Multiple sequence alignment - TraesCS6D01G066900

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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 TraesCS6D01G066900 chr6D 100.000 4998 0 0 1 4998 32867346 32862349 0.000000e+00 9230.0
1 TraesCS6D01G066900 chr6D 100.000 1295 0 0 5318 6612 32862029 32860735 0.000000e+00 2392.0
2 TraesCS6D01G066900 chr6D 77.387 398 73 14 6129 6520 30212078 30212464 3.100000e-53 220.0
3 TraesCS6D01G066900 chr6B 95.905 2442 90 5 2567 4998 69457448 69455007 0.000000e+00 3947.0
4 TraesCS6D01G066900 chr6B 91.107 1563 106 17 463 2014 69459575 69458035 0.000000e+00 2085.0
5 TraesCS6D01G066900 chr6B 92.619 1260 62 14 5318 6558 69454944 69453697 0.000000e+00 1783.0
6 TraesCS6D01G066900 chr6B 96.336 464 16 1 1 463 69460146 69459683 0.000000e+00 761.0
7 TraesCS6D01G066900 chr6B 97.805 410 6 1 2177 2586 69458036 69457630 0.000000e+00 704.0
8 TraesCS6D01G066900 chr6A 95.362 2156 88 6 2542 4697 37441565 37439422 0.000000e+00 3417.0
9 TraesCS6D01G066900 chr6A 92.362 1558 80 10 463 2014 37443698 37442174 0.000000e+00 2182.0
10 TraesCS6D01G066900 chr6A 87.644 1214 106 29 5373 6554 37417200 37415999 0.000000e+00 1371.0
11 TraesCS6D01G066900 chr6A 95.054 465 17 2 1 459 37444274 37443810 0.000000e+00 726.0
12 TraesCS6D01G066900 chr6A 91.016 256 20 2 2269 2524 37441995 37441743 6.350000e-90 342.0
13 TraesCS6D01G066900 chr6A 98.387 62 1 0 6551 6612 37415974 37415913 7.010000e-20 110.0
14 TraesCS6D01G066900 chr6A 96.825 63 2 0 5318 5380 37439279 37439217 9.070000e-19 106.0
15 TraesCS6D01G066900 chr6A 90.625 64 6 0 2177 2240 37442175 37442112 1.180000e-12 86.1
16 TraesCS6D01G066900 chr6A 92.157 51 4 0 5993 6043 259770635 259770585 9.200000e-09 73.1
17 TraesCS6D01G066900 chr3B 74.866 1492 331 40 3194 4657 85059407 85057932 7.230000e-179 638.0
18 TraesCS6D01G066900 chr3B 74.312 654 152 12 2742 3387 85085430 85084785 5.080000e-66 263.0
19 TraesCS6D01G066900 chr5B 88.642 405 33 9 460 858 494709756 494710153 1.290000e-131 481.0
20 TraesCS6D01G066900 chr5B 94.737 57 3 0 2406 2462 136020810 136020754 9.130000e-14 89.8
21 TraesCS6D01G066900 chr5A 99.422 173 0 1 2009 2181 382566806 382566635 4.980000e-81 313.0
22 TraesCS6D01G066900 chr4D 98.851 174 0 2 2010 2182 477898792 477898964 6.440000e-80 309.0
23 TraesCS6D01G066900 chr4D 93.000 200 9 5 1984 2180 70988197 70988000 3.020000e-73 287.0
24 TraesCS6D01G066900 chr4D 94.118 51 1 2 5993 6042 44203998 44203949 7.110000e-10 76.8
25 TraesCS6D01G066900 chr4D 92.308 52 4 0 5993 6044 441486773 441486824 2.560000e-09 75.0
26 TraesCS6D01G066900 chr2B 98.851 174 1 1 2012 2185 174794821 174794993 6.440000e-80 309.0
27 TraesCS6D01G066900 chr2B 98.837 172 1 1 2011 2182 719520671 719520501 8.330000e-79 305.0
28 TraesCS6D01G066900 chr2B 98.276 174 2 1 2008 2181 594833870 594834042 3.000000e-78 303.0
29 TraesCS6D01G066900 chr2B 95.918 49 1 1 5993 6041 734295969 734296016 1.980000e-10 78.7
30 TraesCS6D01G066900 chr1D 98.837 172 1 1 2013 2184 178466470 178466300 8.330000e-79 305.0
31 TraesCS6D01G066900 chr1B 95.745 188 4 4 2008 2194 628050855 628050671 3.880000e-77 300.0
32 TraesCS6D01G066900 chr1B 95.918 49 1 1 5993 6041 562928486 562928439 1.980000e-10 78.7
33 TraesCS6D01G066900 chr1B 95.918 49 1 1 5993 6041 572442106 572442059 1.980000e-10 78.7
34 TraesCS6D01G066900 chr7D 96.685 181 3 3 2013 2193 69592660 69592837 1.390000e-76 298.0
35 TraesCS6D01G066900 chrUn 77.387 398 73 14 6129 6520 71720969 71720583 3.100000e-53 220.0
36 TraesCS6D01G066900 chr4A 75.397 378 67 20 6149 6519 609926201 609926559 6.860000e-35 159.0
37 TraesCS6D01G066900 chr7B 97.778 45 1 0 5993 6037 420072755 420072799 1.980000e-10 78.7
38 TraesCS6D01G066900 chr7B 95.918 49 1 1 5993 6041 463050406 463050359 1.980000e-10 78.7


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 TraesCS6D01G066900 chr6D 32860735 32867346 6611 True 5811.000000 9230 100.000000 1 6612 2 chr6D.!!$R1 6611
1 TraesCS6D01G066900 chr6B 69453697 69460146 6449 True 1856.000000 3947 94.754400 1 6558 5 chr6B.!!$R1 6557
2 TraesCS6D01G066900 chr6A 37439217 37444274 5057 True 1143.183333 3417 93.540667 1 5380 6 chr6A.!!$R3 5379
3 TraesCS6D01G066900 chr6A 37415913 37417200 1287 True 740.500000 1371 93.015500 5373 6612 2 chr6A.!!$R2 1239
4 TraesCS6D01G066900 chr3B 85057932 85059407 1475 True 638.000000 638 74.866000 3194 4657 1 chr3B.!!$R1 1463
5 TraesCS6D01G066900 chr3B 85084785 85085430 645 True 263.000000 263 74.312000 2742 3387 1 chr3B.!!$R2 645

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
986 1113 0.250945 TACACCATTGGAAGCCGCAA 60.251 50.000 10.37 0.00 0.00 4.85 F
1557 1684 0.035534 TGGTGTACCTGCGCATGAAT 60.036 50.000 19.95 3.91 36.82 2.57 F
3090 3564 0.818296 CCGACGAAGAAGGAGGTGAT 59.182 55.000 0.00 0.00 0.00 3.06 F
3541 4024 0.537828 TTCCATCTGCAGTGCAAGCA 60.538 50.000 20.22 13.69 38.41 3.91 F
3981 4467 1.273327 CACCTGCCAAAAGGATGGTTC 59.727 52.381 0.00 0.00 42.75 3.62 F
4990 5495 0.253327 ATGAGACGAAAAGGGGAGGC 59.747 55.000 0.00 0.00 0.00 4.70 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2163 2299 1.067071 CACAACTACTCCCTCCGTTCC 60.067 57.143 0.00 0.00 0.00 3.62 R
3273 3747 0.319469 TGAACATGTTGCGCGAGAGA 60.319 50.000 17.58 0.00 0.00 3.10 R
4497 4983 1.304713 AGGGGCCAATGCACTTGAG 60.305 57.895 4.39 3.19 42.08 3.02 R
4970 5475 1.485066 GCCTCCCCTTTTCGTCTCATA 59.515 52.381 0.00 0.00 0.00 2.15 R
5544 6050 2.298729 TGCAAGAAATTAACCTGGTGGC 59.701 45.455 0.00 0.00 36.63 5.01 R
6404 6957 1.154430 TGGTTAGGCCTTGGGTCTTT 58.846 50.000 12.58 0.00 39.09 2.52 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
68 69 1.682684 ACGGTGGAGCAGAGGTAGG 60.683 63.158 0.00 0.00 0.00 3.18
87 89 2.708325 AGGAAAGACTGAAGAACCAGCT 59.292 45.455 0.00 0.00 37.68 4.24
159 161 1.073923 CAACCACCCCTAGCTTTGACT 59.926 52.381 0.00 0.00 0.00 3.41
170 172 5.105752 CCTAGCTTTGACTGTCAGTATGTC 58.894 45.833 10.77 0.00 37.40 3.06
232 236 1.630369 CTTGGTCATCTGTCCCCTTCA 59.370 52.381 0.00 0.00 0.00 3.02
233 237 1.971149 TGGTCATCTGTCCCCTTCAT 58.029 50.000 0.00 0.00 0.00 2.57
459 467 2.851195 TGTCTTGCTTGAGGTTCTTCC 58.149 47.619 0.00 0.00 0.00 3.46
471 588 1.135170 GGTTCTTCCTAGGTCGTTCGG 60.135 57.143 9.08 0.00 0.00 4.30
493 610 7.325694 TCGGTAATACCCAGAAGTAAGAAAAG 58.674 38.462 3.51 0.00 33.75 2.27
494 611 7.178983 TCGGTAATACCCAGAAGTAAGAAAAGA 59.821 37.037 3.51 0.00 33.75 2.52
552 670 4.379186 GCATCTTGTGATCACTTGGACAAG 60.379 45.833 25.55 18.50 44.39 3.16
574 692 2.125673 CCAGCAGCAAAGCATGGC 60.126 61.111 0.00 0.00 36.85 4.40
628 746 1.999648 TGCTCTGCTTTGGAAACCAT 58.000 45.000 0.00 0.00 31.53 3.55
629 747 1.888512 TGCTCTGCTTTGGAAACCATC 59.111 47.619 0.00 0.00 31.53 3.51
661 779 4.993029 TTGAAGTTCACGAAAATGGGTT 57.007 36.364 4.68 0.00 0.00 4.11
727 845 7.194278 GTCGAAGTCTAGCACATGTTTCTATA 58.806 38.462 0.00 0.00 0.00 1.31
796 919 4.096833 TGCCTACAGAAATGCAAGCATAAG 59.903 41.667 8.12 1.77 35.31 1.73
986 1113 0.250945 TACACCATTGGAAGCCGCAA 60.251 50.000 10.37 0.00 0.00 4.85
987 1114 1.112315 ACACCATTGGAAGCCGCAAA 61.112 50.000 10.37 0.00 0.00 3.68
1080 1207 2.334946 TTCCATGCACGCTTCAGCC 61.335 57.895 0.00 0.00 37.91 4.85
1081 1208 3.057548 CCATGCACGCTTCAGCCA 61.058 61.111 0.00 0.00 37.91 4.75
1082 1209 2.628696 CCATGCACGCTTCAGCCAA 61.629 57.895 0.00 0.00 37.91 4.52
1085 1212 2.050985 GCACGCTTCAGCCAACAC 60.051 61.111 0.00 0.00 37.91 3.32
1097 1224 2.124487 CAACACCACCACCACCGT 60.124 61.111 0.00 0.00 0.00 4.83
1202 1329 4.504916 CGGAGAGGACTGCTGCCG 62.505 72.222 0.00 0.00 32.26 5.69
1322 1449 1.912043 CAACCTCACCTCCCTCAAGAT 59.088 52.381 0.00 0.00 0.00 2.40
1334 1461 1.413445 CCTCAAGATCCTGAGCCTCAG 59.587 57.143 14.99 14.99 43.91 3.35
1352 1479 2.903547 GCACCACACGCATTTCCGT 61.904 57.895 0.00 0.00 43.11 4.69
1359 1486 2.124901 CGCATTTCCGTGGGGCTA 60.125 61.111 0.00 0.00 0.00 3.93
1420 1547 4.361971 ACGGGTCGAGCTCCTGGA 62.362 66.667 15.18 0.00 35.79 3.86
1425 1552 2.119611 TCGAGCTCCTGGAACCCA 59.880 61.111 8.47 0.00 0.00 4.51
1501 1628 5.413309 CCTCGAGGGCTATGATTTATCTT 57.587 43.478 24.62 0.00 0.00 2.40
1510 1637 6.291377 GGCTATGATTTATCTTGGTCACAGA 58.709 40.000 0.00 0.00 0.00 3.41
1557 1684 0.035534 TGGTGTACCTGCGCATGAAT 60.036 50.000 19.95 3.91 36.82 2.57
1578 1705 4.966787 TGCAGTTTCACCGGGCCC 62.967 66.667 13.57 13.57 0.00 5.80
1579 1706 4.966787 GCAGTTTCACCGGGCCCA 62.967 66.667 24.92 0.00 0.00 5.36
1614 1741 1.949525 GGAACTCTTGCAAAGCTGACA 59.050 47.619 0.00 0.00 45.70 3.58
1626 1753 3.423539 AAGCTGACACTGCTGGATTTA 57.576 42.857 4.13 0.00 38.59 1.40
1674 1801 3.555966 GGTTCCTTCATGGATCGGAAAT 58.444 45.455 0.00 0.00 45.68 2.17
1691 1818 4.517453 CGGAAATCTTACCAGGTTGACAAA 59.483 41.667 0.00 0.00 0.00 2.83
1696 1823 4.204012 TCTTACCAGGTTGACAAAGTTGG 58.796 43.478 0.00 10.67 0.00 3.77
1698 1825 1.039856 CCAGGTTGACAAAGTTGGGG 58.960 55.000 0.00 0.00 0.00 4.96
1717 1844 1.728490 GATCCAAGGTTGCCGGCATC 61.728 60.000 33.25 29.26 0.00 3.91
1728 1855 1.526917 CCGGCATCCTGGGTCAATC 60.527 63.158 0.00 0.00 0.00 2.67
1814 1941 5.299531 TCGGTGAGATCCTAACTACAATCTG 59.700 44.000 0.00 0.00 0.00 2.90
1914 2041 9.216117 GTACTGCTAAGAAAAGGAAATTACTCA 57.784 33.333 0.00 0.00 0.00 3.41
1915 2042 8.870075 ACTGCTAAGAAAAGGAAATTACTCAT 57.130 30.769 0.00 0.00 0.00 2.90
1952 2079 3.216800 CAATGAGGTCACCCCATGTATG 58.783 50.000 0.00 0.00 34.66 2.39
1968 2095 7.827236 CCCCATGTATGTACAGAAAGAGTAAAA 59.173 37.037 0.33 0.00 39.92 1.52
1980 2107 8.250332 ACAGAAAGAGTAAAACATTTTTGCAGA 58.750 29.630 0.00 0.00 0.00 4.26
1981 2108 9.086336 CAGAAAGAGTAAAACATTTTTGCAGAA 57.914 29.630 0.00 0.00 0.00 3.02
1982 2109 9.651913 AGAAAGAGTAAAACATTTTTGCAGAAA 57.348 25.926 4.71 4.71 0.00 2.52
2018 2154 9.498176 TTTTTGTACTTGATACTTTCTACTCCC 57.502 33.333 0.00 0.00 34.56 4.30
2019 2155 8.431910 TTTGTACTTGATACTTTCTACTCCCT 57.568 34.615 0.00 0.00 34.56 4.20
2020 2156 7.642082 TGTACTTGATACTTTCTACTCCCTC 57.358 40.000 0.00 0.00 34.56 4.30
2021 2157 6.606395 TGTACTTGATACTTTCTACTCCCTCC 59.394 42.308 0.00 0.00 34.56 4.30
2022 2158 4.645588 ACTTGATACTTTCTACTCCCTCCG 59.354 45.833 0.00 0.00 0.00 4.63
2023 2159 4.246712 TGATACTTTCTACTCCCTCCGT 57.753 45.455 0.00 0.00 0.00 4.69
2024 2160 4.607239 TGATACTTTCTACTCCCTCCGTT 58.393 43.478 0.00 0.00 0.00 4.44
2025 2161 4.643784 TGATACTTTCTACTCCCTCCGTTC 59.356 45.833 0.00 0.00 0.00 3.95
2026 2162 2.177734 ACTTTCTACTCCCTCCGTTCC 58.822 52.381 0.00 0.00 0.00 3.62
2027 2163 2.225318 ACTTTCTACTCCCTCCGTTCCT 60.225 50.000 0.00 0.00 0.00 3.36
2028 2164 3.011032 ACTTTCTACTCCCTCCGTTCCTA 59.989 47.826 0.00 0.00 0.00 2.94
2029 2165 3.744940 TTCTACTCCCTCCGTTCCTAA 57.255 47.619 0.00 0.00 0.00 2.69
2030 2166 3.744940 TCTACTCCCTCCGTTCCTAAA 57.255 47.619 0.00 0.00 0.00 1.85
2031 2167 4.261411 TCTACTCCCTCCGTTCCTAAAT 57.739 45.455 0.00 0.00 0.00 1.40
2032 2168 5.393068 TCTACTCCCTCCGTTCCTAAATA 57.607 43.478 0.00 0.00 0.00 1.40
2033 2169 5.961897 TCTACTCCCTCCGTTCCTAAATAT 58.038 41.667 0.00 0.00 0.00 1.28
2034 2170 6.379579 TCTACTCCCTCCGTTCCTAAATATT 58.620 40.000 0.00 0.00 0.00 1.28
2035 2171 5.970501 ACTCCCTCCGTTCCTAAATATTT 57.029 39.130 5.89 5.89 0.00 1.40
2036 2172 5.681639 ACTCCCTCCGTTCCTAAATATTTG 58.318 41.667 11.05 1.40 0.00 2.32
2037 2173 5.191124 ACTCCCTCCGTTCCTAAATATTTGT 59.809 40.000 11.05 0.00 0.00 2.83
2038 2174 5.677567 TCCCTCCGTTCCTAAATATTTGTC 58.322 41.667 11.05 0.00 0.00 3.18
2039 2175 5.427481 TCCCTCCGTTCCTAAATATTTGTCT 59.573 40.000 11.05 0.00 0.00 3.41
2040 2176 6.069847 TCCCTCCGTTCCTAAATATTTGTCTT 60.070 38.462 11.05 0.00 0.00 3.01
2041 2177 6.602009 CCCTCCGTTCCTAAATATTTGTCTTT 59.398 38.462 11.05 0.00 0.00 2.52
2042 2178 7.201705 CCCTCCGTTCCTAAATATTTGTCTTTC 60.202 40.741 11.05 0.00 0.00 2.62
2043 2179 7.553044 CCTCCGTTCCTAAATATTTGTCTTTCT 59.447 37.037 11.05 0.00 0.00 2.52
2044 2180 9.595823 CTCCGTTCCTAAATATTTGTCTTTCTA 57.404 33.333 11.05 0.00 0.00 2.10
2045 2181 9.595823 TCCGTTCCTAAATATTTGTCTTTCTAG 57.404 33.333 11.05 0.00 0.00 2.43
2046 2182 9.595823 CCGTTCCTAAATATTTGTCTTTCTAGA 57.404 33.333 11.05 0.00 0.00 2.43
2059 2195 8.964476 TTGTCTTTCTAGAGATTTCAACAAGT 57.036 30.769 0.00 0.00 0.00 3.16
2060 2196 8.370493 TGTCTTTCTAGAGATTTCAACAAGTG 57.630 34.615 0.00 0.00 0.00 3.16
2061 2197 8.204160 TGTCTTTCTAGAGATTTCAACAAGTGA 58.796 33.333 0.00 0.00 0.00 3.41
2062 2198 8.491950 GTCTTTCTAGAGATTTCAACAAGTGAC 58.508 37.037 0.00 0.00 35.39 3.67
2063 2199 8.424918 TCTTTCTAGAGATTTCAACAAGTGACT 58.575 33.333 0.00 0.00 35.39 3.41
2064 2200 9.698309 CTTTCTAGAGATTTCAACAAGTGACTA 57.302 33.333 0.00 0.00 35.39 2.59
2065 2201 9.477484 TTTCTAGAGATTTCAACAAGTGACTAC 57.523 33.333 0.00 0.00 35.39 2.73
2066 2202 8.178313 TCTAGAGATTTCAACAAGTGACTACA 57.822 34.615 0.00 0.00 35.39 2.74
2067 2203 8.807118 TCTAGAGATTTCAACAAGTGACTACAT 58.193 33.333 0.00 0.00 35.39 2.29
2069 2205 8.764524 AGAGATTTCAACAAGTGACTACATAC 57.235 34.615 0.00 0.00 35.39 2.39
2070 2206 7.542477 AGAGATTTCAACAAGTGACTACATACG 59.458 37.037 0.00 0.00 35.39 3.06
2071 2207 6.590292 AGATTTCAACAAGTGACTACATACGG 59.410 38.462 0.00 0.00 35.39 4.02
2072 2208 5.456548 TTCAACAAGTGACTACATACGGA 57.543 39.130 0.00 0.00 35.39 4.69
2073 2209 5.055642 TCAACAAGTGACTACATACGGAG 57.944 43.478 0.00 0.00 0.00 4.63
2074 2210 3.505464 ACAAGTGACTACATACGGAGC 57.495 47.619 0.00 0.00 0.00 4.70
2075 2211 2.823747 ACAAGTGACTACATACGGAGCA 59.176 45.455 0.00 0.00 0.00 4.26
2076 2212 3.257375 ACAAGTGACTACATACGGAGCAA 59.743 43.478 0.00 0.00 0.00 3.91
2077 2213 4.242475 CAAGTGACTACATACGGAGCAAA 58.758 43.478 0.00 0.00 0.00 3.68
2078 2214 4.530710 AGTGACTACATACGGAGCAAAA 57.469 40.909 0.00 0.00 0.00 2.44
2079 2215 5.086104 AGTGACTACATACGGAGCAAAAT 57.914 39.130 0.00 0.00 0.00 1.82
2080 2216 4.870426 AGTGACTACATACGGAGCAAAATG 59.130 41.667 0.00 0.00 0.00 2.32
2081 2217 4.868171 GTGACTACATACGGAGCAAAATGA 59.132 41.667 0.00 0.00 0.00 2.57
2082 2218 5.005779 GTGACTACATACGGAGCAAAATGAG 59.994 44.000 0.00 0.00 0.00 2.90
2083 2219 5.086104 ACTACATACGGAGCAAAATGAGT 57.914 39.130 0.00 0.00 0.00 3.41
2084 2220 4.870426 ACTACATACGGAGCAAAATGAGTG 59.130 41.667 0.00 0.00 0.00 3.51
2085 2221 3.937814 ACATACGGAGCAAAATGAGTGA 58.062 40.909 0.00 0.00 0.00 3.41
2086 2222 4.323417 ACATACGGAGCAAAATGAGTGAA 58.677 39.130 0.00 0.00 0.00 3.18
2087 2223 4.943705 ACATACGGAGCAAAATGAGTGAAT 59.056 37.500 0.00 0.00 0.00 2.57
2088 2224 5.065218 ACATACGGAGCAAAATGAGTGAATC 59.935 40.000 0.00 0.00 0.00 2.52
2089 2225 3.679389 ACGGAGCAAAATGAGTGAATCT 58.321 40.909 0.00 0.00 0.00 2.40
2090 2226 4.832248 ACGGAGCAAAATGAGTGAATCTA 58.168 39.130 0.00 0.00 0.00 1.98
2091 2227 4.631813 ACGGAGCAAAATGAGTGAATCTAC 59.368 41.667 0.00 0.00 0.00 2.59
2092 2228 4.631377 CGGAGCAAAATGAGTGAATCTACA 59.369 41.667 0.00 0.00 0.00 2.74
2093 2229 5.446473 CGGAGCAAAATGAGTGAATCTACAC 60.446 44.000 0.00 0.00 40.60 2.90
2127 2263 7.770366 TGTCTTATATACATCCGTATGTGGT 57.230 36.000 3.56 0.00 45.99 4.16
2128 2264 8.866970 TGTCTTATATACATCCGTATGTGGTA 57.133 34.615 3.56 0.00 45.99 3.25
2129 2265 8.953313 TGTCTTATATACATCCGTATGTGGTAG 58.047 37.037 3.56 0.00 45.99 3.18
2130 2266 8.954350 GTCTTATATACATCCGTATGTGGTAGT 58.046 37.037 3.56 0.00 45.99 2.73
2131 2267 9.170734 TCTTATATACATCCGTATGTGGTAGTC 57.829 37.037 3.56 0.00 45.99 2.59
2132 2268 6.770746 ATATACATCCGTATGTGGTAGTCC 57.229 41.667 3.56 0.00 45.99 3.85
2133 2269 2.742348 ACATCCGTATGTGGTAGTCCA 58.258 47.619 0.00 0.00 44.79 4.02
2134 2270 3.305720 ACATCCGTATGTGGTAGTCCAT 58.694 45.455 0.00 0.00 44.79 3.41
2135 2271 3.709653 ACATCCGTATGTGGTAGTCCATT 59.290 43.478 0.00 0.00 44.79 3.16
2136 2272 4.163458 ACATCCGTATGTGGTAGTCCATTT 59.837 41.667 0.00 0.00 44.79 2.32
2137 2273 4.131649 TCCGTATGTGGTAGTCCATTTG 57.868 45.455 0.00 0.00 46.20 2.32
2138 2274 3.770388 TCCGTATGTGGTAGTCCATTTGA 59.230 43.478 0.00 0.00 46.20 2.69
2139 2275 4.223255 TCCGTATGTGGTAGTCCATTTGAA 59.777 41.667 0.00 0.00 46.20 2.69
2140 2276 4.938832 CCGTATGTGGTAGTCCATTTGAAA 59.061 41.667 0.00 0.00 46.20 2.69
2141 2277 5.588648 CCGTATGTGGTAGTCCATTTGAAAT 59.411 40.000 0.00 0.00 46.20 2.17
2142 2278 6.238374 CCGTATGTGGTAGTCCATTTGAAATC 60.238 42.308 0.00 0.00 46.20 2.17
2143 2279 6.538742 CGTATGTGGTAGTCCATTTGAAATCT 59.461 38.462 0.00 0.00 46.20 2.40
2144 2280 7.254455 CGTATGTGGTAGTCCATTTGAAATCTC 60.254 40.741 0.00 0.00 46.20 2.75
2145 2281 6.126863 TGTGGTAGTCCATTTGAAATCTCT 57.873 37.500 0.00 0.00 46.20 3.10
2146 2282 7.252612 TGTGGTAGTCCATTTGAAATCTCTA 57.747 36.000 0.00 0.00 46.20 2.43
2147 2283 7.685481 TGTGGTAGTCCATTTGAAATCTCTAA 58.315 34.615 0.00 0.00 46.20 2.10
2148 2284 8.160765 TGTGGTAGTCCATTTGAAATCTCTAAA 58.839 33.333 0.00 0.00 46.20 1.85
2149 2285 9.010029 GTGGTAGTCCATTTGAAATCTCTAAAA 57.990 33.333 0.00 0.00 46.20 1.52
2150 2286 9.581289 TGGTAGTCCATTTGAAATCTCTAAAAA 57.419 29.630 0.00 0.00 39.03 1.94
2154 2290 9.354673 AGTCCATTTGAAATCTCTAAAAAGACA 57.645 29.630 0.00 0.00 0.00 3.41
2155 2291 9.965824 GTCCATTTGAAATCTCTAAAAAGACAA 57.034 29.630 0.00 0.00 0.00 3.18
2172 2308 7.625828 AAAGACAAATATTTAGGAACGGAGG 57.374 36.000 0.00 0.00 0.00 4.30
2173 2309 5.681639 AGACAAATATTTAGGAACGGAGGG 58.318 41.667 0.00 0.00 0.00 4.30
2174 2310 5.427481 AGACAAATATTTAGGAACGGAGGGA 59.573 40.000 0.00 0.00 0.00 4.20
2175 2311 5.681639 ACAAATATTTAGGAACGGAGGGAG 58.318 41.667 0.00 0.00 0.00 4.30
2628 3099 7.121168 ACACAGTATCACACCTAAAAATCATGG 59.879 37.037 0.00 0.00 0.00 3.66
2713 3184 9.918630 TGTCATAGATACATCAAGATATGTGTG 57.081 33.333 0.00 0.00 40.29 3.82
3090 3564 0.818296 CCGACGAAGAAGGAGGTGAT 59.182 55.000 0.00 0.00 0.00 3.06
3162 3636 2.888414 TCTCACAAAATTTCCGGGTTCC 59.112 45.455 0.00 0.00 0.00 3.62
3253 3727 3.469859 TGGGTATGGGAGAATTGGAAGA 58.530 45.455 0.00 0.00 0.00 2.87
3273 3747 4.723309 AGAACCAGCTTGAGAGTTTGAAT 58.277 39.130 0.00 0.00 0.00 2.57
3341 3815 7.611467 TCTTGTTCATATGCCAAATCTAACTGT 59.389 33.333 0.00 0.00 0.00 3.55
3387 3861 4.699925 TCAAGGCAGTATACCAATACCC 57.300 45.455 0.00 0.00 39.08 3.69
3541 4024 0.537828 TTCCATCTGCAGTGCAAGCA 60.538 50.000 20.22 13.69 38.41 3.91
3726 4212 7.481275 TTTGAACAGAAATCAAATTGAAGGC 57.519 32.000 0.00 0.00 40.75 4.35
3750 4236 6.307155 CGAACTACCAAGATCATTGTCAAAC 58.693 40.000 0.00 0.00 0.00 2.93
3819 4305 2.069775 TCCTTTCCATCTTGGTTGGGA 58.930 47.619 0.00 0.00 39.03 4.37
3895 4381 2.166907 AAGGGATCTCGATGGTGACT 57.833 50.000 0.00 0.00 0.00 3.41
3896 4382 1.407936 AGGGATCTCGATGGTGACTG 58.592 55.000 0.00 0.00 0.00 3.51
3981 4467 1.273327 CACCTGCCAAAAGGATGGTTC 59.727 52.381 0.00 0.00 42.75 3.62
4035 4521 1.481363 GAGGAGGGACGAGTTTTAGGG 59.519 57.143 0.00 0.00 0.00 3.53
4053 4539 4.339872 AGGGTATTACACAAACACGACA 57.660 40.909 0.00 0.00 0.00 4.35
4099 4585 3.189606 ACCATCACACTTAAGGGATCCA 58.810 45.455 12.83 0.00 0.00 3.41
4203 4689 4.082787 TCAATTGGGAATCTTGTTTCGCTC 60.083 41.667 5.42 0.00 38.84 5.03
4497 4983 3.929610 GTGAGACTACAGATTCAACTGCC 59.070 47.826 0.00 0.00 41.06 4.85
4678 5182 4.169059 TGGTAAATCCATGTGCTATGCT 57.831 40.909 0.00 0.00 41.93 3.79
4760 5264 8.136800 TGTTCATAGTTTGTACTTGTTAGACGA 58.863 33.333 0.00 0.00 35.78 4.20
4762 5266 7.310664 TCATAGTTTGTACTTGTTAGACGAGG 58.689 38.462 0.00 0.00 33.85 4.63
4843 5347 8.076178 ACAAAGTACTTGTATGCTTCATTTCAC 58.924 33.333 9.34 0.00 46.75 3.18
4923 5428 9.828039 TGCATTGCATTTTTATTTCATATGGTA 57.172 25.926 7.38 0.00 31.71 3.25
4970 5475 4.894114 AGGCACTAGTGGTATCGACTAAAT 59.106 41.667 23.95 0.00 36.02 1.40
4975 5480 7.751348 GCACTAGTGGTATCGACTAAATATGAG 59.249 40.741 23.95 0.00 0.00 2.90
4990 5495 0.253327 ATGAGACGAAAAGGGGAGGC 59.747 55.000 0.00 0.00 0.00 4.70
4991 5496 1.448013 GAGACGAAAAGGGGAGGCG 60.448 63.158 0.00 0.00 0.00 5.52
4993 5498 3.246880 ACGAAAAGGGGAGGCGGT 61.247 61.111 0.00 0.00 0.00 5.68
4994 5499 2.746277 CGAAAAGGGGAGGCGGTG 60.746 66.667 0.00 0.00 0.00 4.94
4996 5501 3.182996 AAAAGGGGAGGCGGTGGT 61.183 61.111 0.00 0.00 0.00 4.16
4997 5502 3.507377 AAAAGGGGAGGCGGTGGTG 62.507 63.158 0.00 0.00 0.00 4.17
5412 5917 7.728532 TCCTATTGTGCACTCCAGTAGAATATA 59.271 37.037 19.41 0.49 0.00 0.86
5460 5965 4.645535 TGGAGACCAAGAGTGAAATTCAG 58.354 43.478 0.00 0.00 0.00 3.02
5473 5978 6.459066 AGTGAAATTCAGATCGAACTTCTCA 58.541 36.000 16.46 9.01 39.91 3.27
5483 5988 7.169308 TCAGATCGAACTTCTCAGTTTGTTTAC 59.831 37.037 0.00 0.00 43.79 2.01
5495 6001 7.827236 TCTCAGTTTGTTTACTTCTCAGGAAAA 59.173 33.333 0.00 0.00 34.37 2.29
5699 6222 4.370049 CTGATCATCCTACAAGCAGAGTG 58.630 47.826 0.00 0.00 0.00 3.51
5731 6254 9.937175 AAAGTGAGTATTTTTCTTCTTTTCTCG 57.063 29.630 0.00 0.00 0.00 4.04
5773 6297 5.227569 ACATGTACTTGGAGTGATCAACA 57.772 39.130 12.86 0.00 0.00 3.33
5909 6434 4.439776 GTGTTTGTTTTACGAATCACCAGC 59.560 41.667 0.00 0.00 0.00 4.85
6018 6568 5.545658 TCCATTTCTGCGACAAGTAATTC 57.454 39.130 0.00 0.00 0.00 2.17
6019 6569 4.092821 TCCATTTCTGCGACAAGTAATTCG 59.907 41.667 0.00 0.00 38.31 3.34
6020 6570 4.334443 CATTTCTGCGACAAGTAATTCGG 58.666 43.478 0.00 0.00 35.73 4.30
6021 6571 2.004583 TCTGCGACAAGTAATTCGGG 57.995 50.000 0.00 0.00 35.73 5.14
6022 6572 1.546923 TCTGCGACAAGTAATTCGGGA 59.453 47.619 0.00 0.00 35.73 5.14
6023 6573 1.659098 CTGCGACAAGTAATTCGGGAC 59.341 52.381 0.00 0.00 35.73 4.46
6024 6574 1.001068 TGCGACAAGTAATTCGGGACA 59.999 47.619 0.00 0.00 35.73 4.02
6035 6585 0.702902 TTCGGGACAGAGGGAGTAGT 59.297 55.000 0.00 0.00 0.00 2.73
6106 6658 6.100404 ACAATTTTGCACCACTGTCAATAT 57.900 33.333 0.00 0.00 0.00 1.28
6194 6747 1.901591 CCTTGAGCTGTGACACCATT 58.098 50.000 2.45 0.00 0.00 3.16
6228 6781 6.917477 CGTGCCATTGTTAAAAGCATACATAT 59.083 34.615 0.00 0.00 32.97 1.78
6254 6807 3.250323 CTGTCATCGACCAGCGCG 61.250 66.667 0.00 0.00 40.61 6.86
6393 6946 2.194800 ACATGAGTGATACGAGTGCG 57.805 50.000 0.00 0.00 44.79 5.34
6569 7151 7.813645 TGCTTATCTTGCTTATATTGATGCAG 58.186 34.615 0.00 0.00 36.75 4.41
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
68 69 3.733337 TGAGCTGGTTCTTCAGTCTTTC 58.267 45.455 0.00 0.00 37.12 2.62
87 89 7.309133 CCATCTTTACTGGTACAAAAAGCATGA 60.309 37.037 0.00 0.00 39.65 3.07
159 161 3.181500 CCTTCGTCATCGACATACTGACA 60.181 47.826 14.56 1.93 46.03 3.58
170 172 6.530534 ACTTATTAGTGTTTCCTTCGTCATCG 59.469 38.462 0.00 0.00 31.99 3.84
232 236 1.743394 GCGGAAAATTCTCGGTCCAAT 59.257 47.619 0.00 0.00 0.00 3.16
233 237 1.161843 GCGGAAAATTCTCGGTCCAA 58.838 50.000 0.00 0.00 0.00 3.53
459 467 2.951642 TGGGTATTACCGAACGACCTAG 59.048 50.000 6.77 0.00 39.83 3.02
493 610 3.181397 CGAAAATGCACACATCCCATTC 58.819 45.455 0.00 0.00 34.62 2.67
494 611 2.562298 ACGAAAATGCACACATCCCATT 59.438 40.909 0.00 0.00 34.62 3.16
552 670 3.756727 GCTTTGCTGCTGGAGGCC 61.757 66.667 0.00 0.00 40.92 5.19
628 746 3.251729 GTGAACTTCAAAGCAGAGCATGA 59.748 43.478 0.00 0.00 0.00 3.07
629 747 3.562505 GTGAACTTCAAAGCAGAGCATG 58.437 45.455 0.00 0.00 0.00 4.06
661 779 7.465245 GCTCCGATCATTTTGTTTTGTTTTTCA 60.465 33.333 0.00 0.00 0.00 2.69
727 845 3.450817 GGCAAACCTAAGCCCAACAATAT 59.549 43.478 0.00 0.00 45.18 1.28
796 919 1.981256 TGGTTCCTGAAGTCTTTGGC 58.019 50.000 0.00 0.00 0.00 4.52
986 1113 0.034337 CACCATTTTGCTGCTGGCTT 59.966 50.000 5.64 0.00 42.39 4.35
987 1114 1.669440 CACCATTTTGCTGCTGGCT 59.331 52.632 5.64 0.00 42.39 4.75
1080 1207 2.124487 ACGGTGGTGGTGGTGTTG 60.124 61.111 0.00 0.00 0.00 3.33
1081 1208 2.191109 GACGGTGGTGGTGGTGTT 59.809 61.111 0.00 0.00 0.00 3.32
1082 1209 3.084646 TGACGGTGGTGGTGGTGT 61.085 61.111 0.00 0.00 0.00 4.16
1284 1411 4.988716 AGGAGTGCGGGGTCGACA 62.989 66.667 18.91 0.00 39.00 4.35
1322 1449 2.203832 TGGTGCTGAGGCTCAGGA 60.204 61.111 37.73 34.85 44.43 3.86
1334 1461 2.126888 CGGAAATGCGTGTGGTGC 60.127 61.111 0.00 0.00 0.00 5.01
1352 1479 0.833287 GCTCAGTGAAGATAGCCCCA 59.167 55.000 0.00 0.00 0.00 4.96
1359 1486 1.065564 GGGAGCTTGCTCAGTGAAGAT 60.066 52.381 21.97 0.00 0.00 2.40
1425 1552 0.397816 AAGATAGCTCCGGACCTGCT 60.398 55.000 19.35 19.35 40.43 4.24
1427 1554 0.312416 CGAAGATAGCTCCGGACCTG 59.688 60.000 9.67 0.00 0.00 4.00
1510 1637 1.134280 CAGATTGCCGATCCAAGAGGT 60.134 52.381 0.00 0.00 35.21 3.85
1557 1684 0.887387 GCCCGGTGAAACTGCAACTA 60.887 55.000 0.00 0.00 43.57 2.24
1578 1705 3.552875 AGTTCCAATCTGATCAGGCATG 58.447 45.455 22.42 17.01 0.00 4.06
1579 1706 3.458857 AGAGTTCCAATCTGATCAGGCAT 59.541 43.478 22.42 6.98 0.00 4.40
1614 1741 5.726980 TGCAATTTTCTAAATCCAGCAGT 57.273 34.783 0.00 0.00 0.00 4.40
1626 1753 2.556622 CCCGGTGTAGTTGCAATTTTCT 59.443 45.455 0.59 0.00 0.00 2.52
1674 1801 4.204012 CCAACTTTGTCAACCTGGTAAGA 58.796 43.478 12.10 5.68 0.00 2.10
1691 1818 0.251787 GCAACCTTGGATCCCCAACT 60.252 55.000 9.90 0.00 46.94 3.16
1696 1823 2.440247 CCGGCAACCTTGGATCCC 60.440 66.667 9.90 0.00 0.00 3.85
1698 1825 1.728490 GATGCCGGCAACCTTGGATC 61.728 60.000 36.33 20.18 0.00 3.36
1725 1852 2.203209 GCGATTGCCGAGGGGATT 60.203 61.111 0.00 0.00 41.76 3.01
1728 1855 2.749839 TTTGCGATTGCCGAGGGG 60.750 61.111 1.50 0.00 41.78 4.79
1814 1941 7.912773 GCTAGGAACAAAAAGAAGCATTATCTC 59.087 37.037 0.00 0.00 0.00 2.75
1952 2079 9.296400 TGCAAAAATGTTTTACTCTTTCTGTAC 57.704 29.630 0.00 0.00 0.00 2.90
2012 2148 6.384886 ACAAATATTTAGGAACGGAGGGAGTA 59.615 38.462 0.00 0.00 0.00 2.59
2013 2149 5.191124 ACAAATATTTAGGAACGGAGGGAGT 59.809 40.000 0.00 0.00 0.00 3.85
2014 2150 5.681639 ACAAATATTTAGGAACGGAGGGAG 58.318 41.667 0.00 0.00 0.00 4.30
2015 2151 5.427481 AGACAAATATTTAGGAACGGAGGGA 59.573 40.000 0.00 0.00 0.00 4.20
2016 2152 5.681639 AGACAAATATTTAGGAACGGAGGG 58.318 41.667 0.00 0.00 0.00 4.30
2017 2153 7.553044 AGAAAGACAAATATTTAGGAACGGAGG 59.447 37.037 0.00 0.00 0.00 4.30
2018 2154 8.494016 AGAAAGACAAATATTTAGGAACGGAG 57.506 34.615 0.00 0.00 0.00 4.63
2019 2155 9.595823 CTAGAAAGACAAATATTTAGGAACGGA 57.404 33.333 0.00 0.00 0.00 4.69
2020 2156 9.595823 TCTAGAAAGACAAATATTTAGGAACGG 57.404 33.333 0.00 0.00 0.00 4.44
2033 2169 9.396022 ACTTGTTGAAATCTCTAGAAAGACAAA 57.604 29.630 0.00 0.00 0.00 2.83
2034 2170 8.830580 CACTTGTTGAAATCTCTAGAAAGACAA 58.169 33.333 0.00 0.00 0.00 3.18
2035 2171 8.204160 TCACTTGTTGAAATCTCTAGAAAGACA 58.796 33.333 0.00 0.00 0.00 3.41
2036 2172 8.491950 GTCACTTGTTGAAATCTCTAGAAAGAC 58.508 37.037 0.00 0.00 35.39 3.01
2037 2173 8.424918 AGTCACTTGTTGAAATCTCTAGAAAGA 58.575 33.333 0.00 0.00 35.39 2.52
2038 2174 8.600449 AGTCACTTGTTGAAATCTCTAGAAAG 57.400 34.615 0.00 0.00 35.39 2.62
2039 2175 9.477484 GTAGTCACTTGTTGAAATCTCTAGAAA 57.523 33.333 0.00 0.00 35.39 2.52
2040 2176 8.638873 TGTAGTCACTTGTTGAAATCTCTAGAA 58.361 33.333 0.00 0.00 35.39 2.10
2041 2177 8.178313 TGTAGTCACTTGTTGAAATCTCTAGA 57.822 34.615 0.00 0.00 35.39 2.43
2042 2178 8.994429 ATGTAGTCACTTGTTGAAATCTCTAG 57.006 34.615 0.00 0.00 35.39 2.43
2043 2179 9.856488 GTATGTAGTCACTTGTTGAAATCTCTA 57.144 33.333 0.00 0.00 35.39 2.43
2044 2180 7.542477 CGTATGTAGTCACTTGTTGAAATCTCT 59.458 37.037 0.00 0.00 35.39 3.10
2045 2181 7.201444 CCGTATGTAGTCACTTGTTGAAATCTC 60.201 40.741 0.00 0.00 35.39 2.75
2046 2182 6.590292 CCGTATGTAGTCACTTGTTGAAATCT 59.410 38.462 0.00 0.00 35.39 2.40
2047 2183 6.588756 TCCGTATGTAGTCACTTGTTGAAATC 59.411 38.462 0.00 0.00 35.39 2.17
2048 2184 6.460781 TCCGTATGTAGTCACTTGTTGAAAT 58.539 36.000 0.00 0.00 35.39 2.17
2049 2185 5.845103 TCCGTATGTAGTCACTTGTTGAAA 58.155 37.500 0.00 0.00 35.39 2.69
2050 2186 5.456548 TCCGTATGTAGTCACTTGTTGAA 57.543 39.130 0.00 0.00 35.39 2.69
2051 2187 4.617530 GCTCCGTATGTAGTCACTTGTTGA 60.618 45.833 0.00 0.00 0.00 3.18
2052 2188 3.612860 GCTCCGTATGTAGTCACTTGTTG 59.387 47.826 0.00 0.00 0.00 3.33
2053 2189 3.257375 TGCTCCGTATGTAGTCACTTGTT 59.743 43.478 0.00 0.00 0.00 2.83
2054 2190 2.823747 TGCTCCGTATGTAGTCACTTGT 59.176 45.455 0.00 0.00 0.00 3.16
2055 2191 3.503827 TGCTCCGTATGTAGTCACTTG 57.496 47.619 0.00 0.00 0.00 3.16
2056 2192 4.530710 TTTGCTCCGTATGTAGTCACTT 57.469 40.909 0.00 0.00 0.00 3.16
2057 2193 4.530710 TTTTGCTCCGTATGTAGTCACT 57.469 40.909 0.00 0.00 0.00 3.41
2058 2194 4.868171 TCATTTTGCTCCGTATGTAGTCAC 59.132 41.667 0.00 0.00 0.00 3.67
2059 2195 5.079689 TCATTTTGCTCCGTATGTAGTCA 57.920 39.130 0.00 0.00 0.00 3.41
2060 2196 5.005779 CACTCATTTTGCTCCGTATGTAGTC 59.994 44.000 0.00 0.00 0.00 2.59
2061 2197 4.870426 CACTCATTTTGCTCCGTATGTAGT 59.130 41.667 0.00 0.00 0.00 2.73
2062 2198 5.109210 TCACTCATTTTGCTCCGTATGTAG 58.891 41.667 0.00 0.00 0.00 2.74
2063 2199 5.079689 TCACTCATTTTGCTCCGTATGTA 57.920 39.130 0.00 0.00 0.00 2.29
2064 2200 3.937814 TCACTCATTTTGCTCCGTATGT 58.062 40.909 0.00 0.00 0.00 2.29
2065 2201 4.944962 TTCACTCATTTTGCTCCGTATG 57.055 40.909 0.00 0.00 0.00 2.39
2066 2202 5.431765 AGATTCACTCATTTTGCTCCGTAT 58.568 37.500 0.00 0.00 0.00 3.06
2067 2203 4.832248 AGATTCACTCATTTTGCTCCGTA 58.168 39.130 0.00 0.00 0.00 4.02
2068 2204 3.679389 AGATTCACTCATTTTGCTCCGT 58.321 40.909 0.00 0.00 0.00 4.69
2069 2205 4.631377 TGTAGATTCACTCATTTTGCTCCG 59.369 41.667 0.00 0.00 0.00 4.63
2070 2206 5.645497 AGTGTAGATTCACTCATTTTGCTCC 59.355 40.000 0.00 0.00 44.07 4.70
2071 2207 6.734104 AGTGTAGATTCACTCATTTTGCTC 57.266 37.500 0.00 0.00 44.07 4.26
2101 2237 9.470399 ACCACATACGGATGTATATAAGACATA 57.530 33.333 14.23 0.00 44.82 2.29
2102 2238 8.362464 ACCACATACGGATGTATATAAGACAT 57.638 34.615 14.23 3.86 44.82 3.06
2103 2239 7.770366 ACCACATACGGATGTATATAAGACA 57.230 36.000 14.23 0.00 44.82 3.41
2104 2240 8.954350 ACTACCACATACGGATGTATATAAGAC 58.046 37.037 14.23 0.00 44.82 3.01
2105 2241 9.170734 GACTACCACATACGGATGTATATAAGA 57.829 37.037 14.23 0.00 44.82 2.10
2106 2242 8.404000 GGACTACCACATACGGATGTATATAAG 58.596 40.741 14.23 9.25 44.82 1.73
2107 2243 7.889600 TGGACTACCACATACGGATGTATATAA 59.110 37.037 14.23 0.00 44.82 0.98
2108 2244 7.404481 TGGACTACCACATACGGATGTATATA 58.596 38.462 14.23 5.36 44.82 0.86
2109 2245 6.250711 TGGACTACCACATACGGATGTATAT 58.749 40.000 14.23 4.37 44.82 0.86
2110 2246 5.633117 TGGACTACCACATACGGATGTATA 58.367 41.667 14.23 8.27 44.82 1.47
2111 2247 4.476297 TGGACTACCACATACGGATGTAT 58.524 43.478 14.23 7.46 44.82 2.29
2112 2248 3.900971 TGGACTACCACATACGGATGTA 58.099 45.455 14.23 0.00 44.82 2.29
2128 2264 9.354673 TGTCTTTTTAGAGATTTCAAATGGACT 57.645 29.630 0.00 0.00 0.00 3.85
2129 2265 9.965824 TTGTCTTTTTAGAGATTTCAAATGGAC 57.034 29.630 0.00 0.00 0.00 4.02
2146 2282 8.520351 CCTCCGTTCCTAAATATTTGTCTTTTT 58.480 33.333 11.05 0.00 0.00 1.94
2147 2283 7.122204 CCCTCCGTTCCTAAATATTTGTCTTTT 59.878 37.037 11.05 0.00 0.00 2.27
2148 2284 6.602009 CCCTCCGTTCCTAAATATTTGTCTTT 59.398 38.462 11.05 0.00 0.00 2.52
2149 2285 6.069847 TCCCTCCGTTCCTAAATATTTGTCTT 60.070 38.462 11.05 0.00 0.00 3.01
2150 2286 5.427481 TCCCTCCGTTCCTAAATATTTGTCT 59.573 40.000 11.05 0.00 0.00 3.41
2151 2287 5.677567 TCCCTCCGTTCCTAAATATTTGTC 58.322 41.667 11.05 0.00 0.00 3.18
2152 2288 5.191124 ACTCCCTCCGTTCCTAAATATTTGT 59.809 40.000 11.05 0.00 0.00 2.83
2153 2289 5.681639 ACTCCCTCCGTTCCTAAATATTTG 58.318 41.667 11.05 1.40 0.00 2.32
2154 2290 5.970501 ACTCCCTCCGTTCCTAAATATTT 57.029 39.130 5.89 5.89 0.00 1.40
2155 2291 6.141790 ACTACTCCCTCCGTTCCTAAATATT 58.858 40.000 0.00 0.00 0.00 1.28
2156 2292 5.713807 ACTACTCCCTCCGTTCCTAAATAT 58.286 41.667 0.00 0.00 0.00 1.28
2157 2293 5.134725 ACTACTCCCTCCGTTCCTAAATA 57.865 43.478 0.00 0.00 0.00 1.40
2158 2294 3.991683 ACTACTCCCTCCGTTCCTAAAT 58.008 45.455 0.00 0.00 0.00 1.40
2159 2295 3.463048 ACTACTCCCTCCGTTCCTAAA 57.537 47.619 0.00 0.00 0.00 1.85
2160 2296 3.094572 CAACTACTCCCTCCGTTCCTAA 58.905 50.000 0.00 0.00 0.00 2.69
2161 2297 2.042162 ACAACTACTCCCTCCGTTCCTA 59.958 50.000 0.00 0.00 0.00 2.94
2162 2298 1.203149 ACAACTACTCCCTCCGTTCCT 60.203 52.381 0.00 0.00 0.00 3.36
2163 2299 1.067071 CACAACTACTCCCTCCGTTCC 60.067 57.143 0.00 0.00 0.00 3.62
2164 2300 1.617357 ACACAACTACTCCCTCCGTTC 59.383 52.381 0.00 0.00 0.00 3.95
2165 2301 1.713297 ACACAACTACTCCCTCCGTT 58.287 50.000 0.00 0.00 0.00 4.44
2166 2302 2.224967 ACTACACAACTACTCCCTCCGT 60.225 50.000 0.00 0.00 0.00 4.69
2167 2303 2.163815 CACTACACAACTACTCCCTCCG 59.836 54.545 0.00 0.00 0.00 4.63
2168 2304 2.094130 GCACTACACAACTACTCCCTCC 60.094 54.545 0.00 0.00 0.00 4.30
2169 2305 2.826725 AGCACTACACAACTACTCCCTC 59.173 50.000 0.00 0.00 0.00 4.30
2170 2306 2.890814 AGCACTACACAACTACTCCCT 58.109 47.619 0.00 0.00 0.00 4.20
2171 2307 3.326747 CAAGCACTACACAACTACTCCC 58.673 50.000 0.00 0.00 0.00 4.30
2172 2308 2.737252 GCAAGCACTACACAACTACTCC 59.263 50.000 0.00 0.00 0.00 3.85
2173 2309 2.737252 GGCAAGCACTACACAACTACTC 59.263 50.000 0.00 0.00 0.00 2.59
2174 2310 2.368875 AGGCAAGCACTACACAACTACT 59.631 45.455 0.00 0.00 0.00 2.57
2175 2311 2.767505 AGGCAAGCACTACACAACTAC 58.232 47.619 0.00 0.00 0.00 2.73
2535 2783 7.635648 ACTTAAATAACACTACTAATGCCCCA 58.364 34.615 0.00 0.00 0.00 4.96
2612 3083 7.961351 TGAAACAATCCATGATTTTTAGGTGT 58.039 30.769 0.00 0.00 28.87 4.16
2713 3184 9.744468 TTCCAGTGCTTCTAAAAGAAAATTAAC 57.256 29.630 0.00 0.00 33.19 2.01
3084 3558 6.842676 AGGAAGAGAGTTTAAAACATCACCT 58.157 36.000 0.00 0.00 0.00 4.00
3141 3615 2.888414 GGAACCCGGAAATTTTGTGAGA 59.112 45.455 0.73 0.00 0.00 3.27
3162 3636 8.798402 ACGGAAACTTTATCTAGATATCTCAGG 58.202 37.037 13.22 1.99 0.00 3.86
3253 3727 4.723309 AGATTCAAACTCTCAAGCTGGTT 58.277 39.130 0.00 0.00 0.00 3.67
3273 3747 0.319469 TGAACATGTTGCGCGAGAGA 60.319 50.000 17.58 0.00 0.00 3.10
3341 3815 9.167311 GAAGCCTATTAAAACTGAGATCAAGAA 57.833 33.333 0.00 0.00 0.00 2.52
3387 3861 0.676466 TCCCAGGCATTGCAGTTACG 60.676 55.000 11.39 0.00 0.00 3.18
3541 4024 6.821616 AGACAGGTCCAAGATATTGAGATT 57.178 37.500 0.54 0.00 0.00 2.40
3726 4212 6.147821 AGTTTGACAATGATCTTGGTAGTTCG 59.852 38.462 8.95 0.00 0.00 3.95
3819 4305 4.044698 AGGACCCTAAGCTTTGGAAGAATT 59.955 41.667 26.04 5.82 0.00 2.17
3835 4321 1.264295 GACCGTAAGACAAGGACCCT 58.736 55.000 0.00 0.00 43.02 4.34
3885 4371 0.034756 TGGTTCCACAGTCACCATCG 59.965 55.000 0.00 0.00 35.57 3.84
3895 4381 2.582052 GAACTGGTTGATGGTTCCACA 58.418 47.619 0.00 0.00 34.90 4.17
3905 4391 1.754226 GCAAACTTGGGAACTGGTTGA 59.246 47.619 0.00 0.00 35.34 3.18
4035 4521 5.177881 TCCATGTGTCGTGTTTGTGTAATAC 59.822 40.000 0.00 0.00 0.00 1.89
4053 4539 7.765695 AACAGTGTCTTGATAAAATCCATGT 57.234 32.000 0.00 0.00 0.00 3.21
4099 4585 9.588096 AGTTAGAATCTTGGTGAAAATAAGGTT 57.412 29.630 0.00 0.00 0.00 3.50
4203 4689 3.181449 TGGATGACATATTAACCCCGTGG 60.181 47.826 0.00 0.00 37.80 4.94
4497 4983 1.304713 AGGGGCCAATGCACTTGAG 60.305 57.895 4.39 3.19 42.08 3.02
4748 5252 3.470645 AAGTTGCCTCGTCTAACAAGT 57.529 42.857 0.00 0.00 0.00 3.16
4760 5264 9.301897 AGACAAAGAGAATTAAATAAGTTGCCT 57.698 29.630 0.00 0.00 0.00 4.75
4762 5266 9.346725 CCAGACAAAGAGAATTAAATAAGTTGC 57.653 33.333 0.00 0.00 0.00 4.17
4843 5347 8.657074 ATTCATCAATTTTGCAATCCATACAG 57.343 30.769 0.00 0.00 0.00 2.74
4923 5428 8.199449 CCTTCCAGCATGATAAAACAATATGTT 58.801 33.333 0.00 0.00 39.99 2.71
4924 5429 7.685155 GCCTTCCAGCATGATAAAACAATATGT 60.685 37.037 0.00 0.00 39.69 2.29
4970 5475 1.485066 GCCTCCCCTTTTCGTCTCATA 59.515 52.381 0.00 0.00 0.00 2.15
4975 5480 2.436115 CCGCCTCCCCTTTTCGTC 60.436 66.667 0.00 0.00 0.00 4.20
5322 5827 6.785191 AGTGCCATGTAATAAAGTTTGATCG 58.215 36.000 0.00 0.00 0.00 3.69
5460 5965 7.409465 AGTAAACAAACTGAGAAGTTCGATC 57.591 36.000 0.00 0.00 0.00 3.69
5473 5978 8.575649 TTCTTTTCCTGAGAAGTAAACAAACT 57.424 30.769 0.00 0.00 32.35 2.66
5544 6050 2.298729 TGCAAGAAATTAACCTGGTGGC 59.701 45.455 0.00 0.00 36.63 5.01
5545 6051 4.806640 ATGCAAGAAATTAACCTGGTGG 57.193 40.909 0.00 0.00 39.83 4.61
5722 6245 9.677567 CTTGGAATATTTTGTTTCGAGAAAAGA 57.322 29.630 0.00 2.25 31.33 2.52
5773 6297 5.187772 TCTCATCTTGTATGCAACCTACACT 59.812 40.000 0.00 0.00 0.00 3.55
5853 6377 9.029243 TGTTTTATTGTCAAAACTGCACATAAG 57.971 29.630 11.45 0.00 44.86 1.73
5886 6411 4.439776 GCTGGTGATTCGTAAAACAAACAC 59.560 41.667 0.00 0.00 0.00 3.32
5995 6545 5.220662 CGAATTACTTGTCGCAGAAATGGAT 60.221 40.000 0.00 0.00 39.69 3.41
6018 6568 2.299521 CTTACTACTCCCTCTGTCCCG 58.700 57.143 0.00 0.00 0.00 5.14
6019 6569 3.385314 ACTTACTACTCCCTCTGTCCC 57.615 52.381 0.00 0.00 0.00 4.46
6020 6570 6.367161 AGATTACTTACTACTCCCTCTGTCC 58.633 44.000 0.00 0.00 0.00 4.02
6021 6571 7.171337 CGTAGATTACTTACTACTCCCTCTGTC 59.829 44.444 0.00 0.00 37.43 3.51
6022 6572 6.991531 CGTAGATTACTTACTACTCCCTCTGT 59.008 42.308 0.00 0.00 37.43 3.41
6023 6573 6.991531 ACGTAGATTACTTACTACTCCCTCTG 59.008 42.308 0.00 0.00 37.43 3.35
6024 6574 7.135591 ACGTAGATTACTTACTACTCCCTCT 57.864 40.000 0.00 0.00 37.43 3.69
6035 6585 6.985117 ACTGTTGTGGAACGTAGATTACTTA 58.015 36.000 0.00 0.00 42.39 2.24
6106 6658 2.441750 ACTTACCCAACAGAGCAAAGGA 59.558 45.455 0.00 0.00 0.00 3.36
6194 6747 4.071875 AATGGCACGACCGCGGTA 62.072 61.111 34.36 15.86 43.94 4.02
6228 6781 2.046285 TCGATGACAGAGGCGCTCA 61.046 57.895 7.64 2.35 32.06 4.26
6290 6843 1.352622 TGGAGAGCTTTGGTGGTGGT 61.353 55.000 0.00 0.00 0.00 4.16
6404 6957 1.154430 TGGTTAGGCCTTGGGTCTTT 58.846 50.000 12.58 0.00 39.09 2.52
6457 7010 2.420372 GGAGGCTTCTTCGAATTTGACC 59.580 50.000 0.00 0.00 0.00 4.02
6488 7041 1.827344 CTGAGATCAGGGCTGTACACA 59.173 52.381 1.70 0.00 40.20 3.72
6551 7105 7.719778 TCTACACTGCATCAATATAAGCAAG 57.280 36.000 0.00 0.00 36.44 4.01
6554 7108 7.439356 TCTGTTCTACACTGCATCAATATAAGC 59.561 37.037 0.00 0.00 0.00 3.09
6569 7151 8.831550 AGAAAATTTTCACTCTCTGTTCTACAC 58.168 33.333 28.00 0.45 39.61 2.90


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

AutoCloner maintained by Alex Coulton.