Multiple sequence alignment - TraesCS5D01G512200

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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 TraesCS5D01G512200 chr5D 100.000 2605 0 0 1 2605 536533055 536535659 0.000000e+00 4811.0
1 TraesCS5D01G512200 chr5D 88.506 87 10 0 496 582 45178316 45178402 3.550000e-19 106.0
2 TraesCS5D01G512200 chr5B 91.136 1365 49 26 800 2109 677149278 677150625 0.000000e+00 1784.0
3 TraesCS5D01G512200 chr5B 93.553 760 39 6 54 803 677148416 677149175 0.000000e+00 1123.0
4 TraesCS5D01G512200 chr5B 91.358 243 6 6 2034 2272 677151152 677151383 4.180000e-83 318.0
5 TraesCS5D01G512200 chr5B 90.164 244 11 4 2368 2605 677151382 677151618 3.260000e-79 305.0
6 TraesCS5D01G512200 chr5B 90.260 154 14 1 2237 2389 677150965 677151118 1.580000e-47 200.0
7 TraesCS5D01G512200 chr4A 86.661 1207 72 31 691 1862 634743261 634742109 0.000000e+00 1254.0
8 TraesCS5D01G512200 chr4A 88.966 145 15 1 414 557 634743591 634743447 7.410000e-41 178.0
9 TraesCS5D01G512200 chr4A 86.207 87 12 0 496 582 29458515 29458429 7.670000e-16 95.3
10 TraesCS5D01G512200 chr4B 94.000 100 5 1 401 499 475921562 475921463 1.610000e-32 150.0
11 TraesCS5D01G512200 chr7D 93.878 98 5 1 403 499 40863230 40863327 2.090000e-31 147.0
12 TraesCS5D01G512200 chr7D 93.000 100 6 1 401 499 17861472 17861571 7.510000e-31 145.0
13 TraesCS5D01G512200 chr3B 91.429 105 7 2 397 499 817426347 817426243 2.700000e-30 143.0
14 TraesCS5D01G512200 chr3B 91.139 79 7 0 504 582 763250336 763250414 9.860000e-20 108.0
15 TraesCS5D01G512200 chr3B 91.139 79 7 0 504 582 807502466 807502544 9.860000e-20 108.0
16 TraesCS5D01G512200 chrUn 92.079 101 7 1 400 499 283087235 283087135 9.720000e-30 141.0
17 TraesCS5D01G512200 chr7A 91.429 105 5 3 397 499 15772215 15772317 9.720000e-30 141.0
18 TraesCS5D01G512200 chr1D 92.079 101 7 1 400 499 781148 781048 9.720000e-30 141.0
19 TraesCS5D01G512200 chr1D 86.207 87 10 1 496 582 481938765 481938681 2.760000e-15 93.5
20 TraesCS5D01G512200 chr6B 93.056 72 5 0 511 582 646139362 646139291 3.550000e-19 106.0
21 TraesCS5D01G512200 chr2B 89.873 79 8 0 504 582 499563440 499563518 4.590000e-18 102.0
22 TraesCS5D01G512200 chr6D 89.855 69 7 0 1363 1431 433426930 433426862 3.570000e-14 89.8
23 TraesCS5D01G512200 chr6A 90.385 52 4 1 2006 2056 129746858 129746807 1.670000e-07 67.6


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 TraesCS5D01G512200 chr5D 536533055 536535659 2604 False 4811 4811 100.0000 1 2605 1 chr5D.!!$F2 2604
1 TraesCS5D01G512200 chr5B 677148416 677151618 3202 False 746 1784 91.2942 54 2605 5 chr5B.!!$F1 2551
2 TraesCS5D01G512200 chr4A 634742109 634743591 1482 True 716 1254 87.8135 414 1862 2 chr4A.!!$R2 1448

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
34 35 0.185416 CGAGGGCTAGGTAGGGAGAA 59.815 60.0 0.00 0.0 0.00 2.87 F
1438 1742 0.043224 CGACGACGACGAGTAGGATG 60.043 60.0 15.32 0.0 42.66 3.51 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1565 1877 0.321671 TGAGAAGGGAAGGCGAACTG 59.678 55.0 0.0 0.0 0.0 3.16 R
2432 3364 0.253327 CCCCAGAGTAAACCCAGAGC 59.747 60.0 0.0 0.0 0.0 4.09 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
28 29 4.177673 GGGACGAGGGCTAGGTAG 57.822 66.667 0.00 0.00 0.00 3.18
29 30 1.531128 GGGACGAGGGCTAGGTAGG 60.531 68.421 0.00 0.00 0.00 3.18
30 31 1.531128 GGACGAGGGCTAGGTAGGG 60.531 68.421 0.00 0.00 0.00 3.53
31 32 1.535685 GACGAGGGCTAGGTAGGGA 59.464 63.158 0.00 0.00 0.00 4.20
32 33 0.537828 GACGAGGGCTAGGTAGGGAG 60.538 65.000 0.00 0.00 0.00 4.30
33 34 0.992431 ACGAGGGCTAGGTAGGGAGA 60.992 60.000 0.00 0.00 0.00 3.71
34 35 0.185416 CGAGGGCTAGGTAGGGAGAA 59.815 60.000 0.00 0.00 0.00 2.87
35 36 1.707106 GAGGGCTAGGTAGGGAGAAC 58.293 60.000 0.00 0.00 0.00 3.01
36 37 0.265254 AGGGCTAGGTAGGGAGAACC 59.735 60.000 0.00 0.00 40.67 3.62
45 46 3.459063 GGGAGAACCTAGCGCCGT 61.459 66.667 2.29 0.00 35.85 5.68
46 47 2.202756 GGAGAACCTAGCGCCGTG 60.203 66.667 2.29 0.00 0.00 4.94
47 48 2.202756 GAGAACCTAGCGCCGTGG 60.203 66.667 2.29 6.58 0.00 4.94
48 49 2.678934 AGAACCTAGCGCCGTGGA 60.679 61.111 16.23 0.00 0.00 4.02
49 50 2.221906 GAGAACCTAGCGCCGTGGAA 62.222 60.000 16.23 0.00 0.00 3.53
50 51 1.153429 GAACCTAGCGCCGTGGAAT 60.153 57.895 16.23 5.97 0.00 3.01
51 52 1.429148 GAACCTAGCGCCGTGGAATG 61.429 60.000 16.23 0.00 0.00 2.67
52 53 1.895020 AACCTAGCGCCGTGGAATGA 61.895 55.000 16.23 0.00 0.00 2.57
108 110 1.681229 TGGAGTGGGGAATTAAGGCT 58.319 50.000 0.00 0.00 0.00 4.58
111 113 1.564348 GAGTGGGGAATTAAGGCTGGA 59.436 52.381 0.00 0.00 0.00 3.86
114 116 0.629058 GGGGAATTAAGGCTGGACCA 59.371 55.000 0.00 0.00 43.14 4.02
151 153 1.518774 CCAACGTATGTAGCCCCGT 59.481 57.895 0.00 0.00 34.56 5.28
191 194 1.673665 CCTGGCTCTGAGGCACAAC 60.674 63.158 27.63 0.00 46.47 3.32
267 270 4.641989 AGGCTGAAATTACATAGGTGCAAG 59.358 41.667 0.00 0.00 0.00 4.01
291 294 8.959676 AGGTAACCTTGTTTTTATTATGGGAA 57.040 30.769 0.00 0.00 37.17 3.97
297 300 6.986231 CCTTGTTTTTATTATGGGAATGCCTC 59.014 38.462 0.00 0.00 0.00 4.70
300 303 6.829298 TGTTTTTATTATGGGAATGCCTCGTA 59.171 34.615 0.00 0.00 0.00 3.43
306 309 0.674534 GGGAATGCCTCGTATCTCGT 59.325 55.000 0.00 0.00 40.80 4.18
365 368 1.402787 GGCATGATAAACCTGGGTGG 58.597 55.000 0.00 0.00 42.93 4.61
388 391 3.223435 TCACCGTCCCAAAATAAAGCAA 58.777 40.909 0.00 0.00 0.00 3.91
454 458 4.275936 AGTTCGGACTTTTGGATGAGTTTG 59.724 41.667 0.00 0.00 29.87 2.93
475 479 2.286294 GCTGGAGCATGAATTCAGTACG 59.714 50.000 14.54 3.70 41.59 3.67
537 541 5.528690 CAGTTCAGACTTTTGGATGAGTTGA 59.471 40.000 0.00 0.00 32.54 3.18
541 545 4.214971 CAGACTTTTGGATGAGTTGACTGG 59.785 45.833 0.00 0.00 0.00 4.00
552 556 4.401022 TGAGTTGACTGGAGCATGAATTT 58.599 39.130 0.00 0.00 0.00 1.82
557 561 8.757982 AGTTGACTGGAGCATGAATTTAATAT 57.242 30.769 0.00 0.00 0.00 1.28
582 586 2.851195 TCTGAGCCAAAAGGTCTTGAC 58.149 47.619 0.00 0.00 43.71 3.18
588 592 2.893489 GCCAAAAGGTCTTGACCATCTT 59.107 45.455 20.36 8.76 0.00 2.40
619 623 8.492748 CATCAGTTTGGATTTTTGAATGAGTTG 58.507 33.333 0.00 0.00 0.00 3.16
630 634 5.534207 TTGAATGAGTTGGCTGAAACATT 57.466 34.783 0.00 0.00 32.21 2.71
657 662 8.557592 TTCAATAGAATCATAAGCATGCCTAG 57.442 34.615 15.66 2.10 31.73 3.02
658 663 7.108194 TCAATAGAATCATAAGCATGCCTAGG 58.892 38.462 15.66 8.00 31.73 3.02
661 666 4.352001 AGAATCATAAGCATGCCTAGGGAA 59.648 41.667 15.66 0.00 31.73 3.97
733 873 6.966751 TCTTCCCAATTCTTTGAGATCTCAT 58.033 36.000 25.64 8.11 39.64 2.90
831 1084 3.845781 AGCTCCAAAAAGTCAGACTCA 57.154 42.857 2.72 0.00 0.00 3.41
860 1113 3.228188 TGGCCTGAAAACTGATTGACT 57.772 42.857 3.32 0.00 0.00 3.41
890 1157 7.938563 TTAACTGATTGATTTGGGTTTTTCG 57.061 32.000 0.00 0.00 0.00 3.46
891 1158 5.529581 ACTGATTGATTTGGGTTTTTCGT 57.470 34.783 0.00 0.00 0.00 3.85
893 1160 7.045126 ACTGATTGATTTGGGTTTTTCGTTA 57.955 32.000 0.00 0.00 0.00 3.18
894 1161 6.921307 ACTGATTGATTTGGGTTTTTCGTTAC 59.079 34.615 0.00 0.00 0.00 2.50
895 1162 6.806751 TGATTGATTTGGGTTTTTCGTTACA 58.193 32.000 0.00 0.00 0.00 2.41
896 1163 6.697892 TGATTGATTTGGGTTTTTCGTTACAC 59.302 34.615 0.00 0.00 0.00 2.90
897 1164 5.578005 TGATTTGGGTTTTTCGTTACACA 57.422 34.783 0.00 0.00 0.00 3.72
898 1165 5.962433 TGATTTGGGTTTTTCGTTACACAA 58.038 33.333 0.00 0.00 35.97 3.33
900 1167 6.872020 TGATTTGGGTTTTTCGTTACACAAAA 59.128 30.769 6.72 0.00 46.95 2.44
901 1168 7.549488 TGATTTGGGTTTTTCGTTACACAAAAT 59.451 29.630 6.72 0.00 46.95 1.82
902 1169 6.889019 TTGGGTTTTTCGTTACACAAAATC 57.111 33.333 0.00 0.00 34.91 2.17
903 1170 5.962433 TGGGTTTTTCGTTACACAAAATCA 58.038 33.333 2.89 0.00 0.00 2.57
908 1194 4.742438 TTCGTTACACAAAATCAGGCTC 57.258 40.909 0.00 0.00 0.00 4.70
1020 1307 0.530431 CAGGCGCCATAAATTTGGGC 60.530 55.000 31.54 20.07 44.27 5.36
1128 1432 2.103042 GCTGAATCTTGCCGTCGCT 61.103 57.895 0.00 0.00 35.36 4.93
1228 1532 3.393970 TGAGGAAGAGGCTGCCCG 61.394 66.667 16.57 0.00 35.76 6.13
1437 1741 1.150567 CCGACGACGACGAGTAGGAT 61.151 60.000 20.63 0.00 42.66 3.24
1438 1742 0.043224 CGACGACGACGAGTAGGATG 60.043 60.000 15.32 0.00 42.66 3.51
1439 1743 0.304098 GACGACGACGAGTAGGATGG 59.696 60.000 15.32 0.00 42.66 3.51
1440 1744 1.094073 ACGACGACGAGTAGGATGGG 61.094 60.000 15.32 0.00 42.66 4.00
1517 1825 5.387113 TGATATTAGTGGTGGATGCCTTT 57.613 39.130 0.00 0.00 0.00 3.11
1565 1877 6.468956 CGTTGTTGGTACTGATTTGCATATTC 59.531 38.462 0.00 0.00 0.00 1.75
1662 1975 4.638421 TGGACGTATTGATTCATCCAAACC 59.362 41.667 3.90 0.00 33.34 3.27
1773 2089 4.748102 TCCGAAGTCACAACTGAAATGTAC 59.252 41.667 0.00 0.00 35.36 2.90
1818 2135 7.806409 TGATGTGAACTTTTGATCTCTTCAA 57.194 32.000 0.00 0.00 42.62 2.69
1835 2152 3.865011 TCAAGTCATCTCAGACAGAGC 57.135 47.619 0.00 0.00 44.35 4.09
1836 2153 3.160269 TCAAGTCATCTCAGACAGAGCA 58.840 45.455 0.00 0.00 44.35 4.26
1837 2154 3.768215 TCAAGTCATCTCAGACAGAGCAT 59.232 43.478 0.00 0.00 44.35 3.79
2110 3037 4.037089 TCATGCAAAATCATCCTCCAATCG 59.963 41.667 0.00 0.00 0.00 3.34
2111 3038 3.355378 TGCAAAATCATCCTCCAATCGT 58.645 40.909 0.00 0.00 0.00 3.73
2112 3039 3.378112 TGCAAAATCATCCTCCAATCGTC 59.622 43.478 0.00 0.00 0.00 4.20
2113 3040 3.629398 GCAAAATCATCCTCCAATCGTCT 59.371 43.478 0.00 0.00 0.00 4.18
2114 3041 4.497006 GCAAAATCATCCTCCAATCGTCTG 60.497 45.833 0.00 0.00 0.00 3.51
2115 3042 4.494091 AAATCATCCTCCAATCGTCTGT 57.506 40.909 0.00 0.00 0.00 3.41
2116 3043 2.967599 TCATCCTCCAATCGTCTGTG 57.032 50.000 0.00 0.00 0.00 3.66
2117 3044 2.179427 TCATCCTCCAATCGTCTGTGT 58.821 47.619 0.00 0.00 0.00 3.72
2118 3045 2.094026 TCATCCTCCAATCGTCTGTGTG 60.094 50.000 0.00 0.00 0.00 3.82
2119 3046 1.338107 TCCTCCAATCGTCTGTGTGT 58.662 50.000 0.00 0.00 0.00 3.72
2120 3047 2.521126 TCCTCCAATCGTCTGTGTGTA 58.479 47.619 0.00 0.00 0.00 2.90
2121 3048 3.096852 TCCTCCAATCGTCTGTGTGTAT 58.903 45.455 0.00 0.00 0.00 2.29
2122 3049 3.513912 TCCTCCAATCGTCTGTGTGTATT 59.486 43.478 0.00 0.00 0.00 1.89
2123 3050 3.618594 CCTCCAATCGTCTGTGTGTATTG 59.381 47.826 0.00 0.00 0.00 1.90
2124 3051 3.595173 TCCAATCGTCTGTGTGTATTGG 58.405 45.455 0.00 0.00 45.18 3.16
2125 3052 2.677836 CCAATCGTCTGTGTGTATTGGG 59.322 50.000 0.00 0.00 41.80 4.12
2126 3053 2.677836 CAATCGTCTGTGTGTATTGGGG 59.322 50.000 0.00 0.00 0.00 4.96
2127 3054 0.611200 TCGTCTGTGTGTATTGGGGG 59.389 55.000 0.00 0.00 0.00 5.40
2128 3055 1.024579 CGTCTGTGTGTATTGGGGGC 61.025 60.000 0.00 0.00 0.00 5.80
2144 3071 2.441348 GCGGGTGGGGGTAATTGG 60.441 66.667 0.00 0.00 0.00 3.16
2187 3114 4.141756 TGTCCTAACCGGTTTTGTAGTTCA 60.142 41.667 27.64 13.74 0.00 3.18
2188 3115 4.999311 GTCCTAACCGGTTTTGTAGTTCAT 59.001 41.667 27.64 0.00 0.00 2.57
2189 3116 4.998672 TCCTAACCGGTTTTGTAGTTCATG 59.001 41.667 27.64 3.56 0.00 3.07
2215 3142 7.624360 TGGTTGTAAATTTAGCTGACCATAG 57.376 36.000 13.65 0.00 31.47 2.23
2278 3209 8.507470 AAAAAGCACTTATCTCAATTTTCGAC 57.493 30.769 0.00 0.00 0.00 4.20
2279 3210 6.801539 AAGCACTTATCTCAATTTTCGACA 57.198 33.333 0.00 0.00 0.00 4.35
2280 3211 6.170675 AGCACTTATCTCAATTTTCGACAC 57.829 37.500 0.00 0.00 0.00 3.67
2281 3212 5.122396 AGCACTTATCTCAATTTTCGACACC 59.878 40.000 0.00 0.00 0.00 4.16
2282 3213 5.673818 GCACTTATCTCAATTTTCGACACCC 60.674 44.000 0.00 0.00 0.00 4.61
2283 3214 5.643777 CACTTATCTCAATTTTCGACACCCT 59.356 40.000 0.00 0.00 0.00 4.34
2284 3215 6.149474 CACTTATCTCAATTTTCGACACCCTT 59.851 38.462 0.00 0.00 0.00 3.95
2285 3216 7.333423 CACTTATCTCAATTTTCGACACCCTTA 59.667 37.037 0.00 0.00 0.00 2.69
2286 3217 8.047310 ACTTATCTCAATTTTCGACACCCTTAT 58.953 33.333 0.00 0.00 0.00 1.73
2287 3218 9.542462 CTTATCTCAATTTTCGACACCCTTATA 57.458 33.333 0.00 0.00 0.00 0.98
2289 3220 8.608844 ATCTCAATTTTCGACACCCTTATATC 57.391 34.615 0.00 0.00 0.00 1.63
2290 3221 7.561251 TCTCAATTTTCGACACCCTTATATCA 58.439 34.615 0.00 0.00 0.00 2.15
2291 3222 8.044309 TCTCAATTTTCGACACCCTTATATCAA 58.956 33.333 0.00 0.00 0.00 2.57
2292 3223 7.981142 TCAATTTTCGACACCCTTATATCAAC 58.019 34.615 0.00 0.00 0.00 3.18
2293 3224 6.937436 ATTTTCGACACCCTTATATCAACC 57.063 37.500 0.00 0.00 0.00 3.77
2294 3225 5.687166 TTTCGACACCCTTATATCAACCT 57.313 39.130 0.00 0.00 0.00 3.50
2295 3226 5.687166 TTCGACACCCTTATATCAACCTT 57.313 39.130 0.00 0.00 0.00 3.50
2296 3227 6.795144 TTCGACACCCTTATATCAACCTTA 57.205 37.500 0.00 0.00 0.00 2.69
2297 3228 6.989155 TCGACACCCTTATATCAACCTTAT 57.011 37.500 0.00 0.00 0.00 1.73
2298 3229 7.369551 TCGACACCCTTATATCAACCTTATT 57.630 36.000 0.00 0.00 0.00 1.40
2299 3230 7.798071 TCGACACCCTTATATCAACCTTATTT 58.202 34.615 0.00 0.00 0.00 1.40
2300 3231 8.269317 TCGACACCCTTATATCAACCTTATTTT 58.731 33.333 0.00 0.00 0.00 1.82
2301 3232 8.899771 CGACACCCTTATATCAACCTTATTTTT 58.100 33.333 0.00 0.00 0.00 1.94
2303 3234 8.474831 ACACCCTTATATCAACCTTATTTTTGC 58.525 33.333 0.00 0.00 0.00 3.68
2304 3235 8.474025 CACCCTTATATCAACCTTATTTTTGCA 58.526 33.333 0.00 0.00 0.00 4.08
2305 3236 9.212593 ACCCTTATATCAACCTTATTTTTGCAT 57.787 29.630 0.00 0.00 0.00 3.96
2306 3237 9.480053 CCCTTATATCAACCTTATTTTTGCATG 57.520 33.333 0.00 0.00 0.00 4.06
2310 3241 5.404466 TCAACCTTATTTTTGCATGAGGG 57.596 39.130 0.00 0.00 34.77 4.30
2311 3242 4.837860 TCAACCTTATTTTTGCATGAGGGT 59.162 37.500 0.00 0.00 34.77 4.34
2312 3243 6.013379 TCAACCTTATTTTTGCATGAGGGTA 58.987 36.000 0.00 0.00 34.77 3.69
2313 3244 6.667414 TCAACCTTATTTTTGCATGAGGGTAT 59.333 34.615 0.00 0.00 34.77 2.73
2314 3245 6.469782 ACCTTATTTTTGCATGAGGGTATG 57.530 37.500 0.00 0.00 34.77 2.39
2315 3246 5.957774 ACCTTATTTTTGCATGAGGGTATGT 59.042 36.000 0.00 0.00 34.77 2.29
2316 3247 6.127366 ACCTTATTTTTGCATGAGGGTATGTG 60.127 38.462 0.00 0.00 34.77 3.21
2317 3248 3.591196 TTTTTGCATGAGGGTATGTGC 57.409 42.857 0.00 0.00 38.05 4.57
2318 3249 2.512692 TTTGCATGAGGGTATGTGCT 57.487 45.000 0.00 0.00 38.37 4.40
2319 3250 2.042686 TTGCATGAGGGTATGTGCTC 57.957 50.000 0.00 0.00 38.37 4.26
2320 3251 1.206878 TGCATGAGGGTATGTGCTCT 58.793 50.000 0.00 0.00 38.37 4.09
2321 3252 1.561076 TGCATGAGGGTATGTGCTCTT 59.439 47.619 0.00 0.00 38.37 2.85
2322 3253 2.216898 GCATGAGGGTATGTGCTCTTC 58.783 52.381 0.00 0.00 34.85 2.87
2323 3254 2.420547 GCATGAGGGTATGTGCTCTTCA 60.421 50.000 0.00 0.00 34.85 3.02
2324 3255 3.464907 CATGAGGGTATGTGCTCTTCAG 58.535 50.000 0.00 0.00 0.00 3.02
2325 3256 2.540383 TGAGGGTATGTGCTCTTCAGT 58.460 47.619 0.00 0.00 0.00 3.41
2326 3257 2.906389 TGAGGGTATGTGCTCTTCAGTT 59.094 45.455 0.00 0.00 0.00 3.16
2327 3258 4.093743 TGAGGGTATGTGCTCTTCAGTTA 58.906 43.478 0.00 0.00 0.00 2.24
2328 3259 4.716784 TGAGGGTATGTGCTCTTCAGTTAT 59.283 41.667 0.00 0.00 0.00 1.89
2329 3260 5.028549 AGGGTATGTGCTCTTCAGTTATG 57.971 43.478 0.00 0.00 0.00 1.90
2330 3261 4.716784 AGGGTATGTGCTCTTCAGTTATGA 59.283 41.667 0.00 0.00 0.00 2.15
2331 3262 5.189736 AGGGTATGTGCTCTTCAGTTATGAA 59.810 40.000 0.00 0.00 43.20 2.57
2332 3263 6.058183 GGGTATGTGCTCTTCAGTTATGAAT 58.942 40.000 0.00 0.00 44.32 2.57
2333 3264 6.543831 GGGTATGTGCTCTTCAGTTATGAATT 59.456 38.462 0.00 0.00 44.32 2.17
2334 3265 7.067494 GGGTATGTGCTCTTCAGTTATGAATTT 59.933 37.037 0.00 0.00 44.32 1.82
2335 3266 8.462016 GGTATGTGCTCTTCAGTTATGAATTTT 58.538 33.333 0.00 0.00 44.32 1.82
2336 3267 9.495754 GTATGTGCTCTTCAGTTATGAATTTTC 57.504 33.333 0.00 0.00 44.32 2.29
2337 3268 7.750229 TGTGCTCTTCAGTTATGAATTTTCT 57.250 32.000 0.00 0.00 44.32 2.52
2338 3269 8.846943 TGTGCTCTTCAGTTATGAATTTTCTA 57.153 30.769 0.00 0.00 44.32 2.10
2339 3270 9.453572 TGTGCTCTTCAGTTATGAATTTTCTAT 57.546 29.630 0.00 0.00 44.32 1.98
2358 3289 8.809159 TTTCTATTTTGTTTTGCATTCATCGA 57.191 26.923 0.00 0.00 0.00 3.59
2359 3290 7.795431 TCTATTTTGTTTTGCATTCATCGAC 57.205 32.000 0.00 0.00 0.00 4.20
2360 3291 5.844301 ATTTTGTTTTGCATTCATCGACC 57.156 34.783 0.00 0.00 0.00 4.79
2361 3292 3.296322 TTGTTTTGCATTCATCGACCC 57.704 42.857 0.00 0.00 0.00 4.46
2362 3293 2.234143 TGTTTTGCATTCATCGACCCA 58.766 42.857 0.00 0.00 0.00 4.51
2363 3294 2.824936 TGTTTTGCATTCATCGACCCAT 59.175 40.909 0.00 0.00 0.00 4.00
2364 3295 3.181397 GTTTTGCATTCATCGACCCATG 58.819 45.455 0.00 0.00 0.00 3.66
2365 3296 2.416680 TTGCATTCATCGACCCATGA 57.583 45.000 0.00 0.00 0.00 3.07
2366 3297 2.643995 TGCATTCATCGACCCATGAT 57.356 45.000 0.00 0.00 32.69 2.45
2367 3298 3.767902 TGCATTCATCGACCCATGATA 57.232 42.857 0.00 0.00 32.69 2.15
2368 3299 4.290711 TGCATTCATCGACCCATGATAT 57.709 40.909 0.00 0.00 32.69 1.63
2369 3300 4.256110 TGCATTCATCGACCCATGATATC 58.744 43.478 0.00 0.00 32.69 1.63
2370 3301 3.624861 GCATTCATCGACCCATGATATCC 59.375 47.826 0.00 0.00 32.69 2.59
2376 3307 3.797312 TCGACCCATGATATCCCCATTA 58.203 45.455 0.00 0.00 0.00 1.90
2378 3309 4.408921 TCGACCCATGATATCCCCATTATC 59.591 45.833 0.00 0.00 0.00 1.75
2382 3313 7.202130 CGACCCATGATATCCCCATTATCTTAT 60.202 40.741 0.00 0.00 0.00 1.73
2432 3364 1.135689 GCGTGAGGGTATGTTTTGCAG 60.136 52.381 0.00 0.00 0.00 4.41
2526 3463 2.292845 GCAGCTCTTGAATCCTAATGGC 59.707 50.000 0.00 0.00 0.00 4.40
2527 3464 3.818180 CAGCTCTTGAATCCTAATGGCT 58.182 45.455 0.00 0.00 0.00 4.75
2528 3465 3.564644 CAGCTCTTGAATCCTAATGGCTG 59.435 47.826 0.00 0.00 38.57 4.85
2529 3466 3.457380 AGCTCTTGAATCCTAATGGCTGA 59.543 43.478 0.00 0.00 0.00 4.26
2530 3467 4.104420 AGCTCTTGAATCCTAATGGCTGAT 59.896 41.667 0.00 0.00 0.00 2.90
2531 3468 4.455190 GCTCTTGAATCCTAATGGCTGATC 59.545 45.833 0.00 0.00 0.00 2.92
2532 3469 4.635223 TCTTGAATCCTAATGGCTGATCG 58.365 43.478 0.00 0.00 0.00 3.69
2544 3481 0.179124 GCTGATCGAGTTCGCCTTCT 60.179 55.000 0.00 0.00 39.60 2.85
2553 3490 3.427638 CGAGTTCGCCTTCTCTATGTCAA 60.428 47.826 0.00 0.00 0.00 3.18
2566 3503 4.780815 TCTATGTCAATCCCCACATCAAC 58.219 43.478 0.00 0.00 34.92 3.18
2588 3525 8.556194 TCAACCGATTAATATTGATGCAAGTAC 58.444 33.333 0.00 0.00 0.00 2.73
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 1.153823 CTCGTCCCGGTGATGTGTC 60.154 63.158 0.00 0.00 0.00 3.67
1 2 2.646175 CCTCGTCCCGGTGATGTGT 61.646 63.158 0.00 0.00 0.00 3.72
2 3 2.184322 CCTCGTCCCGGTGATGTG 59.816 66.667 0.00 4.13 0.00 3.21
4 5 4.530857 GCCCTCGTCCCGGTGATG 62.531 72.222 0.00 3.09 0.00 3.07
5 6 3.369410 TAGCCCTCGTCCCGGTGAT 62.369 63.158 0.00 0.00 0.00 3.06
6 7 4.051167 TAGCCCTCGTCCCGGTGA 62.051 66.667 0.00 0.00 0.00 4.02
7 8 3.528370 CTAGCCCTCGTCCCGGTG 61.528 72.222 0.00 0.00 0.00 4.94
8 9 4.835891 CCTAGCCCTCGTCCCGGT 62.836 72.222 0.00 0.00 0.00 5.28
9 10 3.426309 TACCTAGCCCTCGTCCCGG 62.426 68.421 0.00 0.00 0.00 5.73
10 11 1.897615 CTACCTAGCCCTCGTCCCG 60.898 68.421 0.00 0.00 0.00 5.14
11 12 1.531128 CCTACCTAGCCCTCGTCCC 60.531 68.421 0.00 0.00 0.00 4.46
12 13 1.531128 CCCTACCTAGCCCTCGTCC 60.531 68.421 0.00 0.00 0.00 4.79
13 14 0.537828 CTCCCTACCTAGCCCTCGTC 60.538 65.000 0.00 0.00 0.00 4.20
14 15 0.992431 TCTCCCTACCTAGCCCTCGT 60.992 60.000 0.00 0.00 0.00 4.18
15 16 0.185416 TTCTCCCTACCTAGCCCTCG 59.815 60.000 0.00 0.00 0.00 4.63
16 17 1.707106 GTTCTCCCTACCTAGCCCTC 58.293 60.000 0.00 0.00 0.00 4.30
17 18 0.265254 GGTTCTCCCTACCTAGCCCT 59.735 60.000 0.00 0.00 32.75 5.19
18 19 0.265254 AGGTTCTCCCTACCTAGCCC 59.735 60.000 0.00 0.00 44.11 5.19
19 20 3.950611 AGGTTCTCCCTACCTAGCC 57.049 57.895 0.00 0.00 44.11 3.93
22 23 1.478288 GCGCTAGGTTCTCCCTACCTA 60.478 57.143 0.00 0.00 44.11 3.08
23 24 0.756070 GCGCTAGGTTCTCCCTACCT 60.756 60.000 0.00 0.00 43.87 3.08
24 25 1.740905 GCGCTAGGTTCTCCCTACC 59.259 63.158 0.00 0.00 43.87 3.18
25 26 1.740905 GGCGCTAGGTTCTCCCTAC 59.259 63.158 7.64 0.00 43.87 3.18
26 27 1.826921 CGGCGCTAGGTTCTCCCTA 60.827 63.158 7.64 0.00 43.87 3.53
28 29 3.459063 ACGGCGCTAGGTTCTCCC 61.459 66.667 6.90 0.00 0.00 4.30
29 30 2.202756 CACGGCGCTAGGTTCTCC 60.203 66.667 6.90 0.00 0.00 3.71
30 31 2.202756 CCACGGCGCTAGGTTCTC 60.203 66.667 6.90 0.00 0.00 2.87
31 32 1.614241 ATTCCACGGCGCTAGGTTCT 61.614 55.000 6.90 0.00 0.00 3.01
32 33 1.153429 ATTCCACGGCGCTAGGTTC 60.153 57.895 6.90 0.00 0.00 3.62
33 34 1.449601 CATTCCACGGCGCTAGGTT 60.450 57.895 6.90 0.00 0.00 3.50
34 35 2.186903 CATTCCACGGCGCTAGGT 59.813 61.111 6.90 0.00 0.00 3.08
35 36 1.592669 CTCATTCCACGGCGCTAGG 60.593 63.158 6.90 7.10 0.00 3.02
36 37 1.592669 CCTCATTCCACGGCGCTAG 60.593 63.158 6.90 4.36 0.00 3.42
37 38 2.355986 ACCTCATTCCACGGCGCTA 61.356 57.895 6.90 0.00 0.00 4.26
38 39 3.706373 ACCTCATTCCACGGCGCT 61.706 61.111 6.90 0.00 0.00 5.92
39 40 3.499737 CACCTCATTCCACGGCGC 61.500 66.667 6.90 0.00 0.00 6.53
40 41 2.819595 CCACCTCATTCCACGGCG 60.820 66.667 4.80 4.80 0.00 6.46
41 42 2.040544 CACCACCTCATTCCACGGC 61.041 63.158 0.00 0.00 0.00 5.68
42 43 0.391661 CTCACCACCTCATTCCACGG 60.392 60.000 0.00 0.00 0.00 4.94
43 44 0.608130 TCTCACCACCTCATTCCACG 59.392 55.000 0.00 0.00 0.00 4.94
44 45 1.902508 TCTCTCACCACCTCATTCCAC 59.097 52.381 0.00 0.00 0.00 4.02
45 46 2.325661 TCTCTCACCACCTCATTCCA 57.674 50.000 0.00 0.00 0.00 3.53
46 47 3.539604 CATTCTCTCACCACCTCATTCC 58.460 50.000 0.00 0.00 0.00 3.01
47 48 3.539604 CCATTCTCTCACCACCTCATTC 58.460 50.000 0.00 0.00 0.00 2.67
48 49 2.240667 CCCATTCTCTCACCACCTCATT 59.759 50.000 0.00 0.00 0.00 2.57
49 50 1.842562 CCCATTCTCTCACCACCTCAT 59.157 52.381 0.00 0.00 0.00 2.90
50 51 1.279496 CCCATTCTCTCACCACCTCA 58.721 55.000 0.00 0.00 0.00 3.86
51 52 0.543749 CCCCATTCTCTCACCACCTC 59.456 60.000 0.00 0.00 0.00 3.85
52 53 0.178861 ACCCCATTCTCTCACCACCT 60.179 55.000 0.00 0.00 0.00 4.00
111 113 1.224592 GCACGGGAGATGGAATGGT 59.775 57.895 0.00 0.00 0.00 3.55
114 116 0.181350 GGAAGCACGGGAGATGGAAT 59.819 55.000 0.00 0.00 0.00 3.01
176 178 1.251251 ATTTGTTGTGCCTCAGAGCC 58.749 50.000 0.00 0.00 0.00 4.70
191 194 3.664107 TGAGGAGGAACGTCTGAATTTG 58.336 45.455 0.00 0.00 34.87 2.32
244 247 4.235079 TGCACCTATGTAATTTCAGCCT 57.765 40.909 0.00 0.00 0.00 4.58
267 270 9.594478 CATTCCCATAATAAAAACAAGGTTACC 57.406 33.333 0.00 0.00 0.00 2.85
282 285 4.382040 CGAGATACGAGGCATTCCCATAAT 60.382 45.833 0.00 0.00 45.77 1.28
286 289 0.673985 CGAGATACGAGGCATTCCCA 59.326 55.000 0.00 0.00 45.77 4.37
291 294 6.080648 TGTAATAAACGAGATACGAGGCAT 57.919 37.500 0.00 0.00 45.77 4.40
345 348 1.402787 CACCCAGGTTTATCATGCCC 58.597 55.000 0.00 0.00 0.00 5.36
365 368 3.442273 TGCTTTATTTTGGGACGGTGATC 59.558 43.478 0.00 0.00 0.00 2.92
415 418 2.357637 CGAACTGATGGAGAGAGAGGAC 59.642 54.545 0.00 0.00 0.00 3.85
416 419 2.649190 CGAACTGATGGAGAGAGAGGA 58.351 52.381 0.00 0.00 0.00 3.71
454 458 2.286294 CGTACTGAATTCATGCTCCAGC 59.714 50.000 8.96 0.00 42.50 4.85
475 479 2.393646 AGACCTCTTGGCTCAGATACC 58.606 52.381 0.00 0.00 36.63 2.73
537 541 6.613699 TCCCATATTAAATTCATGCTCCAGT 58.386 36.000 0.00 0.00 0.00 4.00
541 545 8.571461 TCAGATCCCATATTAAATTCATGCTC 57.429 34.615 0.00 0.00 0.00 4.26
552 556 5.134339 ACCTTTTGGCTCAGATCCCATATTA 59.866 40.000 0.00 0.00 45.59 0.98
557 561 1.004745 GACCTTTTGGCTCAGATCCCA 59.995 52.381 0.00 0.00 45.59 4.37
582 586 7.636150 AATCCAAACTGATGTAGAAAGATGG 57.364 36.000 0.00 0.00 0.00 3.51
588 592 9.695526 CATTCAAAAATCCAAACTGATGTAGAA 57.304 29.630 0.00 0.00 0.00 2.10
657 662 1.821136 CAAGGTGGCTCATTCTTTCCC 59.179 52.381 0.00 0.00 0.00 3.97
658 663 2.519013 ACAAGGTGGCTCATTCTTTCC 58.481 47.619 0.00 0.00 0.00 3.13
661 666 2.036346 GCAAACAAGGTGGCTCATTCTT 59.964 45.455 0.00 0.00 0.00 2.52
733 873 3.734463 TGACCGAGTGCTTTGTGAATTA 58.266 40.909 0.00 0.00 0.00 1.40
822 1075 2.349886 GCCATTCATCGTTGAGTCTGAC 59.650 50.000 0.00 0.00 32.27 3.51
831 1084 3.057315 CAGTTTTCAGGCCATTCATCGTT 60.057 43.478 5.01 0.00 0.00 3.85
889 1156 3.667960 GCAGAGCCTGATTTTGTGTAACG 60.668 47.826 6.40 0.00 34.08 3.18
890 1157 3.667960 CGCAGAGCCTGATTTTGTGTAAC 60.668 47.826 6.40 0.00 32.44 2.50
891 1158 2.483877 CGCAGAGCCTGATTTTGTGTAA 59.516 45.455 6.40 0.00 32.44 2.41
893 1160 0.877071 CGCAGAGCCTGATTTTGTGT 59.123 50.000 6.40 0.00 32.44 3.72
894 1161 0.169672 CCGCAGAGCCTGATTTTGTG 59.830 55.000 6.40 0.00 32.44 3.33
895 1162 0.962356 CCCGCAGAGCCTGATTTTGT 60.962 55.000 6.40 0.00 32.44 2.83
896 1163 0.962356 ACCCGCAGAGCCTGATTTTG 60.962 55.000 6.40 0.00 32.44 2.44
897 1164 0.962356 CACCCGCAGAGCCTGATTTT 60.962 55.000 6.40 0.00 32.44 1.82
898 1165 1.377725 CACCCGCAGAGCCTGATTT 60.378 57.895 6.40 0.00 32.44 2.17
900 1167 2.685017 TCACCCGCAGAGCCTGAT 60.685 61.111 6.40 0.00 32.44 2.90
901 1168 3.695606 GTCACCCGCAGAGCCTGA 61.696 66.667 6.40 0.00 32.44 3.86
902 1169 3.655810 GAGTCACCCGCAGAGCCTG 62.656 68.421 0.00 0.00 34.12 4.85
903 1170 3.386237 GAGTCACCCGCAGAGCCT 61.386 66.667 0.00 0.00 0.00 4.58
1112 1416 0.737367 CTCAGCGACGGCAAGATTCA 60.737 55.000 0.00 0.00 43.41 2.57
1185 1489 1.122632 TCTTGCCGTTCACCACCCTA 61.123 55.000 0.00 0.00 0.00 3.53
1228 1532 4.090057 GCGGCGCACCTTCTTCAC 62.090 66.667 29.21 0.00 0.00 3.18
1437 1741 0.617535 TCCGCTTCATCTTCCTCCCA 60.618 55.000 0.00 0.00 0.00 4.37
1438 1742 0.541863 TTCCGCTTCATCTTCCTCCC 59.458 55.000 0.00 0.00 0.00 4.30
1439 1743 2.403252 TTTCCGCTTCATCTTCCTCC 57.597 50.000 0.00 0.00 0.00 4.30
1440 1744 3.065925 CCAATTTCCGCTTCATCTTCCTC 59.934 47.826 0.00 0.00 0.00 3.71
1517 1825 5.624509 CGAGTCTTCCACCATTCAGATTACA 60.625 44.000 0.00 0.00 0.00 2.41
1565 1877 0.321671 TGAGAAGGGAAGGCGAACTG 59.678 55.000 0.00 0.00 0.00 3.16
1711 2027 5.766150 TTCTTGTTTCGTGATGACCAAAT 57.234 34.783 0.00 0.00 0.00 2.32
1752 2068 5.907197 AGTACATTTCAGTTGTGACTTCG 57.093 39.130 0.00 0.00 32.54 3.79
1818 2135 3.363627 TGATGCTCTGTCTGAGATGACT 58.636 45.455 10.70 0.00 45.39 3.41
1835 2152 3.424703 ACAAGGGGTGAAATCACTGATG 58.575 45.455 12.87 9.55 45.73 3.07
1836 2153 3.814504 ACAAGGGGTGAAATCACTGAT 57.185 42.857 12.87 0.00 45.73 2.90
1837 2154 3.117701 TGAACAAGGGGTGAAATCACTGA 60.118 43.478 12.87 0.00 45.73 3.41
2003 2328 7.346751 GGTTGAAATATGCATTTCTCCCTTA 57.653 36.000 3.54 0.00 46.87 2.69
2005 2330 5.859205 GGTTGAAATATGCATTTCTCCCT 57.141 39.130 3.54 0.00 46.87 4.20
2008 2333 6.455360 TCAGGGTTGAAATATGCATTTCTC 57.545 37.500 3.54 0.00 46.87 2.87
2009 2334 6.438425 AGTTCAGGGTTGAAATATGCATTTCT 59.562 34.615 3.54 0.00 46.87 2.52
2010 2335 6.633856 AGTTCAGGGTTGAAATATGCATTTC 58.366 36.000 3.54 5.04 46.91 2.17
2011 2336 6.438425 AGAGTTCAGGGTTGAAATATGCATTT 59.562 34.615 3.54 0.00 44.49 2.32
2012 2337 5.954150 AGAGTTCAGGGTTGAAATATGCATT 59.046 36.000 3.54 0.00 44.49 3.56
2013 2338 5.513233 AGAGTTCAGGGTTGAAATATGCAT 58.487 37.500 3.79 3.79 44.49 3.96
2014 2339 4.922206 AGAGTTCAGGGTTGAAATATGCA 58.078 39.130 0.00 0.00 44.49 3.96
2015 2340 5.529060 CCTAGAGTTCAGGGTTGAAATATGC 59.471 44.000 0.00 0.00 44.49 3.14
2016 2341 6.058183 CCCTAGAGTTCAGGGTTGAAATATG 58.942 44.000 0.00 0.00 46.77 1.78
2017 2342 6.253946 CCCTAGAGTTCAGGGTTGAAATAT 57.746 41.667 0.00 0.00 46.77 1.28
2018 2343 5.693769 CCCTAGAGTTCAGGGTTGAAATA 57.306 43.478 0.00 0.00 46.77 1.40
2019 2344 4.576330 CCCTAGAGTTCAGGGTTGAAAT 57.424 45.455 0.00 0.00 46.77 2.17
2110 3037 1.024579 CGCCCCCAATACACACAGAC 61.025 60.000 0.00 0.00 0.00 3.51
2111 3038 1.298340 CGCCCCCAATACACACAGA 59.702 57.895 0.00 0.00 0.00 3.41
2112 3039 1.748879 CCGCCCCCAATACACACAG 60.749 63.158 0.00 0.00 0.00 3.66
2113 3040 2.353189 CCGCCCCCAATACACACA 59.647 61.111 0.00 0.00 0.00 3.72
2114 3041 2.439519 CCCGCCCCCAATACACAC 60.440 66.667 0.00 0.00 0.00 3.82
2115 3042 2.936584 ACCCGCCCCCAATACACA 60.937 61.111 0.00 0.00 0.00 3.72
2116 3043 2.439519 CACCCGCCCCCAATACAC 60.440 66.667 0.00 0.00 0.00 2.90
2117 3044 3.733972 CCACCCGCCCCCAATACA 61.734 66.667 0.00 0.00 0.00 2.29
2118 3045 4.516258 CCCACCCGCCCCCAATAC 62.516 72.222 0.00 0.00 0.00 1.89
2125 3052 3.746436 AATTACCCCCACCCGCCC 61.746 66.667 0.00 0.00 0.00 6.13
2126 3053 2.441348 CAATTACCCCCACCCGCC 60.441 66.667 0.00 0.00 0.00 6.13
2127 3054 2.441348 CCAATTACCCCCACCCGC 60.441 66.667 0.00 0.00 0.00 6.13
2128 3055 1.379309 CACCAATTACCCCCACCCG 60.379 63.158 0.00 0.00 0.00 5.28
2141 3068 4.062293 CAACCTCGAACTATCAACACCAA 58.938 43.478 0.00 0.00 0.00 3.67
2144 3071 4.056050 ACACAACCTCGAACTATCAACAC 58.944 43.478 0.00 0.00 0.00 3.32
2187 3114 6.663093 TGGTCAGCTAAATTTACAACCATCAT 59.337 34.615 10.17 0.00 30.91 2.45
2188 3115 6.007076 TGGTCAGCTAAATTTACAACCATCA 58.993 36.000 10.17 0.00 30.91 3.07
2189 3116 6.509418 TGGTCAGCTAAATTTACAACCATC 57.491 37.500 10.17 0.00 30.91 3.51
2215 3142 6.199937 AGTGCATATTTCAACCATGAACTC 57.800 37.500 0.00 0.00 45.01 3.01
2264 3195 8.210946 TGATATAAGGGTGTCGAAAATTGAGAT 58.789 33.333 0.00 0.00 0.00 2.75
2272 3203 5.687166 AGGTTGATATAAGGGTGTCGAAA 57.313 39.130 0.00 0.00 0.00 3.46
2274 3205 6.989155 ATAAGGTTGATATAAGGGTGTCGA 57.011 37.500 0.00 0.00 0.00 4.20
2275 3206 8.446599 AAAATAAGGTTGATATAAGGGTGTCG 57.553 34.615 0.00 0.00 0.00 4.35
2277 3208 8.474831 GCAAAAATAAGGTTGATATAAGGGTGT 58.525 33.333 0.00 0.00 0.00 4.16
2278 3209 8.474025 TGCAAAAATAAGGTTGATATAAGGGTG 58.526 33.333 0.00 0.00 0.00 4.61
2279 3210 8.602472 TGCAAAAATAAGGTTGATATAAGGGT 57.398 30.769 0.00 0.00 0.00 4.34
2280 3211 9.480053 CATGCAAAAATAAGGTTGATATAAGGG 57.520 33.333 0.00 0.00 0.00 3.95
2284 3215 8.859090 CCCTCATGCAAAAATAAGGTTGATATA 58.141 33.333 0.00 0.00 0.00 0.86
2285 3216 7.345392 ACCCTCATGCAAAAATAAGGTTGATAT 59.655 33.333 0.00 0.00 0.00 1.63
2286 3217 6.667414 ACCCTCATGCAAAAATAAGGTTGATA 59.333 34.615 0.00 0.00 0.00 2.15
2287 3218 5.484998 ACCCTCATGCAAAAATAAGGTTGAT 59.515 36.000 0.00 0.00 0.00 2.57
2288 3219 4.837860 ACCCTCATGCAAAAATAAGGTTGA 59.162 37.500 0.00 0.00 0.00 3.18
2289 3220 5.151297 ACCCTCATGCAAAAATAAGGTTG 57.849 39.130 0.00 0.00 0.00 3.77
2290 3221 6.440328 ACATACCCTCATGCAAAAATAAGGTT 59.560 34.615 0.00 0.00 0.00 3.50
2291 3222 5.957774 ACATACCCTCATGCAAAAATAAGGT 59.042 36.000 0.00 0.00 0.00 3.50
2292 3223 6.275335 CACATACCCTCATGCAAAAATAAGG 58.725 40.000 0.00 0.00 0.00 2.69
2293 3224 5.750067 GCACATACCCTCATGCAAAAATAAG 59.250 40.000 0.00 0.00 38.00 1.73
2294 3225 5.421693 AGCACATACCCTCATGCAAAAATAA 59.578 36.000 0.00 0.00 40.63 1.40
2295 3226 4.955450 AGCACATACCCTCATGCAAAAATA 59.045 37.500 0.00 0.00 40.63 1.40
2296 3227 3.770933 AGCACATACCCTCATGCAAAAAT 59.229 39.130 0.00 0.00 40.63 1.82
2297 3228 3.164268 AGCACATACCCTCATGCAAAAA 58.836 40.909 0.00 0.00 40.63 1.94
2298 3229 2.754552 GAGCACATACCCTCATGCAAAA 59.245 45.455 0.00 0.00 40.63 2.44
2299 3230 2.025981 AGAGCACATACCCTCATGCAAA 60.026 45.455 0.00 0.00 40.63 3.68
2300 3231 1.561076 AGAGCACATACCCTCATGCAA 59.439 47.619 0.00 0.00 40.63 4.08
2301 3232 1.206878 AGAGCACATACCCTCATGCA 58.793 50.000 0.00 0.00 40.63 3.96
2302 3233 2.216898 GAAGAGCACATACCCTCATGC 58.783 52.381 0.00 0.00 38.39 4.06
2303 3234 3.118482 ACTGAAGAGCACATACCCTCATG 60.118 47.826 0.00 0.00 0.00 3.07
2304 3235 3.110705 ACTGAAGAGCACATACCCTCAT 58.889 45.455 0.00 0.00 0.00 2.90
2305 3236 2.540383 ACTGAAGAGCACATACCCTCA 58.460 47.619 0.00 0.00 0.00 3.86
2306 3237 3.618690 AACTGAAGAGCACATACCCTC 57.381 47.619 0.00 0.00 0.00 4.30
2307 3238 4.716784 TCATAACTGAAGAGCACATACCCT 59.283 41.667 0.00 0.00 0.00 4.34
2308 3239 5.023533 TCATAACTGAAGAGCACATACCC 57.976 43.478 0.00 0.00 0.00 3.69
2309 3240 7.559590 AATTCATAACTGAAGAGCACATACC 57.440 36.000 0.00 0.00 44.32 2.73
2310 3241 9.495754 GAAAATTCATAACTGAAGAGCACATAC 57.504 33.333 0.00 0.00 44.32 2.39
2311 3242 9.453572 AGAAAATTCATAACTGAAGAGCACATA 57.546 29.630 0.00 0.00 44.32 2.29
2312 3243 8.345724 AGAAAATTCATAACTGAAGAGCACAT 57.654 30.769 0.00 0.00 44.32 3.21
2313 3244 7.750229 AGAAAATTCATAACTGAAGAGCACA 57.250 32.000 0.00 0.00 44.32 4.57
2332 3263 9.254133 TCGATGAATGCAAAACAAAATAGAAAA 57.746 25.926 0.00 0.00 0.00 2.29
2333 3264 8.698854 GTCGATGAATGCAAAACAAAATAGAAA 58.301 29.630 0.00 0.00 0.00 2.52
2334 3265 7.328249 GGTCGATGAATGCAAAACAAAATAGAA 59.672 33.333 0.00 0.00 0.00 2.10
2335 3266 6.806249 GGTCGATGAATGCAAAACAAAATAGA 59.194 34.615 0.00 0.00 0.00 1.98
2336 3267 6.034898 GGGTCGATGAATGCAAAACAAAATAG 59.965 38.462 0.00 0.00 0.00 1.73
2337 3268 5.866633 GGGTCGATGAATGCAAAACAAAATA 59.133 36.000 0.00 0.00 0.00 1.40
2338 3269 4.690280 GGGTCGATGAATGCAAAACAAAAT 59.310 37.500 0.00 0.00 0.00 1.82
2339 3270 4.054671 GGGTCGATGAATGCAAAACAAAA 58.945 39.130 0.00 0.00 0.00 2.44
2340 3271 3.068732 TGGGTCGATGAATGCAAAACAAA 59.931 39.130 0.00 0.00 0.00 2.83
2341 3272 2.625314 TGGGTCGATGAATGCAAAACAA 59.375 40.909 0.00 0.00 0.00 2.83
2342 3273 2.234143 TGGGTCGATGAATGCAAAACA 58.766 42.857 0.00 0.00 0.00 2.83
2343 3274 3.119531 TCATGGGTCGATGAATGCAAAAC 60.120 43.478 0.00 0.00 29.11 2.43
2344 3275 3.087781 TCATGGGTCGATGAATGCAAAA 58.912 40.909 0.00 0.00 29.11 2.44
2345 3276 2.720915 TCATGGGTCGATGAATGCAAA 58.279 42.857 0.00 0.00 29.11 3.68
2346 3277 2.416680 TCATGGGTCGATGAATGCAA 57.583 45.000 0.00 0.00 29.11 4.08
2347 3278 2.643995 ATCATGGGTCGATGAATGCA 57.356 45.000 0.00 0.00 35.97 3.96
2348 3279 3.624861 GGATATCATGGGTCGATGAATGC 59.375 47.826 4.83 0.00 35.97 3.56
2349 3280 4.194640 GGGATATCATGGGTCGATGAATG 58.805 47.826 4.83 0.00 35.97 2.67
2350 3281 3.200825 GGGGATATCATGGGTCGATGAAT 59.799 47.826 4.83 0.00 35.97 2.57
2351 3282 2.571653 GGGGATATCATGGGTCGATGAA 59.428 50.000 4.83 0.00 35.97 2.57
2352 3283 2.187958 GGGGATATCATGGGTCGATGA 58.812 52.381 4.83 0.00 36.78 2.92
2353 3284 1.908619 TGGGGATATCATGGGTCGATG 59.091 52.381 4.83 0.00 0.00 3.84
2354 3285 2.342406 TGGGGATATCATGGGTCGAT 57.658 50.000 4.83 0.00 0.00 3.59
2355 3286 2.342406 ATGGGGATATCATGGGTCGA 57.658 50.000 4.83 0.00 0.00 4.20
2356 3287 4.410228 AGATAATGGGGATATCATGGGTCG 59.590 45.833 4.83 0.00 33.17 4.79
2357 3288 5.983333 AGATAATGGGGATATCATGGGTC 57.017 43.478 4.83 0.00 33.17 4.46
2358 3289 8.284435 CAATAAGATAATGGGGATATCATGGGT 58.716 37.037 4.83 0.00 33.17 4.51
2359 3290 8.284435 ACAATAAGATAATGGGGATATCATGGG 58.716 37.037 4.83 0.00 33.17 4.00
2432 3364 0.253327 CCCCAGAGTAAACCCAGAGC 59.747 60.000 0.00 0.00 0.00 4.09
2495 3432 5.278364 GGATTCAAGAGCTGCATGGATAAAG 60.278 44.000 1.02 0.00 0.00 1.85
2526 3463 1.403679 AGAGAAGGCGAACTCGATCAG 59.596 52.381 2.69 0.00 43.02 2.90
2527 3464 1.464734 AGAGAAGGCGAACTCGATCA 58.535 50.000 2.69 0.00 43.02 2.92
2528 3465 3.003897 ACATAGAGAAGGCGAACTCGATC 59.996 47.826 2.69 0.00 43.02 3.69
2529 3466 2.952978 ACATAGAGAAGGCGAACTCGAT 59.047 45.455 2.69 0.00 43.02 3.59
2530 3467 2.355132 GACATAGAGAAGGCGAACTCGA 59.645 50.000 2.69 0.00 43.02 4.04
2531 3468 2.097629 TGACATAGAGAAGGCGAACTCG 59.902 50.000 0.00 0.00 43.27 4.18
2532 3469 3.784701 TGACATAGAGAAGGCGAACTC 57.215 47.619 0.00 0.00 0.00 3.01
2544 3481 4.385199 GGTTGATGTGGGGATTGACATAGA 60.385 45.833 0.00 0.00 32.85 1.98
2553 3490 3.943671 TTAATCGGTTGATGTGGGGAT 57.056 42.857 0.00 0.00 34.24 3.85
2566 3503 7.117241 ACGTACTTGCATCAATATTAATCGG 57.883 36.000 0.00 0.00 0.00 4.18


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

AutoCloner maintained by Alex Coulton.