Multiple sequence alignment - TraesCS6B01G315800

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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 TraesCS6B01G315800 chr6B 100.000 6381 0 0 1 6381 563994774 564001154 0.000000e+00 11784.0
1 TraesCS6B01G315800 chr6D 95.191 3660 133 25 2156 5793 377544325 377547963 0.000000e+00 5744.0
2 TraesCS6B01G315800 chr6D 89.723 1479 94 29 583 2038 377542881 377544324 0.000000e+00 1836.0
3 TraesCS6B01G315800 chr6D 94.624 558 25 5 5825 6381 377548333 377548886 0.000000e+00 859.0
4 TraesCS6B01G315800 chr6D 96.226 53 0 1 529 579 377541724 377541776 1.140000e-12 86.1
5 TraesCS6B01G315800 chr6A 94.592 3661 155 23 2109 5757 519206455 519210084 0.000000e+00 5624.0
6 TraesCS6B01G315800 chr6A 95.323 1176 42 6 889 2061 519205290 519206455 0.000000e+00 1855.0
7 TraesCS6B01G315800 chr6A 85.516 504 49 12 1 484 519204349 519204848 7.380000e-139 505.0
8 TraesCS6B01G315800 chr6A 95.833 48 2 0 824 871 519205255 519205302 1.910000e-10 78.7
9 TraesCS6B01G315800 chr6A 73.869 199 37 14 555 745 604584970 604584779 1.480000e-06 65.8
10 TraesCS6B01G315800 chr4B 85.859 198 20 5 1825 2020 493764672 493764863 3.020000e-48 204.0
11 TraesCS6B01G315800 chrUn 87.952 166 20 0 5241 5406 51474383 51474548 5.050000e-46 196.0
12 TraesCS6B01G315800 chrUn 87.952 166 20 0 5241 5406 339606595 339606760 5.050000e-46 196.0
13 TraesCS6B01G315800 chr2A 86.061 165 23 0 5240 5404 116733675 116733511 1.830000e-40 178.0
14 TraesCS6B01G315800 chr2A 100.000 34 0 0 562 595 734252466 734252433 5.340000e-06 63.9
15 TraesCS6B01G315800 chr2A 97.059 34 1 0 569 602 25582278 25582311 2.480000e-04 58.4
16 TraesCS6B01G315800 chr2D 87.919 149 18 0 5240 5388 346421404 346421552 6.580000e-40 176.0
17 TraesCS6B01G315800 chr1D 89.344 122 10 3 2012 2133 275135689 275135807 3.990000e-32 150.0
18 TraesCS6B01G315800 chr1D 87.395 119 12 2 2019 2134 3824150 3824268 4.010000e-27 134.0
19 TraesCS6B01G315800 chr1D 86.667 120 12 2 2020 2135 212424821 212424940 5.190000e-26 130.0
20 TraesCS6B01G315800 chr1D 86.325 117 16 0 2016 2132 479527104 479527220 1.870000e-25 128.0
21 TraesCS6B01G315800 chr2B 88.235 119 9 2 2019 2132 534232740 534232622 3.100000e-28 137.0
22 TraesCS6B01G315800 chr2B 88.136 118 10 2 2019 2132 777495025 777494908 3.100000e-28 137.0
23 TraesCS6B01G315800 chr2B 80.519 77 13 2 577 652 667821235 667821310 2.480000e-04 58.4
24 TraesCS6B01G315800 chr2B 100.000 28 0 0 380 407 371896231 371896258 1.200000e-02 52.8
25 TraesCS6B01G315800 chr7D 88.034 117 11 1 2016 2132 335401378 335401491 1.120000e-27 135.0
26 TraesCS6B01G315800 chr7D 86.441 118 12 2 2019 2132 485101804 485101687 6.720000e-25 126.0
27 TraesCS6B01G315800 chr7D 86.667 60 4 2 363 421 27818841 27818897 5.340000e-06 63.9
28 TraesCS6B01G315800 chr3D 87.288 118 14 1 2015 2132 138182974 138182858 4.010000e-27 134.0
29 TraesCS6B01G315800 chr7B 92.593 54 3 1 549 601 440182419 440182366 6.860000e-10 76.8
30 TraesCS6B01G315800 chr7A 79.167 96 19 1 520 614 638232267 638232172 1.480000e-06 65.8
31 TraesCS6B01G315800 chr1B 94.595 37 1 1 553 589 4201634 4201669 8.940000e-04 56.5


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS6B01G315800 chr6B 563994774 564001154 6380 False 11784.000 11784 100.000 1 6381 1 chr6B.!!$F1 6380
1 TraesCS6B01G315800 chr6D 377541724 377548886 7162 False 2131.275 5744 93.941 529 6381 4 chr6D.!!$F1 5852
2 TraesCS6B01G315800 chr6A 519204349 519210084 5735 False 2015.675 5624 92.816 1 5757 4 chr6A.!!$F1 5756

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
194 196 0.037232 AGTTAGTGCTCCGGTTCAGC 60.037 55.000 6.68 6.68 37.40 4.26 F
743 1970 0.102663 TTTCAAAACCGGCCGAAACC 59.897 50.000 30.73 0.00 0.00 3.27 F
1668 2939 0.179056 CTGGTATAGCCCCACGGTTG 60.179 60.000 0.00 0.00 36.04 3.77 F
1682 2953 1.081242 GGTTGCTGTTGCCATGACG 60.081 57.895 0.00 0.00 38.71 4.35 F
2407 3680 1.757682 AGGAGAGGAAGTCGCTACTG 58.242 55.000 0.00 0.00 35.02 2.74 F
2632 3905 3.244215 TGCTTATCTGATAGCCCTTTCCG 60.244 47.826 13.06 0.00 0.00 4.30 F
3408 4692 3.715495 CTGTGTCTCTGCATCTATCCAC 58.285 50.000 0.00 0.00 0.00 4.02 F
4129 5417 1.407258 CCCTGCTCACGTTTTGGAAAA 59.593 47.619 0.00 0.00 0.00 2.29 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1425 2692 0.840617 TGAATGCCGCTAATGGGGTA 59.159 50.000 0.00 0.00 46.69 3.69 R
2530 3803 1.895798 AGACGTGAGAAGAGAATGCCA 59.104 47.619 0.00 0.00 0.00 4.92 R
3616 4904 1.003118 TCACCACTGGATTTCTTCCCG 59.997 52.381 0.71 0.00 44.77 5.14 R
3676 4964 8.766000 TGAATTCAACTGAATCATTTGGATTG 57.234 30.769 20.16 3.76 46.17 2.67 R
4041 5329 0.109153 AGCACCAAGACACTCATGCA 59.891 50.000 0.00 0.00 35.51 3.96 R
4042 5330 1.242076 AAGCACCAAGACACTCATGC 58.758 50.000 0.00 0.00 0.00 4.06 R
5150 6440 0.904649 TCCTCCGTTCACTGATGCAT 59.095 50.000 0.00 0.00 0.00 3.96 R
5815 7117 0.111253 AAGAGCTCTGTGTTTGGGGG 59.889 55.000 19.06 0.00 0.00 5.40 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
23 24 0.105039 GATGGCTCCTACTGGTTCGG 59.895 60.000 0.00 0.00 34.23 4.30
45 46 8.767478 TCGGTAAACCTTAGTTCTTAAATGAG 57.233 34.615 0.00 0.00 34.19 2.90
79 80 7.907841 TTCTGCTACTATATTACTTCACCCA 57.092 36.000 0.00 0.00 0.00 4.51
81 82 8.492415 TCTGCTACTATATTACTTCACCCATT 57.508 34.615 0.00 0.00 0.00 3.16
84 85 8.585881 TGCTACTATATTACTTCACCCATTCTC 58.414 37.037 0.00 0.00 0.00 2.87
88 89 9.213777 ACTATATTACTTCACCCATTCTCTTCA 57.786 33.333 0.00 0.00 0.00 3.02
89 90 9.703892 CTATATTACTTCACCCATTCTCTTCAG 57.296 37.037 0.00 0.00 0.00 3.02
106 108 7.056635 TCTCTTCAGAAAAATCCAACAACTCT 58.943 34.615 0.00 0.00 0.00 3.24
110 112 7.364522 TCAGAAAAATCCAACAACTCTATCG 57.635 36.000 0.00 0.00 0.00 2.92
111 113 6.024049 CAGAAAAATCCAACAACTCTATCGC 58.976 40.000 0.00 0.00 0.00 4.58
165 167 5.385509 ACAACTAAACTTTGTGCACTTGT 57.614 34.783 19.41 13.33 35.82 3.16
175 177 5.356751 ACTTTGTGCACTTGTAGAACATCAA 59.643 36.000 19.41 0.00 0.00 2.57
194 196 0.037232 AGTTAGTGCTCCGGTTCAGC 60.037 55.000 6.68 6.68 37.40 4.26
203 205 1.082104 CCGGTTCAGCTTTGCGTTC 60.082 57.895 0.00 0.00 0.00 3.95
226 228 2.971330 TGTTTGGCATGGGAAATGAGTT 59.029 40.909 0.00 0.00 0.00 3.01
227 229 3.244146 TGTTTGGCATGGGAAATGAGTTG 60.244 43.478 0.00 0.00 0.00 3.16
252 254 5.541868 AGGATTGGAGATCCTACATGTACTG 59.458 44.000 0.08 0.00 46.11 2.74
253 255 5.540337 GGATTGGAGATCCTACATGTACTGA 59.460 44.000 0.08 2.15 35.36 3.41
309 320 5.766222 AGTGATCGGTTATACGGTTATGTC 58.234 41.667 0.00 0.00 0.00 3.06
310 321 4.919754 GTGATCGGTTATACGGTTATGTCC 59.080 45.833 0.00 0.00 0.00 4.02
315 326 5.244402 TCGGTTATACGGTTATGTCCATGAT 59.756 40.000 0.00 0.00 0.00 2.45
735 1962 2.855370 CGTGAAACCTTTTCAAAACCGG 59.145 45.455 0.00 0.00 0.00 5.28
736 1963 2.605818 GTGAAACCTTTTCAAAACCGGC 59.394 45.455 0.00 0.00 0.00 6.13
737 1964 2.206750 GAAACCTTTTCAAAACCGGCC 58.793 47.619 0.00 0.00 0.00 6.13
738 1965 0.103390 AACCTTTTCAAAACCGGCCG 59.897 50.000 21.04 21.04 0.00 6.13
741 1968 1.202428 CCTTTTCAAAACCGGCCGAAA 60.202 47.619 30.73 15.47 0.00 3.46
742 1969 1.855978 CTTTTCAAAACCGGCCGAAAC 59.144 47.619 30.73 0.00 0.00 2.78
743 1970 0.102663 TTTCAAAACCGGCCGAAACC 59.897 50.000 30.73 0.00 0.00 3.27
754 1981 3.982576 GGCCGAAACCGATGAAATATT 57.017 42.857 0.00 0.00 0.00 1.28
755 1982 4.301637 GGCCGAAACCGATGAAATATTT 57.698 40.909 0.00 0.00 0.00 1.40
756 1983 4.287720 GGCCGAAACCGATGAAATATTTC 58.712 43.478 19.37 19.37 37.69 2.17
782 2009 1.366679 TGCAAAACCGTTCGTGTACA 58.633 45.000 0.00 0.00 0.00 2.90
788 2015 4.977741 AAACCGTTCGTGTACATGTTAG 57.022 40.909 14.63 7.11 0.00 2.34
800 2027 3.043999 ATGTTAGCTGGGCCGGACC 62.044 63.158 23.70 23.70 37.93 4.46
815 2062 1.376942 GACCCGGTCGAGAGAGTCA 60.377 63.158 0.65 0.00 43.49 3.41
840 2087 1.197721 CCATCGTCACAACAAGCCTTC 59.802 52.381 0.00 0.00 0.00 3.46
871 2118 3.217599 GAAAACGGAGATTTCAAGCCC 57.782 47.619 0.00 0.00 46.42 5.19
872 2119 2.586648 AAACGGAGATTTCAAGCCCT 57.413 45.000 0.00 0.00 0.00 5.19
873 2120 2.586648 AACGGAGATTTCAAGCCCTT 57.413 45.000 0.00 0.00 0.00 3.95
874 2121 2.586648 ACGGAGATTTCAAGCCCTTT 57.413 45.000 0.00 0.00 0.00 3.11
875 2122 2.876581 ACGGAGATTTCAAGCCCTTTT 58.123 42.857 0.00 0.00 0.00 2.27
876 2123 2.558359 ACGGAGATTTCAAGCCCTTTTG 59.442 45.455 0.00 0.00 0.00 2.44
877 2124 2.558359 CGGAGATTTCAAGCCCTTTTGT 59.442 45.455 0.00 0.00 0.00 2.83
878 2125 3.005791 CGGAGATTTCAAGCCCTTTTGTT 59.994 43.478 0.00 0.00 0.00 2.83
879 2126 4.501400 CGGAGATTTCAAGCCCTTTTGTTT 60.501 41.667 0.00 0.00 0.00 2.83
880 2127 5.368145 GGAGATTTCAAGCCCTTTTGTTTT 58.632 37.500 0.00 0.00 0.00 2.43
881 2128 5.237127 GGAGATTTCAAGCCCTTTTGTTTTG 59.763 40.000 0.00 0.00 0.00 2.44
882 2129 5.988287 AGATTTCAAGCCCTTTTGTTTTGA 58.012 33.333 0.00 0.00 0.00 2.69
883 2130 6.413892 AGATTTCAAGCCCTTTTGTTTTGAA 58.586 32.000 0.00 0.00 36.35 2.69
884 2131 6.883756 AGATTTCAAGCCCTTTTGTTTTGAAA 59.116 30.769 11.58 11.58 45.89 2.69
885 2132 7.643569 ATTTCAAGCCCTTTTGTTTTGAAAT 57.356 28.000 14.35 14.35 45.71 2.17
886 2133 6.434018 TTCAAGCCCTTTTGTTTTGAAATG 57.566 33.333 0.00 0.00 35.51 2.32
887 2134 5.738909 TCAAGCCCTTTTGTTTTGAAATGA 58.261 33.333 0.00 0.00 0.00 2.57
888 2135 5.816777 TCAAGCCCTTTTGTTTTGAAATGAG 59.183 36.000 0.00 0.00 0.00 2.90
889 2136 5.612725 AGCCCTTTTGTTTTGAAATGAGA 57.387 34.783 0.00 0.00 0.00 3.27
890 2137 5.604565 AGCCCTTTTGTTTTGAAATGAGAG 58.395 37.500 0.00 0.00 0.00 3.20
891 2138 5.363580 AGCCCTTTTGTTTTGAAATGAGAGA 59.636 36.000 0.00 0.00 0.00 3.10
892 2139 6.042437 AGCCCTTTTGTTTTGAAATGAGAGAT 59.958 34.615 0.00 0.00 0.00 2.75
893 2140 6.707608 GCCCTTTTGTTTTGAAATGAGAGATT 59.292 34.615 0.00 0.00 0.00 2.40
894 2141 7.227314 GCCCTTTTGTTTTGAAATGAGAGATTT 59.773 33.333 0.00 0.00 0.00 2.17
895 2142 8.768019 CCCTTTTGTTTTGAAATGAGAGATTTC 58.232 33.333 0.00 0.00 38.23 2.17
896 2143 9.316730 CCTTTTGTTTTGAAATGAGAGATTTCA 57.683 29.630 5.86 5.86 43.71 2.69
1010 2259 2.825836 CTTCGCCATGGCCACCTC 60.826 66.667 30.79 2.65 37.98 3.85
1011 2260 3.329889 TTCGCCATGGCCACCTCT 61.330 61.111 30.79 0.00 37.98 3.69
1021 2276 2.978824 CCACCTCTACCACCACCG 59.021 66.667 0.00 0.00 0.00 4.94
1335 2602 2.430244 GCGCTCAAGAACGTCCGA 60.430 61.111 0.00 0.00 0.00 4.55
1404 2671 5.521516 CCGATTCGGTAGAAATGATCATG 57.478 43.478 17.08 0.00 42.73 3.07
1405 2672 4.389992 CCGATTCGGTAGAAATGATCATGG 59.610 45.833 17.08 0.00 42.73 3.66
1411 2678 7.539034 TCGGTAGAAATGATCATGGAATCTA 57.461 36.000 9.46 11.74 0.00 1.98
1425 2692 6.781507 TCATGGAATCTATCTCATCAGTCACT 59.218 38.462 0.00 0.00 0.00 3.41
1435 2702 4.895889 TCTCATCAGTCACTACCCCATTAG 59.104 45.833 0.00 0.00 0.00 1.73
1517 2788 2.046314 CGCGAGGTTGGGGATGTT 60.046 61.111 0.00 0.00 0.00 2.71
1668 2939 0.179056 CTGGTATAGCCCCACGGTTG 60.179 60.000 0.00 0.00 36.04 3.77
1675 2946 3.977244 CCCCACGGTTGCTGTTGC 61.977 66.667 0.00 0.00 40.20 4.17
1676 2947 3.977244 CCCACGGTTGCTGTTGCC 61.977 66.667 0.00 0.00 38.71 4.52
1682 2953 1.081242 GGTTGCTGTTGCCATGACG 60.081 57.895 0.00 0.00 38.71 4.35
1750 3021 5.010012 CCTGTACAGCCTTTCTTTGTCATTT 59.990 40.000 17.86 0.00 0.00 2.32
1867 3139 6.308282 GTGTCTATCTGTTTTTGTCCTAGTCG 59.692 42.308 0.00 0.00 0.00 4.18
1870 3142 5.924475 ATCTGTTTTTGTCCTAGTCGTTG 57.076 39.130 0.00 0.00 0.00 4.10
2053 3325 5.823353 TCCAAAATACTTGTCGTGGTTTTC 58.177 37.500 0.00 0.00 0.00 2.29
2055 3327 3.531262 AATACTTGTCGTGGTTTTCGC 57.469 42.857 0.00 0.00 0.00 4.70
2061 3333 1.944024 TGTCGTGGTTTTCGCTCAAAT 59.056 42.857 0.00 0.00 0.00 2.32
2062 3334 2.356382 TGTCGTGGTTTTCGCTCAAATT 59.644 40.909 0.00 0.00 0.00 1.82
2063 3335 3.560481 TGTCGTGGTTTTCGCTCAAATTA 59.440 39.130 0.00 0.00 0.00 1.40
2065 3337 5.151389 GTCGTGGTTTTCGCTCAAATTAAT 58.849 37.500 0.00 0.00 0.00 1.40
2066 3338 6.073167 TGTCGTGGTTTTCGCTCAAATTAATA 60.073 34.615 0.00 0.00 0.00 0.98
2067 3339 6.247791 GTCGTGGTTTTCGCTCAAATTAATAC 59.752 38.462 0.00 0.00 0.00 1.89
2068 3340 6.148150 TCGTGGTTTTCGCTCAAATTAATACT 59.852 34.615 0.00 0.00 0.00 2.12
2069 3341 6.799925 CGTGGTTTTCGCTCAAATTAATACTT 59.200 34.615 0.00 0.00 0.00 2.24
2070 3342 7.958567 CGTGGTTTTCGCTCAAATTAATACTTA 59.041 33.333 0.00 0.00 0.00 2.24
2071 3343 9.783256 GTGGTTTTCGCTCAAATTAATACTTAT 57.217 29.630 0.00 0.00 0.00 1.73
2072 3344 9.997482 TGGTTTTCGCTCAAATTAATACTTATC 57.003 29.630 0.00 0.00 0.00 1.75
2073 3345 9.155053 GGTTTTCGCTCAAATTAATACTTATCG 57.845 33.333 0.00 0.00 0.00 2.92
2074 3346 9.698617 GTTTTCGCTCAAATTAATACTTATCGT 57.301 29.630 0.00 0.00 0.00 3.73
2075 3347 9.697250 TTTTCGCTCAAATTAATACTTATCGTG 57.303 29.630 0.00 0.00 0.00 4.35
2076 3348 7.402811 TCGCTCAAATTAATACTTATCGTGG 57.597 36.000 0.00 0.00 0.00 4.94
2077 3349 6.982141 TCGCTCAAATTAATACTTATCGTGGT 59.018 34.615 0.00 0.00 0.00 4.16
2078 3350 7.493320 TCGCTCAAATTAATACTTATCGTGGTT 59.507 33.333 0.00 0.00 0.00 3.67
2079 3351 8.120465 CGCTCAAATTAATACTTATCGTGGTTT 58.880 33.333 0.00 0.00 0.00 3.27
2080 3352 9.783256 GCTCAAATTAATACTTATCGTGGTTTT 57.217 29.630 0.00 0.00 0.00 2.43
2092 3364 9.458374 ACTTATCGTGGTTTTAGTTCAAATTTG 57.542 29.630 12.15 12.15 0.00 2.32
2093 3365 9.672086 CTTATCGTGGTTTTAGTTCAAATTTGA 57.328 29.630 16.91 16.91 34.92 2.69
2107 3379 7.743520 TTCAAATTTGAACTAAAACCACGAC 57.256 32.000 26.01 0.00 41.88 4.34
2108 3380 6.853720 TCAAATTTGAACTAAAACCACGACA 58.146 32.000 18.45 0.00 33.55 4.35
2109 3381 7.313646 TCAAATTTGAACTAAAACCACGACAA 58.686 30.769 18.45 0.00 33.55 3.18
2110 3382 7.486551 TCAAATTTGAACTAAAACCACGACAAG 59.513 33.333 18.45 0.00 33.55 3.16
2111 3383 5.883503 TTTGAACTAAAACCACGACAAGT 57.116 34.783 0.00 0.00 0.00 3.16
2112 3384 6.981762 TTTGAACTAAAACCACGACAAGTA 57.018 33.333 0.00 0.00 0.00 2.24
2113 3385 7.556733 TTTGAACTAAAACCACGACAAGTAT 57.443 32.000 0.00 0.00 0.00 2.12
2123 3395 3.495377 CCACGACAAGTATTTTGGAACGA 59.505 43.478 0.00 0.00 0.00 3.85
2213 3485 5.590530 TCACGGGGATTCCATTTTATTTG 57.409 39.130 4.80 0.00 34.36 2.32
2407 3680 1.757682 AGGAGAGGAAGTCGCTACTG 58.242 55.000 0.00 0.00 35.02 2.74
2480 3753 4.478206 TTGATTTTTGAGTTTGGTGCCA 57.522 36.364 0.00 0.00 0.00 4.92
2530 3803 5.843019 TGGAGAACTTTAGATGGTCCTTT 57.157 39.130 0.00 0.00 0.00 3.11
2632 3905 3.244215 TGCTTATCTGATAGCCCTTTCCG 60.244 47.826 13.06 0.00 0.00 4.30
2669 3942 3.856267 GCTTTTGCTCTCCTTTTCTGCTG 60.856 47.826 0.00 0.00 43.35 4.41
2677 3950 5.546526 CTCTCCTTTTCTGCTGTAAGAACT 58.453 41.667 8.83 0.00 35.92 3.01
2854 4130 4.523943 TGGAATTATGAAGCACAGCAAGTT 59.476 37.500 0.00 0.00 0.00 2.66
2873 4149 6.672147 CAAGTTCCACATTTCTCCTGTTTAG 58.328 40.000 0.00 0.00 0.00 1.85
2874 4150 6.187727 AGTTCCACATTTCTCCTGTTTAGA 57.812 37.500 0.00 0.00 0.00 2.10
2942 4218 4.681074 TTGGACAATTTCCCACCTTTTC 57.319 40.909 4.78 0.00 45.17 2.29
2958 4234 4.095946 CCTTTTCCCATCATTTCCCAAGA 58.904 43.478 0.00 0.00 0.00 3.02
2965 4241 4.079787 CCCATCATTTCCCAAGACTTCCTA 60.080 45.833 0.00 0.00 0.00 2.94
2968 4244 6.608808 CCATCATTTCCCAAGACTTCCTAAAT 59.391 38.462 0.00 0.00 0.00 1.40
3072 4348 4.363999 GAATAGTCTTCACCACTGATCGG 58.636 47.826 0.00 0.00 0.00 4.18
3182 4458 3.784763 AGTCCATCAGTCCTCATCCATTT 59.215 43.478 0.00 0.00 0.00 2.32
3199 4475 7.342541 TCATCCATTTGTAATTGTCATGTCCAT 59.657 33.333 0.00 0.00 0.00 3.41
3217 4493 6.652053 TGTCCATGACACTAATGATGATCAA 58.348 36.000 0.00 0.00 37.67 2.57
3284 4560 6.133356 TCTTTTGGTTTTACAGAACTGGGAT 58.867 36.000 6.76 0.00 34.19 3.85
3338 4614 6.823689 AGTATATTGTGCACCCTTTTCTGTAG 59.176 38.462 15.69 0.00 0.00 2.74
3408 4692 3.715495 CTGTGTCTCTGCATCTATCCAC 58.285 50.000 0.00 0.00 0.00 4.02
3476 4763 8.303876 CACTGTACTTATTTTATTGTGGCCTTT 58.696 33.333 3.32 0.00 0.00 3.11
3493 4780 5.046448 TGGCCTTTATCATTTTCTGCATGTT 60.046 36.000 3.32 0.00 0.00 2.71
3616 4904 6.347859 CCTCCTCAGGTGTTTATATCCTAC 57.652 45.833 0.00 0.00 34.60 3.18
3701 4989 7.820386 CCAATCCAAATGATTCAGTTGAATTCA 59.180 33.333 24.20 3.38 44.14 2.57
3718 5006 7.815840 TGAATTCATGGTGTCTCTTAACAAA 57.184 32.000 3.38 0.00 0.00 2.83
4041 5329 3.440173 GTGTCGATGGTGTTGATCCATTT 59.560 43.478 0.00 0.00 44.52 2.32
4042 5330 3.439825 TGTCGATGGTGTTGATCCATTTG 59.560 43.478 0.00 0.00 44.52 2.32
4043 5331 2.423185 TCGATGGTGTTGATCCATTTGC 59.577 45.455 0.00 0.00 44.52 3.68
4044 5332 2.164017 CGATGGTGTTGATCCATTTGCA 59.836 45.455 0.00 0.00 44.52 4.08
4129 5417 1.407258 CCCTGCTCACGTTTTGGAAAA 59.593 47.619 0.00 0.00 0.00 2.29
4213 5501 2.039084 GGAAGAGAAAACTCTCCCAGCA 59.961 50.000 0.00 0.00 37.46 4.41
4282 5571 2.142319 CCAAAAGGGCAACGAAAATGG 58.858 47.619 0.00 0.00 37.60 3.16
4326 5615 3.508845 ATGCTCAACACCACCTAAACT 57.491 42.857 0.00 0.00 0.00 2.66
4413 5703 7.639113 TTCTTGTCAGTGTCACCTTATTTTT 57.361 32.000 0.00 0.00 0.00 1.94
4595 5885 3.181443 GGTCTGAAAGTTTCCCCTTGAGA 60.181 47.826 13.01 5.22 33.76 3.27
4925 6215 2.533916 AGAGGTGAGATCTTGTCTGCA 58.466 47.619 0.00 0.00 37.29 4.41
5022 6312 6.912082 TCATAATCATTCGGCACCAATATTG 58.088 36.000 8.58 8.58 0.00 1.90
5027 6317 4.704540 TCATTCGGCACCAATATTGTTTCT 59.295 37.500 14.25 0.00 0.00 2.52
5048 6338 9.689075 GTTTCTTTGAAATGTCAGTTTTTAAGC 57.311 29.630 0.00 0.00 34.49 3.09
5050 6340 6.695278 TCTTTGAAATGTCAGTTTTTAAGCCG 59.305 34.615 0.00 0.00 34.49 5.52
5060 6350 6.526674 GTCAGTTTTTAAGCCGACCAATAATG 59.473 38.462 0.00 0.00 0.00 1.90
5090 6380 1.986882 CCAAGGGTTCTGCAGAAGTT 58.013 50.000 29.13 18.92 34.27 2.66
5150 6440 7.411486 ACTAAAACAGCTAGCAAGAGATCTA 57.589 36.000 18.83 0.00 0.00 1.98
5159 6449 4.959560 AGCAAGAGATCTATGCATCAGT 57.040 40.909 26.22 9.68 42.45 3.41
5172 6462 1.137872 GCATCAGTGAACGGAGGATCT 59.862 52.381 0.00 0.00 33.73 2.75
5259 6549 1.093972 CATGCGGTTATTCTGTGGCA 58.906 50.000 0.00 0.00 34.60 4.92
5270 6560 6.350445 GGTTATTCTGTGGCATCTCACATTTT 60.350 38.462 0.00 0.00 45.26 1.82
5279 6569 3.191371 GCATCTCACATTTTCTCCCGTTT 59.809 43.478 0.00 0.00 0.00 3.60
5389 6679 9.745018 AGAAATCTCTTCAAATAAACAGATGGA 57.255 29.630 0.00 0.00 0.00 3.41
5442 6732 1.738099 AATGCTCGTGTGTCTCCGC 60.738 57.895 0.00 0.00 0.00 5.54
5471 6761 5.419542 TGGTAAATTCTCAATCTGTCCTCG 58.580 41.667 0.00 0.00 0.00 4.63
5494 6792 2.825861 TTTACCACCTTCGTCTGTCC 57.174 50.000 0.00 0.00 0.00 4.02
5497 6795 0.834612 ACCACCTTCGTCTGTCCAAA 59.165 50.000 0.00 0.00 0.00 3.28
5500 6798 0.250338 ACCTTCGTCTGTCCAAAGCC 60.250 55.000 0.00 0.00 0.00 4.35
5553 6851 1.603739 GTTCCACCTCCCTGTTGCC 60.604 63.158 0.00 0.00 0.00 4.52
5563 6861 3.114616 CTGTTGCCGGTGAGCTCG 61.115 66.667 9.64 0.00 0.00 5.03
5661 6963 5.633830 AACTCGCAAAAGATTGATGTGAT 57.366 34.783 0.00 0.00 38.94 3.06
5715 7017 0.723414 CTGAGCTTGGCATACGTGTG 59.277 55.000 8.09 8.09 0.00 3.82
5763 7065 6.308766 CGCATCTGTTTATCTTTTCTTTTGGG 59.691 38.462 0.00 0.00 0.00 4.12
5805 7107 9.751542 ATCCATGTAAAATTCTTCTACGAGTAG 57.248 33.333 3.98 3.98 34.56 2.57
5806 7108 8.746530 TCCATGTAAAATTCTTCTACGAGTAGT 58.253 33.333 9.75 0.00 34.84 2.73
5815 7117 9.636879 AATTCTTCTACGAGTAGTACTTTTTCC 57.363 33.333 0.00 0.00 34.84 3.13
5816 7118 7.150783 TCTTCTACGAGTAGTACTTTTTCCC 57.849 40.000 0.00 0.00 34.84 3.97
5817 7119 5.904362 TCTACGAGTAGTACTTTTTCCCC 57.096 43.478 0.00 0.00 34.84 4.81
5818 7120 3.969287 ACGAGTAGTACTTTTTCCCCC 57.031 47.619 0.00 0.00 0.00 5.40
5854 7494 0.037975 TTTTCGGGTCGCCTGTACTC 60.038 55.000 0.00 0.00 0.00 2.59
5880 7520 0.249447 TCTATCATGCCCAAGACGCG 60.249 55.000 3.53 3.53 0.00 6.01
5903 7543 2.509336 ATTCGCGCTTCCTGTCCG 60.509 61.111 5.56 0.00 0.00 4.79
5982 7623 1.593006 GGACACGCTATCGAAACATGG 59.407 52.381 0.00 0.00 39.41 3.66
6017 7658 6.128849 ACGCCATTGAAAAATCGAGAAAATTG 60.129 34.615 0.00 0.00 0.00 2.32
6053 7694 8.430801 AAGTTGAGAATATCAGAACACATAGC 57.569 34.615 0.00 0.00 39.68 2.97
6092 7733 2.163815 CCTGAGCTCAAATGCTTCTTGG 59.836 50.000 18.85 7.39 44.17 3.61
6106 7747 7.759489 ATGCTTCTTGGTGAACAGTAAAATA 57.241 32.000 0.00 0.00 0.00 1.40
6107 7748 7.575414 TGCTTCTTGGTGAACAGTAAAATAA 57.425 32.000 0.00 0.00 0.00 1.40
6196 7837 6.804770 TTTATGCTTGCAAAATTTCAGCAT 57.195 29.167 20.20 20.20 42.92 3.79
6224 7865 0.257328 TTGTGGAAGGTGTGGCAAGA 59.743 50.000 0.00 0.00 0.00 3.02
6229 7870 2.430332 TGGAAGGTGTGGCAAGAAAAAG 59.570 45.455 0.00 0.00 0.00 2.27
6322 7963 5.233957 TCCATGAATGTAATTTCGTGCTG 57.766 39.130 0.00 0.00 40.00 4.41
6338 7979 3.663233 CGTGCTGAAATTTTGCAAGCATG 60.663 43.478 17.39 17.08 38.50 4.06
6339 7980 3.249080 GTGCTGAAATTTTGCAAGCATGT 59.751 39.130 17.39 0.00 38.50 3.21
6355 7996 8.710551 TGCAAGCATGTAAAATATTTGTCAAAG 58.289 29.630 0.39 3.72 0.00 2.77
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
5 6 0.617820 ACCGAACCAGTAGGAGCCAT 60.618 55.000 0.00 0.00 38.69 4.40
23 24 9.511272 TTCCCTCATTTAAGAACTAAGGTTTAC 57.489 33.333 0.00 0.00 35.58 2.01
53 54 8.934697 TGGGTGAAGTAATATAGTAGCAGAAAT 58.065 33.333 0.00 0.00 0.00 2.17
55 56 7.907841 TGGGTGAAGTAATATAGTAGCAGAA 57.092 36.000 0.00 0.00 0.00 3.02
63 64 9.703892 CTGAAGAGAATGGGTGAAGTAATATAG 57.296 37.037 0.00 0.00 0.00 1.31
79 80 8.242729 AGTTGTTGGATTTTTCTGAAGAGAAT 57.757 30.769 0.00 0.00 38.05 2.40
81 82 7.056635 AGAGTTGTTGGATTTTTCTGAAGAGA 58.943 34.615 0.00 0.00 0.00 3.10
84 85 7.959651 CGATAGAGTTGTTGGATTTTTCTGAAG 59.040 37.037 0.00 0.00 39.76 3.02
88 89 5.163854 CGCGATAGAGTTGTTGGATTTTTCT 60.164 40.000 0.00 0.00 39.76 2.52
89 90 5.022021 CGCGATAGAGTTGTTGGATTTTTC 58.978 41.667 0.00 0.00 39.76 2.29
132 134 9.931710 CACAAAGTTTAGTTGTTAACTTTTTCG 57.068 29.630 7.22 3.56 46.75 3.46
133 135 9.735646 GCACAAAGTTTAGTTGTTAACTTTTTC 57.264 29.630 7.22 1.08 46.75 2.29
141 143 6.915349 ACAAGTGCACAAAGTTTAGTTGTTA 58.085 32.000 21.04 0.00 37.09 2.41
143 145 5.385509 ACAAGTGCACAAAGTTTAGTTGT 57.614 34.783 21.04 13.95 39.79 3.32
144 146 6.781138 TCTACAAGTGCACAAAGTTTAGTTG 58.219 36.000 21.04 13.29 0.00 3.16
145 147 6.995511 TCTACAAGTGCACAAAGTTTAGTT 57.004 33.333 21.04 0.00 0.00 2.24
152 154 5.422666 TGATGTTCTACAAGTGCACAAAG 57.577 39.130 21.04 10.58 0.00 2.77
165 167 4.381612 CCGGAGCACTAACTTGATGTTCTA 60.382 45.833 0.00 0.00 39.89 2.10
175 177 0.037232 GCTGAACCGGAGCACTAACT 60.037 55.000 9.46 0.00 36.40 2.24
181 183 2.260869 GCAAAGCTGAACCGGAGCA 61.261 57.895 9.46 4.37 39.05 4.26
194 196 0.524392 TGCCAAACACGAACGCAAAG 60.524 50.000 0.00 0.00 0.00 2.77
203 205 1.271934 TCATTTCCCATGCCAAACACG 59.728 47.619 0.00 0.00 0.00 4.49
226 228 4.560739 ACATGTAGGATCTCCAATCCTCA 58.439 43.478 9.79 8.68 44.86 3.86
227 229 5.777732 AGTACATGTAGGATCTCCAATCCTC 59.222 44.000 5.62 3.87 44.86 3.71
252 254 2.595009 CTTGGGCGGCCTCTACCTTC 62.595 65.000 29.87 0.00 0.00 3.46
253 255 2.609610 TTGGGCGGCCTCTACCTT 60.610 61.111 29.87 0.00 0.00 3.50
442 455 2.449464 CTTGAGCATTTCCATGGTGGA 58.551 47.619 12.58 0.00 46.61 4.02
444 457 2.094390 CACCTTGAGCATTTCCATGGTG 60.094 50.000 12.58 3.82 45.61 4.17
445 458 2.173519 CACCTTGAGCATTTCCATGGT 58.826 47.619 12.58 0.00 44.10 3.55
447 460 3.129287 GGTACACCTTGAGCATTTCCATG 59.871 47.826 0.00 0.00 0.00 3.66
448 461 3.010584 AGGTACACCTTGAGCATTTCCAT 59.989 43.478 0.00 0.00 46.09 3.41
449 462 2.375174 AGGTACACCTTGAGCATTTCCA 59.625 45.455 0.00 0.00 46.09 3.53
450 463 3.073274 AGGTACACCTTGAGCATTTCC 57.927 47.619 0.00 0.00 46.09 3.13
451 464 6.569179 TTTTAGGTACACCTTGAGCATTTC 57.431 37.500 6.17 0.00 46.09 2.17
721 1948 0.386113 TTCGGCCGGTTTTGAAAAGG 59.614 50.000 27.83 0.00 0.00 3.11
735 1962 4.915704 TGAAATATTTCATCGGTTTCGGC 58.084 39.130 23.86 0.00 41.88 5.54
736 1963 7.192913 TGATTGAAATATTTCATCGGTTTCGG 58.807 34.615 27.11 0.00 45.65 4.30
737 1964 8.786937 ATGATTGAAATATTTCATCGGTTTCG 57.213 30.769 27.11 0.00 45.65 3.46
741 1968 7.490840 TGCAATGATTGAAATATTTCATCGGT 58.509 30.769 27.11 15.60 45.65 4.69
742 1969 7.933728 TGCAATGATTGAAATATTTCATCGG 57.066 32.000 27.11 18.88 45.65 4.18
746 1973 8.441608 CGGTTTTGCAATGATTGAAATATTTCA 58.558 29.630 23.86 23.86 44.78 2.69
747 1974 8.442384 ACGGTTTTGCAATGATTGAAATATTTC 58.558 29.630 19.37 19.37 37.69 2.17
748 1975 8.321650 ACGGTTTTGCAATGATTGAAATATTT 57.678 26.923 9.76 0.00 0.00 1.40
749 1976 7.903995 ACGGTTTTGCAATGATTGAAATATT 57.096 28.000 9.76 0.00 0.00 1.28
750 1977 7.201427 CGAACGGTTTTGCAATGATTGAAATAT 60.201 33.333 9.76 0.00 0.00 1.28
751 1978 6.088749 CGAACGGTTTTGCAATGATTGAAATA 59.911 34.615 9.76 0.00 0.00 1.40
752 1979 5.107530 CGAACGGTTTTGCAATGATTGAAAT 60.108 36.000 9.76 0.00 0.00 2.17
753 1980 4.208047 CGAACGGTTTTGCAATGATTGAAA 59.792 37.500 9.76 1.02 0.00 2.69
754 1981 3.733224 CGAACGGTTTTGCAATGATTGAA 59.267 39.130 9.76 0.00 0.00 2.69
755 1982 3.243234 ACGAACGGTTTTGCAATGATTGA 60.243 39.130 9.76 0.00 0.00 2.57
756 1983 3.049206 ACGAACGGTTTTGCAATGATTG 58.951 40.909 0.00 0.00 0.00 2.67
757 1984 3.049206 CACGAACGGTTTTGCAATGATT 58.951 40.909 0.00 0.00 0.00 2.57
761 1988 2.355132 TGTACACGAACGGTTTTGCAAT 59.645 40.909 0.00 0.00 0.00 3.56
782 2009 2.590092 GTCCGGCCCAGCTAACAT 59.410 61.111 0.00 0.00 0.00 2.71
800 2027 2.785921 CGTGACTCTCTCGACCGG 59.214 66.667 0.00 0.00 35.64 5.28
801 2028 2.098680 GCGTGACTCTCTCGACCG 59.901 66.667 0.00 0.00 35.64 4.79
802 2029 2.486042 GGCGTGACTCTCTCGACC 59.514 66.667 0.00 0.00 35.55 4.79
803 2030 2.486042 GGGCGTGACTCTCTCGAC 59.514 66.667 0.00 0.00 40.35 4.20
840 2087 0.882927 TCCGTTTTCGTGGGCTTGAG 60.883 55.000 0.00 0.00 42.35 3.02
869 2116 8.667076 AAATCTCTCATTTCAAAACAAAAGGG 57.333 30.769 0.00 0.00 0.00 3.95
870 2117 9.316730 TGAAATCTCTCATTTCAAAACAAAAGG 57.683 29.630 7.20 0.00 42.82 3.11
880 2127 4.703575 CAGGGCTTGAAATCTCTCATTTCA 59.296 41.667 5.79 5.79 43.71 2.69
881 2128 4.439837 GCAGGGCTTGAAATCTCTCATTTC 60.440 45.833 0.00 0.89 38.23 2.17
882 2129 3.446516 GCAGGGCTTGAAATCTCTCATTT 59.553 43.478 0.00 0.00 0.00 2.32
883 2130 3.022406 GCAGGGCTTGAAATCTCTCATT 58.978 45.455 0.00 0.00 0.00 2.57
884 2131 2.652590 GCAGGGCTTGAAATCTCTCAT 58.347 47.619 0.00 0.00 0.00 2.90
885 2132 1.340405 GGCAGGGCTTGAAATCTCTCA 60.340 52.381 0.00 0.00 0.00 3.27
886 2133 1.387539 GGCAGGGCTTGAAATCTCTC 58.612 55.000 0.00 0.00 0.00 3.20
887 2134 0.033699 GGGCAGGGCTTGAAATCTCT 60.034 55.000 0.00 0.00 0.00 3.10
888 2135 1.379642 CGGGCAGGGCTTGAAATCTC 61.380 60.000 0.00 0.00 0.00 2.75
889 2136 1.379044 CGGGCAGGGCTTGAAATCT 60.379 57.895 0.00 0.00 0.00 2.40
890 2137 0.393808 TACGGGCAGGGCTTGAAATC 60.394 55.000 0.00 0.00 0.00 2.17
891 2138 0.039035 TTACGGGCAGGGCTTGAAAT 59.961 50.000 0.00 0.00 0.00 2.17
892 2139 0.608035 CTTACGGGCAGGGCTTGAAA 60.608 55.000 0.00 0.00 0.00 2.69
893 2140 1.002624 CTTACGGGCAGGGCTTGAA 60.003 57.895 0.00 0.00 0.00 2.69
894 2141 1.899437 CTCTTACGGGCAGGGCTTGA 61.899 60.000 0.00 0.00 0.00 3.02
895 2142 1.450312 CTCTTACGGGCAGGGCTTG 60.450 63.158 0.00 0.00 0.00 4.01
896 2143 1.198759 TTCTCTTACGGGCAGGGCTT 61.199 55.000 0.00 0.00 0.00 4.35
897 2144 1.198759 TTTCTCTTACGGGCAGGGCT 61.199 55.000 0.00 0.00 0.00 5.19
898 2145 1.025113 GTTTCTCTTACGGGCAGGGC 61.025 60.000 0.00 0.00 0.00 5.19
899 2146 0.739813 CGTTTCTCTTACGGGCAGGG 60.740 60.000 0.00 0.00 35.47 4.45
1006 2255 3.001406 GGCGGTGGTGGTAGAGGT 61.001 66.667 0.00 0.00 0.00 3.85
1007 2256 3.000819 TGGCGGTGGTGGTAGAGG 61.001 66.667 0.00 0.00 0.00 3.69
1008 2257 2.264794 GTGGCGGTGGTGGTAGAG 59.735 66.667 0.00 0.00 0.00 2.43
1009 2258 3.315949 GGTGGCGGTGGTGGTAGA 61.316 66.667 0.00 0.00 0.00 2.59
1010 2259 4.752879 CGGTGGCGGTGGTGGTAG 62.753 72.222 0.00 0.00 0.00 3.18
1096 2351 3.760035 GCGGACGCTGGAGGAAGA 61.760 66.667 9.76 0.00 38.26 2.87
1097 2352 4.821589 GGCGGACGCTGGAGGAAG 62.822 72.222 16.72 0.00 41.60 3.46
1335 2602 3.717452 AAGAGCAGCTTCTCTCCATTT 57.283 42.857 16.52 0.00 42.25 2.32
1404 2671 6.071616 GGGTAGTGACTGATGAGATAGATTCC 60.072 46.154 0.00 0.00 0.00 3.01
1405 2672 6.071616 GGGGTAGTGACTGATGAGATAGATTC 60.072 46.154 0.00 0.00 0.00 2.52
1411 2678 3.404869 TGGGGTAGTGACTGATGAGAT 57.595 47.619 0.00 0.00 0.00 2.75
1425 2692 0.840617 TGAATGCCGCTAATGGGGTA 59.159 50.000 0.00 0.00 46.69 3.69
1435 2702 2.132740 TTGTGAAAACTGAATGCCGC 57.867 45.000 0.00 0.00 0.00 6.53
1517 2788 3.031736 GGGCACAGAGTACCTCTTCATA 58.968 50.000 0.00 0.00 38.99 2.15
1675 2946 1.942657 CTTATCACTTGGGCGTCATGG 59.057 52.381 0.00 0.00 0.00 3.66
1676 2947 2.609459 GTCTTATCACTTGGGCGTCATG 59.391 50.000 0.00 0.00 0.00 3.07
1682 2953 2.271800 CACTCGTCTTATCACTTGGGC 58.728 52.381 0.00 0.00 0.00 5.36
1727 2998 5.695851 AATGACAAAGAAAGGCTGTACAG 57.304 39.130 18.93 18.93 0.00 2.74
1750 3021 4.152284 TCTATCTCAGTGCGAGTCCTAA 57.848 45.455 0.00 0.00 42.88 2.69
1867 3139 7.332182 CAGAGGAGAAAACTTAGTATGGTCAAC 59.668 40.741 0.00 0.00 0.00 3.18
1870 3142 6.937392 ACAGAGGAGAAAACTTAGTATGGTC 58.063 40.000 0.00 0.00 0.00 4.02
2053 3325 7.173863 ACCACGATAAGTATTAATTTGAGCG 57.826 36.000 0.00 0.00 32.17 5.03
2066 3338 9.458374 CAAATTTGAACTAAAACCACGATAAGT 57.542 29.630 13.08 0.00 0.00 2.24
2067 3339 9.672086 TCAAATTTGAACTAAAACCACGATAAG 57.328 29.630 18.45 0.00 33.55 1.73
2083 3355 7.313646 TGTCGTGGTTTTAGTTCAAATTTGAA 58.686 30.769 26.01 26.01 44.31 2.69
2084 3356 6.853720 TGTCGTGGTTTTAGTTCAAATTTGA 58.146 32.000 16.91 16.91 34.92 2.69
2085 3357 7.274686 ACTTGTCGTGGTTTTAGTTCAAATTTG 59.725 33.333 12.15 12.15 0.00 2.32
2086 3358 7.317390 ACTTGTCGTGGTTTTAGTTCAAATTT 58.683 30.769 0.00 0.00 0.00 1.82
2087 3359 6.859017 ACTTGTCGTGGTTTTAGTTCAAATT 58.141 32.000 0.00 0.00 0.00 1.82
2088 3360 6.445357 ACTTGTCGTGGTTTTAGTTCAAAT 57.555 33.333 0.00 0.00 0.00 2.32
2089 3361 5.883503 ACTTGTCGTGGTTTTAGTTCAAA 57.116 34.783 0.00 0.00 0.00 2.69
2090 3362 7.556733 AATACTTGTCGTGGTTTTAGTTCAA 57.443 32.000 0.00 0.00 0.00 2.69
2091 3363 7.556733 AAATACTTGTCGTGGTTTTAGTTCA 57.443 32.000 0.00 0.00 0.00 3.18
2092 3364 7.377662 CCAAAATACTTGTCGTGGTTTTAGTTC 59.622 37.037 0.00 0.00 0.00 3.01
2093 3365 7.067251 TCCAAAATACTTGTCGTGGTTTTAGTT 59.933 33.333 0.00 0.00 0.00 2.24
2094 3366 6.543100 TCCAAAATACTTGTCGTGGTTTTAGT 59.457 34.615 0.00 0.00 0.00 2.24
2095 3367 6.961576 TCCAAAATACTTGTCGTGGTTTTAG 58.038 36.000 0.00 0.00 0.00 1.85
2096 3368 6.939132 TCCAAAATACTTGTCGTGGTTTTA 57.061 33.333 0.00 0.00 0.00 1.52
2097 3369 5.838531 TCCAAAATACTTGTCGTGGTTTT 57.161 34.783 0.00 0.00 0.00 2.43
2098 3370 5.584442 GTTCCAAAATACTTGTCGTGGTTT 58.416 37.500 0.00 0.00 0.00 3.27
2099 3371 4.260866 CGTTCCAAAATACTTGTCGTGGTT 60.261 41.667 0.00 0.00 0.00 3.67
2100 3372 3.249080 CGTTCCAAAATACTTGTCGTGGT 59.751 43.478 0.00 0.00 0.00 4.16
2101 3373 3.495377 TCGTTCCAAAATACTTGTCGTGG 59.505 43.478 0.00 0.00 0.00 4.94
2102 3374 4.718858 TCGTTCCAAAATACTTGTCGTG 57.281 40.909 0.00 0.00 0.00 4.35
2103 3375 5.051816 TCTTCGTTCCAAAATACTTGTCGT 58.948 37.500 0.00 0.00 0.00 4.34
2104 3376 5.404366 TCTCTTCGTTCCAAAATACTTGTCG 59.596 40.000 0.00 0.00 0.00 4.35
2105 3377 6.424207 ACTCTCTTCGTTCCAAAATACTTGTC 59.576 38.462 0.00 0.00 0.00 3.18
2106 3378 6.289064 ACTCTCTTCGTTCCAAAATACTTGT 58.711 36.000 0.00 0.00 0.00 3.16
2107 3379 6.787085 ACTCTCTTCGTTCCAAAATACTTG 57.213 37.500 0.00 0.00 0.00 3.16
2108 3380 7.668492 ACTACTCTCTTCGTTCCAAAATACTT 58.332 34.615 0.00 0.00 0.00 2.24
2109 3381 7.229581 ACTACTCTCTTCGTTCCAAAATACT 57.770 36.000 0.00 0.00 0.00 2.12
2110 3382 7.886405 AACTACTCTCTTCGTTCCAAAATAC 57.114 36.000 0.00 0.00 0.00 1.89
2111 3383 9.985730 TTAAACTACTCTCTTCGTTCCAAAATA 57.014 29.630 0.00 0.00 0.00 1.40
2112 3384 8.897872 TTAAACTACTCTCTTCGTTCCAAAAT 57.102 30.769 0.00 0.00 0.00 1.82
2113 3385 8.606602 GTTTAAACTACTCTCTTCGTTCCAAAA 58.393 33.333 11.18 0.00 0.00 2.44
2277 3550 4.640201 TGCTTCTGTGTATAGAAATTGGGC 59.360 41.667 0.00 0.00 36.34 5.36
2530 3803 1.895798 AGACGTGAGAAGAGAATGCCA 59.104 47.619 0.00 0.00 0.00 4.92
2656 3929 5.561725 GCAAGTTCTTACAGCAGAAAAGGAG 60.562 44.000 0.00 0.00 34.50 3.69
2819 4094 9.585099 TGCTTCATAATTCCATACAACAATTTC 57.415 29.630 0.00 0.00 0.00 2.17
2823 4098 7.459795 TGTGCTTCATAATTCCATACAACAA 57.540 32.000 0.00 0.00 0.00 2.83
2854 4130 7.287061 TCTTTTCTAAACAGGAGAAATGTGGA 58.713 34.615 9.49 1.41 41.37 4.02
2902 4178 5.505173 CCAATATGTGGTGCTTAAGGAAG 57.495 43.478 4.29 0.00 43.20 3.46
2932 4208 2.501316 GGAAATGATGGGAAAAGGTGGG 59.499 50.000 0.00 0.00 0.00 4.61
2942 4218 3.026694 GGAAGTCTTGGGAAATGATGGG 58.973 50.000 0.00 0.00 0.00 4.00
2958 4234 6.392354 CATGACATTGTGCAATTTAGGAAGT 58.608 36.000 0.00 0.00 0.00 3.01
2995 4271 6.624423 CATCTACCTGGAAAGTTGATTTTGG 58.376 40.000 0.00 0.00 29.07 3.28
3072 4348 1.067142 TGCTCACCTGGTTGATACGAC 60.067 52.381 0.00 0.00 0.00 4.34
3199 4475 9.452287 TGAAGATTTTGATCATCATTAGTGTCA 57.548 29.630 0.00 0.00 0.00 3.58
3217 4493 6.863126 CCGAAAACAAGCAATAGTGAAGATTT 59.137 34.615 0.00 0.00 0.00 2.17
3338 4614 6.036735 TCGTACTTTAAATGCCAGTCTATTGC 59.963 38.462 0.00 0.00 0.00 3.56
3476 4763 6.851609 AGCGTAAAACATGCAGAAAATGATA 58.148 32.000 0.00 0.00 42.04 2.15
3493 4780 2.096248 CTAATTGGCCCCAAGCGTAAA 58.904 47.619 0.00 0.00 45.17 2.01
3573 4861 5.163457 GGAGGTCAAACAAGAAATGGACAAA 60.163 40.000 0.00 0.00 0.00 2.83
3579 4867 4.217118 CCTGAGGAGGTCAAACAAGAAATG 59.783 45.833 0.00 0.00 33.60 2.32
3616 4904 1.003118 TCACCACTGGATTTCTTCCCG 59.997 52.381 0.71 0.00 44.77 5.14
3676 4964 8.766000 TGAATTCAACTGAATCATTTGGATTG 57.234 30.769 20.16 3.76 46.17 2.67
3701 4989 7.397221 TCATCAGATTTGTTAAGAGACACCAT 58.603 34.615 0.00 0.00 0.00 3.55
3718 5006 5.929058 TCTCTTTGTAGCACTCATCAGAT 57.071 39.130 0.00 0.00 0.00 2.90
4041 5329 0.109153 AGCACCAAGACACTCATGCA 59.891 50.000 0.00 0.00 35.51 3.96
4042 5330 1.242076 AAGCACCAAGACACTCATGC 58.758 50.000 0.00 0.00 0.00 4.06
4043 5331 3.402110 TGTAAGCACCAAGACACTCATG 58.598 45.455 0.00 0.00 0.00 3.07
4044 5332 3.769739 TGTAAGCACCAAGACACTCAT 57.230 42.857 0.00 0.00 0.00 2.90
4213 5501 8.148437 ACTATATGCATCTCAAGATTCCAGAT 57.852 34.615 0.19 0.00 31.21 2.90
4282 5571 4.261801 TCTCCAGTTTTTATGTGGCTAGC 58.738 43.478 6.04 6.04 0.00 3.42
4296 5585 2.887152 GGTGTTGAGCATTTCTCCAGTT 59.113 45.455 0.00 0.00 41.18 3.16
4326 5615 1.557371 TGCCACGATCTTTATGTCCCA 59.443 47.619 0.00 0.00 0.00 4.37
4595 5885 2.078665 AACTGGCCACCCTGTGACT 61.079 57.895 0.00 0.00 41.83 3.41
4750 6040 8.690203 TGCACAAATAAGTTATATAGGCATGT 57.310 30.769 0.00 0.00 0.00 3.21
5022 6312 9.689075 GCTTAAAAACTGACATTTCAAAGAAAC 57.311 29.630 0.00 0.00 0.00 2.78
5027 6317 6.474102 GTCGGCTTAAAAACTGACATTTCAAA 59.526 34.615 6.82 0.00 41.05 2.69
5048 6338 2.099098 GCCCTGAAACATTATTGGTCGG 59.901 50.000 0.00 0.00 0.00 4.79
5050 6340 2.479560 GCGCCCTGAAACATTATTGGTC 60.480 50.000 0.00 0.00 0.00 4.02
5060 6350 3.373565 CCCTTGGCGCCCTGAAAC 61.374 66.667 26.77 0.00 0.00 2.78
5084 6374 6.071728 CCTGCTTTGTATTGATGGAAACTTCT 60.072 38.462 0.00 0.00 35.62 2.85
5090 6380 2.760092 GGCCTGCTTTGTATTGATGGAA 59.240 45.455 0.00 0.00 0.00 3.53
5150 6440 0.904649 TCCTCCGTTCACTGATGCAT 59.095 50.000 0.00 0.00 0.00 3.96
5172 6462 7.587392 CCGTCTTACGTATTGTGAACGATATAA 59.413 37.037 0.00 0.00 42.90 0.98
5195 6485 2.047465 CTGCAAGAGCTCTGCCGT 60.047 61.111 25.45 7.61 42.74 5.68
5222 6512 4.845580 ATGCGCGGAGGGAAGCAG 62.846 66.667 8.83 0.00 46.37 4.24
5238 6528 1.949525 GCCACAGAATAACCGCATGAT 59.050 47.619 0.00 0.00 0.00 2.45
5254 6544 2.424956 GGGAGAAAATGTGAGATGCCAC 59.575 50.000 0.00 0.00 37.55 5.01
5259 6549 6.540189 CAGATAAACGGGAGAAAATGTGAGAT 59.460 38.462 0.00 0.00 0.00 2.75
5270 6560 1.207089 CTGCACCAGATAAACGGGAGA 59.793 52.381 0.00 0.00 37.30 3.71
5296 6586 2.526888 TGTCCCTCAATCTCCTACGT 57.473 50.000 0.00 0.00 0.00 3.57
5442 6732 5.643777 ACAGATTGAGAATTTACCAAGTCGG 59.356 40.000 0.00 0.00 42.50 4.79
5490 6788 3.252215 CAGTGAAAATACGGCTTTGGACA 59.748 43.478 0.00 0.00 0.00 4.02
5491 6789 3.500680 TCAGTGAAAATACGGCTTTGGAC 59.499 43.478 0.00 0.00 0.00 4.02
5492 6790 3.745799 TCAGTGAAAATACGGCTTTGGA 58.254 40.909 0.00 0.00 0.00 3.53
5493 6791 4.226761 GTTCAGTGAAAATACGGCTTTGG 58.773 43.478 7.25 0.00 0.00 3.28
5494 6792 4.675114 GTGTTCAGTGAAAATACGGCTTTG 59.325 41.667 7.25 0.00 0.00 2.77
5497 6795 2.812011 GGTGTTCAGTGAAAATACGGCT 59.188 45.455 7.25 0.00 0.00 5.52
5500 6798 4.804608 TGTGGTGTTCAGTGAAAATACG 57.195 40.909 7.25 0.00 0.00 3.06
5553 6851 2.357517 AAACAGCCGAGCTCACCG 60.358 61.111 15.40 0.00 36.40 4.94
5661 6963 4.069304 ACAACTCGCAGCTATTTTTGGTA 58.931 39.130 0.00 0.00 0.00 3.25
5715 7017 4.244066 CTGCAGCATCCTAGATCACATAC 58.756 47.826 0.00 0.00 0.00 2.39
5793 7095 6.328714 GGGGAAAAAGTACTACTCGTAGAAG 58.671 44.000 10.83 0.00 36.97 2.85
5794 7096 5.185828 GGGGGAAAAAGTACTACTCGTAGAA 59.814 44.000 10.83 0.00 36.97 2.10
5795 7097 4.706962 GGGGGAAAAAGTACTACTCGTAGA 59.293 45.833 10.83 0.00 36.97 2.59
5796 7098 5.003692 GGGGGAAAAAGTACTACTCGTAG 57.996 47.826 0.00 2.66 39.04 3.51
5798 7100 3.969287 GGGGGAAAAAGTACTACTCGT 57.031 47.619 0.00 0.00 0.00 4.18
5815 7117 0.111253 AAGAGCTCTGTGTTTGGGGG 59.889 55.000 19.06 0.00 0.00 5.40
5816 7118 1.986882 AAAGAGCTCTGTGTTTGGGG 58.013 50.000 19.06 0.00 0.00 4.96
5854 7494 3.133542 TCTTGGGCATGATAGACAGACAG 59.866 47.826 0.00 0.00 0.00 3.51
5880 7520 1.520342 AGGAAGCGCGAATGCTCTC 60.520 57.895 12.10 0.00 46.60 3.20
5903 7543 1.509923 CGAGTCCACCGGTAGAACC 59.490 63.158 6.87 0.00 34.05 3.62
5982 7623 3.829886 TTCAATGGCGTTGAGTGATTC 57.170 42.857 20.42 0.00 46.85 2.52
6017 7658 8.994429 TGATATTCTCAACTTCTCTTTCTGTC 57.006 34.615 0.00 0.00 0.00 3.51
6053 7694 5.521906 TCAGGATCAGAATAGAACTTCCG 57.478 43.478 0.00 0.00 0.00 4.30
6196 7837 4.039004 CCACACCTTCCACAAATGATTTCA 59.961 41.667 0.00 0.00 0.00 2.69


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

AutoCloner maintained by Alex Coulton.