00 0.00 36.32 5.07
2235 2285 2.501223 CTTTCGCACCAGGGACGCTA 62.501 60.000 0.00 0.00 36.32 4.26
2236 2286 2.501223 TTTCGCACCAGGGACGCTAG 62.501 60.000 0.00 0.00 36.32 3.42
2237 2287 3.449227 CGCACCAGGGACGCTAGA 61.449 66.667 0.00 0.00 0.00 2.43
2238 2288 2.184579 GCACCAGGGACGCTAGAC 59.815 66.667 0.00 0.00 0.00 2.59
2239 2289 2.646175 GCACCAGGGACGCTAGACA 61.646 63.158 0.00 0.00 0.00 3.41
2240 2290 1.513158 CACCAGGGACGCTAGACAG 59.487 63.158 0.00 0.00 0.00 3.51
2241 2291 2.352032 ACCAGGGACGCTAGACAGC 61.352 63.158 0.00 0.00 44.90 4.40
2242 2292 2.055042 CCAGGGACGCTAGACAGCT 61.055 63.158 0.00 0.00 46.26 4.24
2243 2293 1.608717 CCAGGGACGCTAGACAGCTT 61.609 60.000 0.00 0.00 46.26 3.74
2244 2294 0.459237 CAGGGACGCTAGACAGCTTG 60.459 60.000 0.00 0.00 46.26 4.01
2245 2295 0.612174 AGGGACGCTAGACAGCTTGA 60.612 55.000 0.00 0.00 46.26 3.02
2246 2296 0.461961 GGGACGCTAGACAGCTTGAT 59.538 55.000 0.00 0.00 46.26 2.57
2247 2297 1.565305 GGACGCTAGACAGCTTGATG 58.435 55.000 0.00 0.00 46.26 3.07
2248 2298 1.565305 GACGCTAGACAGCTTGATGG 58.435 55.000 0.00 0.00 46.26 3.51
2249 2299 0.176680 ACGCTAGACAGCTTGATGGG 59.823 55.000 0.00 0.00 46.26 4.00
2250 2300 1.156645 CGCTAGACAGCTTGATGGGC 61.157 60.000 0.00 0.00 46.26 5.36
2251 2301 0.179936 GCTAGACAGCTTGATGGGCT 59.820 55.000 0.00 0.00 44.93 5.19
2252 2302 1.407989 GCTAGACAGCTTGATGGGCTT 60.408 52.381 0.00 0.00 44.93 4.35
2253 2303 2.158900 GCTAGACAGCTTGATGGGCTTA 60.159 50.000 0.00 0.00 44.93 3.09
2254 2304 3.495806 GCTAGACAGCTTGATGGGCTTAT 60.496 47.826 0.00 0.00 44.93 1.73
2255 2305 3.659183 AGACAGCTTGATGGGCTTATT 57.341 42.857 0.00 0.00 38.03 1.40
2256 2306 3.973425 AGACAGCTTGATGGGCTTATTT 58.027 40.909 0.00 0.00 38.03 1.40
2257 2307 3.698040 AGACAGCTTGATGGGCTTATTTG 59.302 43.478 0.00 0.00 38.03 2.32
2258 2308 3.434309 ACAGCTTGATGGGCTTATTTGT 58.566 40.909 0.00 0.00 38.03 2.83
2259 2309 3.834231 ACAGCTTGATGGGCTTATTTGTT 59.166 39.130 0.00 0.00 38.03 2.83
2260 2310 4.284234 ACAGCTTGATGGGCTTATTTGTTT 59.716 37.500 0.00 0.00 38.03 2.83
2261 2311 4.628333 CAGCTTGATGGGCTTATTTGTTTG 59.372 41.667 0.00 0.00 38.03 2.93
2262 2312 4.527816 AGCTTGATGGGCTTATTTGTTTGA 59.472 37.500 0.00 0.00 36.56 2.69
2263 2313 4.627035 GCTTGATGGGCTTATTTGTTTGAC 59.373 41.667 0.00 0.00 0.00 3.18
2264 2314 5.567423 GCTTGATGGGCTTATTTGTTTGACT 60.567 40.000 0.00 0.00 0.00 3.41
2265 2315 5.389859 TGATGGGCTTATTTGTTTGACTG 57.610 39.130 0.00 0.00 0.00 3.51
2266 2316 3.658757 TGGGCTTATTTGTTTGACTGC 57.341 42.857 0.00 0.00 0.00 4.40
2267 2317 2.961741 TGGGCTTATTTGTTTGACTGCA 59.038 40.909 0.00 0.00 0.00 4.41
2268 2318 3.005684 TGGGCTTATTTGTTTGACTGCAG 59.994 43.478 13.48 13.48 0.00 4.41
2269 2319 2.989166 GGCTTATTTGTTTGACTGCAGC 59.011 45.455 15.27 7.45 0.00 5.25
2270 2320 2.989166 GCTTATTTGTTTGACTGCAGCC 59.011 45.455 15.27 2.30 0.00 4.85
2271 2321 3.578688 CTTATTTGTTTGACTGCAGCCC 58.421 45.455 15.27 6.70 0.00 5.19
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
34 35 2.883386 CTGGATTAGAGAATTGGCTGGC 59.117 50.000 0.00 0.00 0.00 4.85
48 49 8.792633 CAATTAACTCCTGAACAAACTGGATTA 58.207 33.333 0.00 0.00 37.29 1.75
52 53 6.633500 TCAATTAACTCCTGAACAAACTGG 57.367 37.500 0.00 0.00 0.00 4.00
158 159 0.824109 TCTCCTCCACCATTGCGTAG 59.176 55.000 0.00 0.00 0.00 3.51
299 304 2.029918 TCCACGTCTGTTGATCTGTCTG 60.030 50.000 0.00 0.00 0.00 3.51
394 399 1.210478 TGCTTCAGGGTAGCTTCATCC 59.790 52.381 0.00 0.00 39.38 3.51
632 657 4.281182 ACGAGGTCTAAATAGCCCACATAG 59.719 45.833 0.00 0.00 0.00 2.23
647 672 3.231736 ACCGGTTGCACGAGGTCT 61.232 61.111 0.00 0.00 35.47 3.85
655 680 2.515057 GTGTGTCCACCGGTTGCA 60.515 61.111 2.97 0.43 35.44 4.08
777 802 2.943978 AAGTTCGGGCGGTCTCCAG 61.944 63.158 0.00 0.00 0.00 3.86
834 859 1.153289 CCCTGCCACTCCTGAATCG 60.153 63.158 0.00 0.00 0.00 3.34
879 904 2.373707 CCAGGCTGCTAGAAGGGCT 61.374 63.158 9.56 0.17 36.29 5.19
934 959 2.163815 CTCGTAGTGACAAGGATTCGGT 59.836 50.000 0.00 0.00 0.00 4.69
1158 1206 1.375396 AGGCACGCTTCGCACATAA 60.375 52.632 0.00 0.00 0.00 1.90
1345 1393 1.303236 CATCGTGGCCCACCTTTGA 60.303 57.895 8.62 0.00 36.63 2.69
1347 1395 2.676471 GCATCGTGGCCCACCTTT 60.676 61.111 8.62 0.00 36.63 3.11
1348 1396 3.965258 TGCATCGTGGCCCACCTT 61.965 61.111 8.62 0.00 36.63 3.50
1349 1397 4.722700 GTGCATCGTGGCCCACCT 62.723 66.667 8.62 0.00 36.63 4.00
1358 1406 4.722700 GTGGCCAGGGTGCATCGT 62.723 66.667 5.11 0.00 0.00 3.73
1361 1409 4.284550 AACGTGGCCAGGGTGCAT 62.285 61.111 28.01 5.00 0.00 3.96
1381 1429 3.357079 CACAACTGCGGTGGAGCC 61.357 66.667 7.18 0.00 36.02 4.70
1390 1438 1.174712 ATCCACCACTGCACAACTGC 61.175 55.000 0.00 0.00 44.52 4.40
1424 1472 6.614694 TTGTTTTGTAGATAGCCTGACCTA 57.385 37.500 0.00 0.00 0.00 3.08
1428 1476 9.109393 GTTATCATTGTTTTGTAGATAGCCTGA 57.891 33.333 0.00 0.00 0.00 3.86
1429 1477 8.892723 TGTTATCATTGTTTTGTAGATAGCCTG 58.107 33.333 0.00 0.00 0.00 4.85
1623 1673 8.397906 GTTCAGCTATGTTTGATACTAATGCAA 58.602 33.333 0.00 0.00 0.00 4.08
1686 1736 6.019779 TGGTCCCTAATTTTGTCAATTTCG 57.980 37.500 0.00 0.00 0.00 3.46
1694 1744 6.950860 AATTTCCATGGTCCCTAATTTTGT 57.049 33.333 12.58 0.00 0.00 2.83
1709 1759 7.996644 ACATGTACGGTTATCCTAAATTTCCAT 59.003 33.333 0.00 0.00 0.00 3.41
1719 1769 3.243301 CGCTACACATGTACGGTTATCCT 60.243 47.826 0.00 0.00 0.00 3.24
1724 1774 1.000060 ACACGCTACACATGTACGGTT 60.000 47.619 0.00 0.00 33.02 4.44
1739 1789 0.094046 CGTCCCACGATTAAACACGC 59.906 55.000 0.00 0.00 46.05 5.34
1740 1790 0.717224 CCGTCCCACGATTAAACACG 59.283 55.000 0.00 0.00 46.05 4.49
1793 1843 2.787473 ACCTTGCACTATAGCAGCAA 57.213 45.000 23.72 23.72 46.54 3.91
1851 1901 1.139095 CTAGTCCTGTTCGGCGGTC 59.861 63.158 7.21 0.64 0.00 4.79
1870 1920 3.866582 AGCCGCCCAGTCCATAGC 61.867 66.667 0.00 0.00 0.00 2.97
1910 1960 2.591429 CCTCACACGCAACTGCCA 60.591 61.111 0.00 0.00 37.91 4.92
1911 1961 1.845809 CTTCCTCACACGCAACTGCC 61.846 60.000 0.00 0.00 37.91 4.85
1912 1962 1.571460 CTTCCTCACACGCAACTGC 59.429 57.895 0.00 0.00 37.78 4.40
1937 1987 1.078143 GCTTCATTCCCTGCCTCGT 60.078 57.895 0.00 0.00 0.00 4.18
1939 1989 1.821332 CCGCTTCATTCCCTGCCTC 60.821 63.158 0.00 0.00 0.00 4.70
2012 2062 6.496338 AATCCAAGACAAGTAATTCGGAAC 57.504 37.500 0.00 0.00 0.00 3.62
2013 2063 6.488683 ACAAATCCAAGACAAGTAATTCGGAA 59.511 34.615 0.00 0.00 0.00 4.30
2014 2064 6.001460 ACAAATCCAAGACAAGTAATTCGGA 58.999 36.000 0.00 0.00 0.00 4.55
2015 2065 6.149474 AGACAAATCCAAGACAAGTAATTCGG 59.851 38.462 0.00 0.00 0.00 4.30
2016 2066 7.133891 AGACAAATCCAAGACAAGTAATTCG 57.866 36.000 0.00 0.00 0.00 3.34
2017 2067 9.436957 TCTAGACAAATCCAAGACAAGTAATTC 57.563 33.333 0.00 0.00 0.00 2.17
2018 2068 9.965902 ATCTAGACAAATCCAAGACAAGTAATT 57.034 29.630 0.00 0.00 0.00 1.40
2020 2070 9.871238 GTATCTAGACAAATCCAAGACAAGTAA 57.129 33.333 0.00 0.00 0.00 2.24
2021 2071 8.188799 CGTATCTAGACAAATCCAAGACAAGTA 58.811 37.037 0.00 0.00 0.00 2.24
2022 2072 7.036220 CGTATCTAGACAAATCCAAGACAAGT 58.964 38.462 0.00 0.00 0.00 3.16
2023 2073 6.477033 CCGTATCTAGACAAATCCAAGACAAG 59.523 42.308 0.00 0.00 0.00 3.16
2024 2074 6.153851 TCCGTATCTAGACAAATCCAAGACAA 59.846 38.462 0.00 0.00 0.00 3.18
2025 2075 5.655090 TCCGTATCTAGACAAATCCAAGACA 59.345 40.000 0.00 0.00 0.00 3.41
2026 2076 6.145338 TCCGTATCTAGACAAATCCAAGAC 57.855 41.667 0.00 0.00 0.00 3.01
2027 2077 6.323996 ACATCCGTATCTAGACAAATCCAAGA 59.676 38.462 0.00 0.00 0.00 3.02
2028 2078 6.516718 ACATCCGTATCTAGACAAATCCAAG 58.483 40.000 0.00 0.00 0.00 3.61
2029 2079 6.479972 ACATCCGTATCTAGACAAATCCAA 57.520 37.500 0.00 0.00 0.00 3.53
2030 2080 7.776618 ATACATCCGTATCTAGACAAATCCA 57.223 36.000 0.00 0.00 32.66 3.41
2068 2118 8.670490 TGTCTAGATATGGAGGTATCTAACACT 58.330 37.037 0.00 0.00 41.00 3.55
2069 2119 8.865420 TGTCTAGATATGGAGGTATCTAACAC 57.135 38.462 0.00 5.83 41.00 3.32
2070 2120 9.877222 TTTGTCTAGATATGGAGGTATCTAACA 57.123 33.333 0.00 8.70 41.00 2.41
2074 2124 9.607333 TGAATTTGTCTAGATATGGAGGTATCT 57.393 33.333 0.00 2.43 42.50 1.98
2077 2127 9.434275 TCTTGAATTTGTCTAGATATGGAGGTA 57.566 33.333 0.00 0.00 33.79 3.08
2078 2128 8.207545 GTCTTGAATTTGTCTAGATATGGAGGT 58.792 37.037 0.00 0.00 39.77 3.85
2079 2129 8.206867 TGTCTTGAATTTGTCTAGATATGGAGG 58.793 37.037 0.00 0.00 39.77 4.30
2080 2130 9.605275 TTGTCTTGAATTTGTCTAGATATGGAG 57.395 33.333 0.00 0.00 39.77 3.86
2081 2131 9.605275 CTTGTCTTGAATTTGTCTAGATATGGA 57.395 33.333 0.00 0.00 39.77 3.41
2082 2132 9.388506 ACTTGTCTTGAATTTGTCTAGATATGG 57.611 33.333 0.00 0.00 39.77 2.74
2090 2140 9.342308 TCTGAATTACTTGTCTTGAATTTGTCT 57.658 29.630 0.00 0.00 0.00 3.41
2091 2141 9.950680 TTCTGAATTACTTGTCTTGAATTTGTC 57.049 29.630 0.00 0.00 0.00 3.18
2092 2142 9.736023 GTTCTGAATTACTTGTCTTGAATTTGT 57.264 29.630 0.00 0.00 0.00 2.83
2093 2143 8.895845 CGTTCTGAATTACTTGTCTTGAATTTG 58.104 33.333 0.00 0.00 0.00 2.32
2094 2144 8.076178 CCGTTCTGAATTACTTGTCTTGAATTT 58.924 33.333 0.00 0.00 0.00 1.82
2095 2145 7.444183 TCCGTTCTGAATTACTTGTCTTGAATT 59.556 33.333 0.00 0.00 0.00 2.17
2096 2146 6.934645 TCCGTTCTGAATTACTTGTCTTGAAT 59.065 34.615 0.00 0.00 0.00 2.57
2097 2147 6.285224 TCCGTTCTGAATTACTTGTCTTGAA 58.715 36.000 0.00 0.00 0.00 2.69
2098 2148 5.849510 TCCGTTCTGAATTACTTGTCTTGA 58.150 37.500 0.00 0.00 0.00 3.02
2099 2149 6.147821 ACATCCGTTCTGAATTACTTGTCTTG 59.852 38.462 0.00 0.00 0.00 3.02
2100 2150 6.147821 CACATCCGTTCTGAATTACTTGTCTT 59.852 38.462 0.00 0.00 0.00 3.01
2101 2151 5.639506 CACATCCGTTCTGAATTACTTGTCT 59.360 40.000 0.00 0.00 0.00 3.41
2102 2152 5.163854 CCACATCCGTTCTGAATTACTTGTC 60.164 44.000 0.00 0.00 0.00 3.18
2103 2153 4.695455 CCACATCCGTTCTGAATTACTTGT 59.305 41.667 0.00 0.00 0.00 3.16
2104 2154 4.695455 ACCACATCCGTTCTGAATTACTTG 59.305 41.667 0.00 0.00 0.00 3.16
2105 2155 4.906618 ACCACATCCGTTCTGAATTACTT 58.093 39.130 0.00 0.00 0.00 2.24
2106 2156 4.553330 ACCACATCCGTTCTGAATTACT 57.447 40.909 0.00 0.00 0.00 2.24
2107 2157 5.416947 ACTACCACATCCGTTCTGAATTAC 58.583 41.667 0.00 0.00 0.00 1.89
2108 2158 5.670792 ACTACCACATCCGTTCTGAATTA 57.329 39.130 0.00 0.00 0.00 1.40
2109 2159 4.553330 ACTACCACATCCGTTCTGAATT 57.447 40.909 0.00 0.00 0.00 2.17
2110 2160 4.253685 CAACTACCACATCCGTTCTGAAT 58.746 43.478 0.00 0.00 0.00 2.57
2111 2161 3.556213 CCAACTACCACATCCGTTCTGAA 60.556 47.826 0.00 0.00 0.00 3.02
2112 2162 2.028476 CCAACTACCACATCCGTTCTGA 60.028 50.000 0.00 0.00 0.00 3.27
2113 2163 2.346803 CCAACTACCACATCCGTTCTG 58.653 52.381 0.00 0.00 0.00 3.02
2114 2164 1.278127 CCCAACTACCACATCCGTTCT 59.722 52.381 0.00 0.00 0.00 3.01
2115 2165 1.276989 TCCCAACTACCACATCCGTTC 59.723 52.381 0.00 0.00 0.00 3.95
2116 2166 1.354101 TCCCAACTACCACATCCGTT 58.646 50.000 0.00 0.00 0.00 4.44
2117 2167 1.278127 CTTCCCAACTACCACATCCGT 59.722 52.381 0.00 0.00 0.00 4.69
2118 2168 2.012051 GCTTCCCAACTACCACATCCG 61.012 57.143 0.00 0.00 0.00 4.18
2119 2169 1.751437 GCTTCCCAACTACCACATCC 58.249 55.000 0.00 0.00 0.00 3.51
2120 2170 1.369625 CGCTTCCCAACTACCACATC 58.630 55.000 0.00 0.00 0.00 3.06
2121 2171 0.035439 CCGCTTCCCAACTACCACAT 60.035 55.000 0.00 0.00 0.00 3.21
2122 2172 1.373435 CCGCTTCCCAACTACCACA 59.627 57.895 0.00 0.00 0.00 4.17
2123 2173 2.038837 GCCGCTTCCCAACTACCAC 61.039 63.158 0.00 0.00 0.00 4.16
2124 2174 2.221299 AGCCGCTTCCCAACTACCA 61.221 57.895 0.00 0.00 0.00 3.25
2125 2175 1.745489 CAGCCGCTTCCCAACTACC 60.745 63.158 0.00 0.00 0.00 3.18
2126 2176 1.745489 CCAGCCGCTTCCCAACTAC 60.745 63.158 0.00 0.00 0.00 2.73
2127 2177 2.668632 CCAGCCGCTTCCCAACTA 59.331 61.111 0.00 0.00 0.00 2.24
2140 2190 1.366111 TATTTGAACTCGCCGCCAGC 61.366 55.000 0.00 0.00 38.52 4.85
2141 2191 1.003545 CATATTTGAACTCGCCGCCAG 60.004 52.381 0.00 0.00 0.00 4.85
2142 2192 1.013596 CATATTTGAACTCGCCGCCA 58.986 50.000 0.00 0.00 0.00 5.69
2143 2193 0.307760 CCATATTTGAACTCGCCGCC 59.692 55.000 0.00 0.00 0.00 6.13
2144 2194 1.295792 TCCATATTTGAACTCGCCGC 58.704 50.000 0.00 0.00 0.00 6.53
2145 2195 3.788797 GCTTTCCATATTTGAACTCGCCG 60.789 47.826 0.00 0.00 0.00 6.46
2146 2196 3.489229 GGCTTTCCATATTTGAACTCGCC 60.489 47.826 0.00 0.00 0.00 5.54
2147 2197 3.128589 TGGCTTTCCATATTTGAACTCGC 59.871 43.478 0.00 0.00 37.47 5.03
2148 2198 4.963276 TGGCTTTCCATATTTGAACTCG 57.037 40.909 0.00 0.00 37.47 4.18
2161 2211 0.179073 TGCTCGCTCTATGGCTTTCC 60.179 55.000 0.00 0.00 0.00 3.13
2162 2212 1.202463 TCTGCTCGCTCTATGGCTTTC 60.202 52.381 0.00 0.00 0.00 2.62
2163 2213 0.826715 TCTGCTCGCTCTATGGCTTT 59.173 50.000 0.00 0.00 0.00 3.51
2164 2214 0.388659 CTCTGCTCGCTCTATGGCTT 59.611 55.000 0.00 0.00 0.00 4.35
2165 2215 0.467106 TCTCTGCTCGCTCTATGGCT 60.467 55.000 0.00 0.00 0.00 4.75
2166 2216 0.039256 CTCTCTGCTCGCTCTATGGC 60.039 60.000 0.00 0.00 0.00 4.40
2167 2217 0.597568 CCTCTCTGCTCGCTCTATGG 59.402 60.000 0.00 0.00 0.00 2.74
2168 2218 1.603456 TCCTCTCTGCTCGCTCTATG 58.397 55.000 0.00 0.00 0.00 2.23
2169 2219 2.356665 TTCCTCTCTGCTCGCTCTAT 57.643 50.000 0.00 0.00 0.00 1.98
2170 2220 2.356665 ATTCCTCTCTGCTCGCTCTA 57.643 50.000 0.00 0.00 0.00 2.43
2171 2221 2.356665 TATTCCTCTCTGCTCGCTCT 57.643 50.000 0.00 0.00 0.00 4.09
2172 2222 2.288152 CCTTATTCCTCTCTGCTCGCTC 60.288 54.545 0.00 0.00 0.00 5.03
2173 2223 1.686052 CCTTATTCCTCTCTGCTCGCT 59.314 52.381 0.00 0.00 0.00 4.93
2174 2224 1.270041 CCCTTATTCCTCTCTGCTCGC 60.270 57.143 0.00 0.00 0.00 5.03
2175 2225 2.035321 GTCCCTTATTCCTCTCTGCTCG 59.965 54.545 0.00 0.00 0.00 5.03
2176 2226 3.069443 CAGTCCCTTATTCCTCTCTGCTC 59.931 52.174 0.00 0.00 0.00 4.26
2177 2227 3.037549 CAGTCCCTTATTCCTCTCTGCT 58.962 50.000 0.00 0.00 0.00 4.24
2178 2228 2.103941 CCAGTCCCTTATTCCTCTCTGC 59.896 54.545 0.00 0.00 0.00 4.26
2179 2229 2.703007 CCCAGTCCCTTATTCCTCTCTG 59.297 54.545 0.00 0.00 0.00 3.35
2180 2230 2.961977 GCCCAGTCCCTTATTCCTCTCT 60.962 54.545 0.00 0.00 0.00 3.10
2181 2231 1.418264 GCCCAGTCCCTTATTCCTCTC 59.582 57.143 0.00 0.00 0.00 3.20
2182 2232 1.512735 GCCCAGTCCCTTATTCCTCT 58.487 55.000 0.00 0.00 0.00 3.69
2183 2233 0.474614 GGCCCAGTCCCTTATTCCTC 59.525 60.000 0.00 0.00 0.00 3.71
2184 2234 0.253630 TGGCCCAGTCCCTTATTCCT 60.254 55.000 0.00 0.00 0.00 3.36
2185 2235 0.106669 GTGGCCCAGTCCCTTATTCC 60.107 60.000 0.00 0.00 0.00 3.01
2186 2236 0.919710 AGTGGCCCAGTCCCTTATTC 59.080 55.000 0.00 0.00 0.00 1.75
2187 2237 0.919710 GAGTGGCCCAGTCCCTTATT 59.080 55.000 7.38 0.00 0.00 1.40
2188 2238 1.338136 CGAGTGGCCCAGTCCCTTAT 61.338 60.000 12.98 0.00 30.70 1.73
2189 2239 1.987855 CGAGTGGCCCAGTCCCTTA 60.988 63.158 12.98 0.00 30.70 2.69
2190 2240 3.322466 CGAGTGGCCCAGTCCCTT 61.322 66.667 12.98 0.00 30.70 3.95
2194 2244 4.394712 CACCCGAGTGGCCCAGTC 62.395 72.222 8.63 8.63 40.55 3.51
2195 2245 4.954118 TCACCCGAGTGGCCCAGT 62.954 66.667 0.00 0.00 44.64 4.00
2196 2246 4.087892 CTCACCCGAGTGGCCCAG 62.088 72.222 0.00 0.00 44.64 4.45
2204 2254 1.446272 GCGAAAGGACTCACCCGAG 60.446 63.158 0.00 0.00 45.49 4.63
2205 2255 2.204461 TGCGAAAGGACTCACCCGA 61.204 57.895 0.00 0.00 40.05 5.14
2206 2256 2.342279 TGCGAAAGGACTCACCCG 59.658 61.111 0.00 0.00 40.05 5.28
2214 2264 2.747686 GTCCCTGGTGCGAAAGGA 59.252 61.111 0.16 0.00 35.40 3.36
2215 2265 2.742372 CGTCCCTGGTGCGAAAGG 60.742 66.667 1.62 0.00 0.00 3.11
2216 2266 2.501223 TAGCGTCCCTGGTGCGAAAG 62.501 60.000 10.60 0.00 0.00 2.62
2217 2267 2.501223 CTAGCGTCCCTGGTGCGAAA 62.501 60.000 10.60 0.00 0.00 3.46
2218 2268 2.992689 TAGCGTCCCTGGTGCGAA 60.993 61.111 10.60 0.00 0.00 4.70
2219 2269 3.449227 CTAGCGTCCCTGGTGCGA 61.449 66.667 10.60 0.00 0.00 5.10
2220 2270 3.449227 TCTAGCGTCCCTGGTGCG 61.449 66.667 0.00 0.00 0.00 5.34
2221 2271 2.184579 GTCTAGCGTCCCTGGTGC 59.815 66.667 0.00 0.00 0.00 5.01
2222 2272 1.513158 CTGTCTAGCGTCCCTGGTG 59.487 63.158 0.00 0.00 0.00 4.17
2223 2273 2.352032 GCTGTCTAGCGTCCCTGGT 61.352 63.158 0.00 0.00 40.67 4.00
2224 2274 2.496817 GCTGTCTAGCGTCCCTGG 59.503 66.667 0.00 0.00 40.67 4.45
2233 2283 2.706339 AAGCCCATCAAGCTGTCTAG 57.294 50.000 0.00 0.00 40.49 2.43
2234 2284 4.778213 AATAAGCCCATCAAGCTGTCTA 57.222 40.909 0.00 0.00 40.49 2.59
2235 2285 3.659183 AATAAGCCCATCAAGCTGTCT 57.341 42.857 0.00 0.00 40.49 3.41
2236 2286 3.445096 ACAAATAAGCCCATCAAGCTGTC 59.555 43.478 0.00 0.00 40.49 3.51
2237 2287 3.434309 ACAAATAAGCCCATCAAGCTGT 58.566 40.909 0.00 0.00 40.49 4.40
2238 2288 4.460948 AACAAATAAGCCCATCAAGCTG 57.539 40.909 0.00 0.00 40.49 4.24
2239 2289 4.527816 TCAAACAAATAAGCCCATCAAGCT 59.472 37.500 0.00 0.00 44.19 3.74
2240 2290 4.627035 GTCAAACAAATAAGCCCATCAAGC 59.373 41.667 0.00 0.00 0.00 4.01
2241 2291 5.865552 CAGTCAAACAAATAAGCCCATCAAG 59.134 40.000 0.00 0.00 0.00 3.02
2242 2292 5.782047 CAGTCAAACAAATAAGCCCATCAA 58.218 37.500 0.00 0.00 0.00 2.57
2243 2293 4.321899 GCAGTCAAACAAATAAGCCCATCA 60.322 41.667 0.00 0.00 0.00 3.07
2244 2294 4.176271 GCAGTCAAACAAATAAGCCCATC 58.824 43.478 0.00 0.00 0.00 3.51
2245 2295 3.577848 TGCAGTCAAACAAATAAGCCCAT 59.422 39.130 0.00 0.00 0.00 4.00
2246 2296 2.961741 TGCAGTCAAACAAATAAGCCCA 59.038 40.909 0.00 0.00 0.00 5.36
2247 2297 3.578688 CTGCAGTCAAACAAATAAGCCC 58.421 45.455 5.25 0.00 0.00 5.19
2248 2298 2.989166 GCTGCAGTCAAACAAATAAGCC 59.011 45.455 16.64 0.00 0.00 4.35
2249 2299 2.989166 GGCTGCAGTCAAACAAATAAGC 59.011 45.455 14.88 0.00 0.00 3.09
2250 2300 3.578688 GGGCTGCAGTCAAACAAATAAG 58.421 45.455 21.89 0.00 0.00 1.73
2251 2301 3.658757 GGGCTGCAGTCAAACAAATAA 57.341 42.857 21.89 0.00 0.00 1.40


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

AutoCloner maintained by Alex Coulton.