Multiple sequence alignment - TraesCS5A01G497500

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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 TraesCS5A01G497500 chr5A 100.000 2418 0 0 1 2418 664556243 664553826 0.000000e+00 4466.0
1 TraesCS5A01G497500 chr5A 92.500 40 0 3 1954 1991 13409912 13409950 1.000000e-03 54.7
2 TraesCS5A01G497500 chr4B 93.269 1768 74 23 231 1969 615835799 615834048 0.000000e+00 2564.0
3 TraesCS5A01G497500 chr4B 93.722 223 14 0 1 223 615836439 615836217 3.850000e-88 335.0
4 TraesCS5A01G497500 chr4B 95.349 129 6 0 2290 2418 615834049 615833921 3.150000e-49 206.0
5 TraesCS5A01G497500 chr4D 91.357 1747 73 29 231 1969 484295022 484293346 0.000000e+00 2318.0
6 TraesCS5A01G497500 chr4D 96.413 223 8 0 1 223 484295290 484295068 3.800000e-98 368.0
7 TraesCS5A01G497500 chr4D 89.048 210 23 0 1 210 21153962 21154171 6.630000e-66 261.0
8 TraesCS5A01G497500 chr4D 100.000 31 0 0 1961 1991 404113625 404113655 9.340000e-05 58.4
9 TraesCS5A01G497500 chr3B 97.925 241 5 0 1992 2232 650648312 650648552 3.720000e-113 418.0
10 TraesCS5A01G497500 chr3B 94.779 249 12 1 1984 2232 12175022 12174775 1.050000e-103 387.0
11 TraesCS5A01G497500 chr3B 94.286 245 14 0 1992 2236 742449919 742450163 2.270000e-100 375.0
12 TraesCS5A01G497500 chr3B 100.000 30 0 0 1962 1991 409607211 409607240 3.360000e-04 56.5
13 TraesCS5A01G497500 chr3B 96.875 32 0 1 1960 1991 246108976 246109006 4.000000e-03 52.8
14 TraesCS5A01G497500 chr2B 97.131 244 7 0 1989 2232 400605672 400605915 1.730000e-111 412.0
15 TraesCS5A01G497500 chr2B 89.048 210 23 0 1 210 11185480 11185689 6.630000e-66 261.0
16 TraesCS5A01G497500 chr2B 88.571 210 24 0 1 210 95552963 95552754 3.080000e-64 255.0
17 TraesCS5A01G497500 chr6A 95.122 246 12 0 1988 2233 111203267 111203022 2.920000e-104 388.0
18 TraesCS5A01G497500 chr6A 92.720 261 18 1 1989 2249 408339324 408339065 2.270000e-100 375.0
19 TraesCS5A01G497500 chr6A 82.535 355 51 8 221 568 2839780 2839430 3.910000e-78 302.0
20 TraesCS5A01G497500 chr6A 86.124 209 29 0 2 210 524735739 524735947 2.420000e-55 226.0
21 TraesCS5A01G497500 chr1B 94.094 254 15 0 1979 2232 152079878 152079625 1.050000e-103 387.0
22 TraesCS5A01G497500 chr1B 82.254 355 50 10 221 568 185544969 185544621 6.540000e-76 294.0
23 TraesCS5A01G497500 chr1B 93.151 73 3 1 2232 2304 142723516 142723446 3.290000e-19 106.0
24 TraesCS5A01G497500 chr1B 88.372 86 6 4 2232 2314 520467845 520467761 1.530000e-17 100.0
25 TraesCS5A01G497500 chr7A 94.737 247 13 0 1986 2232 668310249 668310495 3.770000e-103 385.0
26 TraesCS5A01G497500 chr7A 80.952 357 64 4 238 593 244709436 244709083 1.830000e-71 279.0
27 TraesCS5A01G497500 chr7A 89.048 210 23 0 1 210 244709712 244709503 6.630000e-66 261.0
28 TraesCS5A01G497500 chr3A 95.436 241 11 0 1992 2232 449125448 449125688 3.770000e-103 385.0
29 TraesCS5A01G497500 chr3A 97.059 34 1 0 1958 1991 695773560 695773527 9.340000e-05 58.4
30 TraesCS5A01G497500 chr6D 82.817 355 50 8 221 568 38228017 38228367 8.400000e-80 307.0
31 TraesCS5A01G497500 chr6D 81.319 364 64 4 231 593 424710314 424710674 2.350000e-75 292.0
32 TraesCS5A01G497500 chr6D 80.381 367 62 9 231 593 455748141 455748501 1.100000e-68 270.0
33 TraesCS5A01G497500 chr6D 89.524 210 22 0 1 210 424710045 424710254 1.430000e-67 267.0
34 TraesCS5A01G497500 chr6D 88.095 210 25 0 1 210 27660991 27660782 1.440000e-62 250.0
35 TraesCS5A01G497500 chr6D 87.204 211 26 1 1 210 455747871 455748081 3.110000e-59 239.0
36 TraesCS5A01G497500 chr6D 85.922 206 28 1 5 210 38227767 38227971 4.050000e-53 219.0
37 TraesCS5A01G497500 chr6D 100.000 63 0 0 2232 2294 77219248 77219310 1.520000e-22 117.0
38 TraesCS5A01G497500 chr6D 92.308 78 3 2 2232 2309 149721690 149721764 9.140000e-20 108.0
39 TraesCS5A01G497500 chr7D 82.934 334 54 3 236 568 518273955 518273624 5.050000e-77 298.0
40 TraesCS5A01G497500 chr5B 80.220 364 68 4 231 593 55612473 55612113 1.100000e-68 270.0
41 TraesCS5A01G497500 chr5B 88.095 210 25 0 1 210 662343108 662342899 1.440000e-62 250.0
42 TraesCS5A01G497500 chr5B 86.667 210 28 0 1 210 55612742 55612533 1.450000e-57 233.0
43 TraesCS5A01G497500 chr5B 100.000 30 0 0 1962 1991 121201254 121201283 3.360000e-04 56.5
44 TraesCS5A01G497500 chr5B 96.970 33 1 0 1959 1991 704452597 704452629 3.360000e-04 56.5
45 TraesCS5A01G497500 chr4A 88.571 210 24 0 1 210 591692716 591692507 3.080000e-64 255.0
46 TraesCS5A01G497500 chr1D 88.571 210 24 0 1 210 452129255 452129464 3.080000e-64 255.0
47 TraesCS5A01G497500 chr1D 81.443 291 51 3 304 593 336512127 336512415 4.020000e-58 235.0
48 TraesCS5A01G497500 chr1D 82.051 195 34 1 231 425 452129524 452129717 5.350000e-37 165.0
49 TraesCS5A01G497500 chr5D 86.935 199 26 0 12 210 425895274 425895076 8.700000e-55 224.0
50 TraesCS5A01G497500 chr5D 95.714 70 2 1 2232 2300 301581344 301581413 7.070000e-21 111.0
51 TraesCS5A01G497500 chr2A 98.438 64 1 0 2232 2295 71560775 71560838 1.960000e-21 113.0
52 TraesCS5A01G497500 chr2D 96.923 65 2 0 2232 2296 178776480 178776544 2.540000e-20 110.0
53 TraesCS5A01G497500 chr2D 96.970 33 1 0 1959 1991 23143408 23143440 3.360000e-04 56.5
54 TraesCS5A01G497500 chr6B 94.286 70 4 0 2232 2301 503547593 503547524 9.140000e-20 108.0
55 TraesCS5A01G497500 chr3D 100.000 31 0 0 1961 1991 131227865 131227835 9.340000e-05 58.4


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 TraesCS5A01G497500 chr5A 664553826 664556243 2417 True 4466.0 4466 100.000000 1 2418 1 chr5A.!!$R1 2417
1 TraesCS5A01G497500 chr4B 615833921 615836439 2518 True 1035.0 2564 94.113333 1 2418 3 chr4B.!!$R1 2417
2 TraesCS5A01G497500 chr4D 484293346 484295290 1944 True 1343.0 2318 93.885000 1 1969 2 chr4D.!!$R1 1968
3 TraesCS5A01G497500 chr7A 244709083 244709712 629 True 270.0 279 85.000000 1 593 2 chr7A.!!$R1 592
4 TraesCS5A01G497500 chr6D 424710045 424710674 629 False 279.5 292 85.421500 1 593 2 chr6D.!!$F4 592
5 TraesCS5A01G497500 chr6D 38227767 38228367 600 False 263.0 307 84.369500 5 568 2 chr6D.!!$F3 563
6 TraesCS5A01G497500 chr6D 455747871 455748501 630 False 254.5 270 83.792500 1 593 2 chr6D.!!$F5 592
7 TraesCS5A01G497500 chr5B 55612113 55612742 629 True 251.5 270 83.443500 1 593 2 chr5B.!!$R2 592

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
72 73 0.874390 TCTCGGCAAGTTCAACATGC 59.126 50.0 9.31 9.31 41.60 4.06 F
1272 1690 0.899019 AAAGAGAAGGTCGGAGAGGC 59.101 55.0 0.00 0.00 36.95 4.70 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1327 1745 0.036858 GCTTCTTCGCCTTCAGGTCT 60.037 55.0 0.0 0.0 37.57 3.85 R
2073 2523 0.102300 ATAATTTTTGCTCCCGCCGC 59.898 50.0 0.0 0.0 34.43 6.53 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
72 73 0.874390 TCTCGGCAAGTTCAACATGC 59.126 50.000 9.31 9.31 41.60 4.06
132 133 5.845103 TCAAGAAAAGCAATGCATCTCAAA 58.155 33.333 8.35 0.00 0.00 2.69
139 140 7.681939 AAAGCAATGCATCTCAAAAATTGAT 57.318 28.000 8.35 0.00 39.30 2.57
211 213 6.541969 TGCACAACACTGAATATTTCATACG 58.458 36.000 0.00 0.00 39.30 3.06
227 601 5.208624 TCATACGTGTAGTAGTGAACGAC 57.791 43.478 12.23 0.00 38.94 4.34
228 602 2.977405 ACGTGTAGTAGTGAACGACC 57.023 50.000 12.23 0.00 39.27 4.79
229 603 2.498167 ACGTGTAGTAGTGAACGACCT 58.502 47.619 12.23 0.00 39.27 3.85
270 683 4.375272 TGTTTGGCAATGTAATGTTGTGG 58.625 39.130 0.00 0.00 0.00 4.17
316 731 4.044065 TCTTTCATGGGGTGATACCAACTT 59.956 41.667 0.00 0.00 41.02 2.66
351 766 2.798976 TGAAGTTTCTGCAATGTGGC 57.201 45.000 0.00 0.00 0.00 5.01
690 1108 5.245301 TGTCGAGACTTTTCCTCTTATCCAA 59.755 40.000 4.78 0.00 0.00 3.53
775 1193 7.090173 CCAACACAACTATAAAACTGGATTGG 58.910 38.462 0.00 0.00 0.00 3.16
850 1268 9.144747 CACTTATATAGGGATCAATCTGAAACG 57.855 37.037 0.00 0.00 0.00 3.60
919 1337 1.613437 GGCAAGTTAGCTTCCTTTGCA 59.387 47.619 19.58 0.00 31.49 4.08
984 1402 1.016627 GCTAATCTTGTGGCATCGCA 58.983 50.000 0.00 0.00 0.00 5.10
1055 1473 4.893829 AGGAGAAGAAGGACAAGGTAAC 57.106 45.455 0.00 0.00 0.00 2.50
1162 1580 9.297586 GTCTGATGAACACATACGTTCTTATTA 57.702 33.333 0.00 0.00 44.59 0.98
1163 1581 9.297586 TCTGATGAACACATACGTTCTTATTAC 57.702 33.333 0.00 0.00 44.59 1.89
1177 1595 6.464311 GTTCTTATTACTTAAGGAACACGCG 58.536 40.000 3.53 3.53 38.29 6.01
1249 1667 1.077858 GAGCAAGGAGGGCAAGGAG 60.078 63.158 0.00 0.00 0.00 3.69
1272 1690 0.899019 AAAGAGAAGGTCGGAGAGGC 59.101 55.000 0.00 0.00 36.95 4.70
1436 1854 2.487762 TGAGATTTCGATGGGTTGTTGC 59.512 45.455 0.00 0.00 0.00 4.17
1460 1879 6.510536 CCTTGAGAAGAATGAAACAGCTTTT 58.489 36.000 0.00 0.00 0.00 2.27
1513 1932 2.102925 CCACAAGTTGGTGCAGGAATTT 59.897 45.455 7.96 0.00 41.10 1.82
1520 1939 5.744171 AGTTGGTGCAGGAATTTTTCTTTT 58.256 33.333 0.00 0.00 0.00 2.27
1634 2057 4.881273 TCCATCTTGTATCAAATTCGTGGG 59.119 41.667 0.00 0.00 0.00 4.61
1643 2066 3.546724 TCAAATTCGTGGGAAACTGTGA 58.453 40.909 0.00 0.00 35.40 3.58
1680 2103 9.025041 CCTCTTAAAGATTTTTGGTATTGGACT 57.975 33.333 0.00 0.00 0.00 3.85
1697 2120 6.391227 TTGGACTTGACCTTTCTTGAAATC 57.609 37.500 0.00 0.00 0.00 2.17
1760 2183 1.149174 AGGGTGTGAACCTGTGCTG 59.851 57.895 0.00 0.00 36.85 4.41
1832 2282 9.075519 CAATGAACGCACACAAAATCTAAATAT 57.924 29.630 0.00 0.00 0.00 1.28
1873 2323 5.075493 AGTAGTAAGAACGAGAAACTGGGA 58.925 41.667 0.00 0.00 0.00 4.37
1900 2350 8.391075 CCTATTCGGCTAAATTTCAATAGGAA 57.609 34.615 17.75 8.35 42.81 3.36
1935 2385 6.290605 ACAATCTCCAAAATTCCAAGGTTTG 58.709 36.000 0.00 0.00 33.06 2.93
1943 2393 6.479990 CCAAAATTCCAAGGTTTGAAAGAGTC 59.520 38.462 3.12 0.00 34.80 3.36
1974 2424 6.622427 AAAACTAGTAGCAACATACTCCCT 57.378 37.500 0.00 0.00 37.24 4.20
1975 2425 5.855740 AACTAGTAGCAACATACTCCCTC 57.144 43.478 0.00 0.00 37.24 4.30
1976 2426 4.216708 ACTAGTAGCAACATACTCCCTCC 58.783 47.826 0.00 0.00 37.24 4.30
1977 2427 2.032620 AGTAGCAACATACTCCCTCCG 58.967 52.381 0.00 0.00 29.89 4.63
1978 2428 1.755380 GTAGCAACATACTCCCTCCGT 59.245 52.381 0.00 0.00 0.00 4.69
1979 2429 0.824759 AGCAACATACTCCCTCCGTC 59.175 55.000 0.00 0.00 0.00 4.79
1980 2430 0.179081 GCAACATACTCCCTCCGTCC 60.179 60.000 0.00 0.00 0.00 4.79
1981 2431 0.464452 CAACATACTCCCTCCGTCCC 59.536 60.000 0.00 0.00 0.00 4.46
1982 2432 0.042131 AACATACTCCCTCCGTCCCA 59.958 55.000 0.00 0.00 0.00 4.37
1983 2433 0.264955 ACATACTCCCTCCGTCCCAT 59.735 55.000 0.00 0.00 0.00 4.00
1984 2434 1.502039 ACATACTCCCTCCGTCCCATA 59.498 52.381 0.00 0.00 0.00 2.74
1985 2435 2.090943 ACATACTCCCTCCGTCCCATAA 60.091 50.000 0.00 0.00 0.00 1.90
1986 2436 3.173965 CATACTCCCTCCGTCCCATAAT 58.826 50.000 0.00 0.00 0.00 1.28
1987 2437 4.202749 ACATACTCCCTCCGTCCCATAATA 60.203 45.833 0.00 0.00 0.00 0.98
1988 2438 3.562108 ACTCCCTCCGTCCCATAATAT 57.438 47.619 0.00 0.00 0.00 1.28
1989 2439 4.687262 ACTCCCTCCGTCCCATAATATA 57.313 45.455 0.00 0.00 0.00 0.86
1990 2440 5.019657 ACTCCCTCCGTCCCATAATATAA 57.980 43.478 0.00 0.00 0.00 0.98
1991 2441 5.600749 ACTCCCTCCGTCCCATAATATAAT 58.399 41.667 0.00 0.00 0.00 1.28
1992 2442 6.748969 ACTCCCTCCGTCCCATAATATAATA 58.251 40.000 0.00 0.00 0.00 0.98
1993 2443 6.610425 ACTCCCTCCGTCCCATAATATAATAC 59.390 42.308 0.00 0.00 0.00 1.89
1994 2444 6.748969 TCCCTCCGTCCCATAATATAATACT 58.251 40.000 0.00 0.00 0.00 2.12
1995 2445 7.194050 TCCCTCCGTCCCATAATATAATACTT 58.806 38.462 0.00 0.00 0.00 2.24
1996 2446 7.343833 TCCCTCCGTCCCATAATATAATACTTC 59.656 40.741 0.00 0.00 0.00 3.01
1997 2447 7.418712 CCCTCCGTCCCATAATATAATACTTCC 60.419 44.444 0.00 0.00 0.00 3.46
1998 2448 7.344871 CCTCCGTCCCATAATATAATACTTCCT 59.655 40.741 0.00 0.00 0.00 3.36
1999 2449 8.302515 TCCGTCCCATAATATAATACTTCCTC 57.697 38.462 0.00 0.00 0.00 3.71
2000 2450 7.343833 TCCGTCCCATAATATAATACTTCCTCC 59.656 40.741 0.00 0.00 0.00 4.30
2001 2451 7.125204 CCGTCCCATAATATAATACTTCCTCCA 59.875 40.741 0.00 0.00 0.00 3.86
2002 2452 8.705594 CGTCCCATAATATAATACTTCCTCCAT 58.294 37.037 0.00 0.00 0.00 3.41
2005 2455 9.853177 CCCATAATATAATACTTCCTCCATTCC 57.147 37.037 0.00 0.00 0.00 3.01
2011 2461 9.745018 ATATAATACTTCCTCCATTCCACAATG 57.255 33.333 0.00 0.00 39.45 2.82
2012 2462 3.814504 ACTTCCTCCATTCCACAATGT 57.185 42.857 0.00 0.00 38.22 2.71
2013 2463 4.927267 ACTTCCTCCATTCCACAATGTA 57.073 40.909 0.00 0.00 38.22 2.29
2014 2464 4.848357 ACTTCCTCCATTCCACAATGTAG 58.152 43.478 0.00 0.00 38.22 2.74
2015 2465 4.289672 ACTTCCTCCATTCCACAATGTAGT 59.710 41.667 0.00 0.00 38.22 2.73
2016 2466 4.220693 TCCTCCATTCCACAATGTAGTG 57.779 45.455 0.00 0.00 38.22 2.74
2017 2467 2.684881 CCTCCATTCCACAATGTAGTGC 59.315 50.000 0.00 0.00 38.22 4.40
2018 2468 3.614092 CTCCATTCCACAATGTAGTGCT 58.386 45.455 0.00 0.00 38.22 4.40
2019 2469 4.012374 CTCCATTCCACAATGTAGTGCTT 58.988 43.478 0.00 0.00 38.22 3.91
2020 2470 4.009675 TCCATTCCACAATGTAGTGCTTC 58.990 43.478 0.00 0.00 38.22 3.86
2021 2471 3.129287 CCATTCCACAATGTAGTGCTTCC 59.871 47.826 0.00 0.00 38.22 3.46
2022 2472 3.788227 TTCCACAATGTAGTGCTTCCT 57.212 42.857 0.00 0.00 38.18 3.36
2023 2473 3.334583 TCCACAATGTAGTGCTTCCTC 57.665 47.619 0.00 0.00 38.18 3.71
2024 2474 2.906389 TCCACAATGTAGTGCTTCCTCT 59.094 45.455 0.00 0.00 38.18 3.69
2025 2475 4.093743 TCCACAATGTAGTGCTTCCTCTA 58.906 43.478 0.00 0.00 38.18 2.43
2026 2476 4.716784 TCCACAATGTAGTGCTTCCTCTAT 59.283 41.667 0.00 0.00 38.18 1.98
2027 2477 5.189736 TCCACAATGTAGTGCTTCCTCTATT 59.810 40.000 0.00 0.00 38.18 1.73
2028 2478 5.525378 CCACAATGTAGTGCTTCCTCTATTC 59.475 44.000 0.00 0.00 38.18 1.75
2029 2479 5.525378 CACAATGTAGTGCTTCCTCTATTCC 59.475 44.000 0.00 0.00 32.04 3.01
2030 2480 4.965200 ATGTAGTGCTTCCTCTATTCCC 57.035 45.455 0.00 0.00 0.00 3.97
2031 2481 2.693591 TGTAGTGCTTCCTCTATTCCCG 59.306 50.000 0.00 0.00 0.00 5.14
2032 2482 1.867363 AGTGCTTCCTCTATTCCCGT 58.133 50.000 0.00 0.00 0.00 5.28
2033 2483 1.482593 AGTGCTTCCTCTATTCCCGTG 59.517 52.381 0.00 0.00 0.00 4.94
2034 2484 0.178068 TGCTTCCTCTATTCCCGTGC 59.822 55.000 0.00 0.00 0.00 5.34
2035 2485 0.466124 GCTTCCTCTATTCCCGTGCT 59.534 55.000 0.00 0.00 0.00 4.40
2036 2486 1.134371 GCTTCCTCTATTCCCGTGCTT 60.134 52.381 0.00 0.00 0.00 3.91
2037 2487 2.827652 CTTCCTCTATTCCCGTGCTTC 58.172 52.381 0.00 0.00 0.00 3.86
2038 2488 1.860641 TCCTCTATTCCCGTGCTTCA 58.139 50.000 0.00 0.00 0.00 3.02
2039 2489 2.184533 TCCTCTATTCCCGTGCTTCAA 58.815 47.619 0.00 0.00 0.00 2.69
2040 2490 2.093658 TCCTCTATTCCCGTGCTTCAAC 60.094 50.000 0.00 0.00 0.00 3.18
2041 2491 2.093447 CCTCTATTCCCGTGCTTCAACT 60.093 50.000 0.00 0.00 0.00 3.16
2042 2492 3.600388 CTCTATTCCCGTGCTTCAACTT 58.400 45.455 0.00 0.00 0.00 2.66
2043 2493 4.003648 CTCTATTCCCGTGCTTCAACTTT 58.996 43.478 0.00 0.00 0.00 2.66
2044 2494 3.751175 TCTATTCCCGTGCTTCAACTTTG 59.249 43.478 0.00 0.00 0.00 2.77
2045 2495 2.045561 TTCCCGTGCTTCAACTTTGA 57.954 45.000 0.00 0.00 34.92 2.69
2046 2496 1.305201 TCCCGTGCTTCAACTTTGAC 58.695 50.000 0.00 0.00 36.83 3.18
2047 2497 0.310854 CCCGTGCTTCAACTTTGACC 59.689 55.000 0.00 0.00 36.83 4.02
2048 2498 0.041312 CCGTGCTTCAACTTTGACCG 60.041 55.000 0.00 0.00 36.83 4.79
2049 2499 0.655733 CGTGCTTCAACTTTGACCGT 59.344 50.000 0.00 0.00 36.83 4.83
2050 2500 1.862201 CGTGCTTCAACTTTGACCGTA 59.138 47.619 0.00 0.00 36.83 4.02
2051 2501 2.285756 CGTGCTTCAACTTTGACCGTAA 59.714 45.455 0.00 0.00 36.83 3.18
2052 2502 3.242478 CGTGCTTCAACTTTGACCGTAAA 60.242 43.478 0.00 0.00 36.83 2.01
2053 2503 4.553938 CGTGCTTCAACTTTGACCGTAAAT 60.554 41.667 0.00 0.00 36.83 1.40
2054 2504 5.278604 GTGCTTCAACTTTGACCGTAAATT 58.721 37.500 0.00 0.00 36.83 1.82
2055 2505 5.746721 GTGCTTCAACTTTGACCGTAAATTT 59.253 36.000 0.00 0.00 36.83 1.82
2056 2506 6.913673 GTGCTTCAACTTTGACCGTAAATTTA 59.086 34.615 0.00 0.00 36.83 1.40
2057 2507 7.432838 GTGCTTCAACTTTGACCGTAAATTTAA 59.567 33.333 0.00 0.00 36.83 1.52
2058 2508 7.432838 TGCTTCAACTTTGACCGTAAATTTAAC 59.567 33.333 0.00 0.00 36.83 2.01
2059 2509 7.646526 GCTTCAACTTTGACCGTAAATTTAACT 59.353 33.333 0.00 0.00 36.83 2.24
2068 2518 9.896263 TTGACCGTAAATTTAACTATCAAAACC 57.104 29.630 0.00 0.00 0.00 3.27
2069 2519 8.229137 TGACCGTAAATTTAACTATCAAAACCG 58.771 33.333 0.00 0.00 0.00 4.44
2070 2520 8.321650 ACCGTAAATTTAACTATCAAAACCGA 57.678 30.769 0.00 0.00 0.00 4.69
2071 2521 8.949177 ACCGTAAATTTAACTATCAAAACCGAT 58.051 29.630 0.00 0.00 0.00 4.18
2072 2522 9.777575 CCGTAAATTTAACTATCAAAACCGATT 57.222 29.630 0.00 0.00 0.00 3.34
2075 2525 7.734538 AATTTAACTATCAAAACCGATTGCG 57.265 32.000 0.00 0.00 37.24 4.85
2100 2550 6.618287 CGGGAGCAAAAATTATATCAGTGA 57.382 37.500 0.00 0.00 0.00 3.41
2101 2551 7.026631 CGGGAGCAAAAATTATATCAGTGAA 57.973 36.000 0.00 0.00 0.00 3.18
2102 2552 7.651808 CGGGAGCAAAAATTATATCAGTGAAT 58.348 34.615 0.00 0.00 0.00 2.57
2103 2553 8.137437 CGGGAGCAAAAATTATATCAGTGAATT 58.863 33.333 0.00 0.00 0.00 2.17
2104 2554 9.468532 GGGAGCAAAAATTATATCAGTGAATTC 57.531 33.333 0.00 0.00 0.00 2.17
2105 2555 9.173939 GGAGCAAAAATTATATCAGTGAATTCG 57.826 33.333 0.00 0.00 0.00 3.34
2106 2556 9.722056 GAGCAAAAATTATATCAGTGAATTCGT 57.278 29.630 0.00 0.00 0.00 3.85
2152 2602 4.783667 TTTTTCTACCGCCGCAGT 57.216 50.000 0.00 0.00 0.00 4.40
2153 2603 3.009612 TTTTTCTACCGCCGCAGTT 57.990 47.368 0.00 0.00 0.00 3.16
2154 2604 0.589223 TTTTTCTACCGCCGCAGTTG 59.411 50.000 0.00 0.00 0.00 3.16
2155 2605 1.231958 TTTTCTACCGCCGCAGTTGG 61.232 55.000 0.00 0.00 0.00 3.77
2156 2606 2.386064 TTTCTACCGCCGCAGTTGGT 62.386 55.000 0.00 0.00 39.80 3.67
2157 2607 2.775032 TTCTACCGCCGCAGTTGGTC 62.775 60.000 0.00 0.00 37.20 4.02
2158 2608 3.296709 CTACCGCCGCAGTTGGTCT 62.297 63.158 0.00 0.00 37.20 3.85
2159 2609 3.291101 TACCGCCGCAGTTGGTCTC 62.291 63.158 0.00 0.00 37.20 3.36
2160 2610 4.680237 CCGCCGCAGTTGGTCTCA 62.680 66.667 0.00 0.00 0.00 3.27
2161 2611 2.434884 CGCCGCAGTTGGTCTCAT 60.435 61.111 0.00 0.00 0.00 2.90
2162 2612 2.034879 CGCCGCAGTTGGTCTCATT 61.035 57.895 0.00 0.00 0.00 2.57
2163 2613 1.503542 GCCGCAGTTGGTCTCATTG 59.496 57.895 0.00 0.00 0.00 2.82
2164 2614 0.955428 GCCGCAGTTGGTCTCATTGA 60.955 55.000 0.00 0.00 0.00 2.57
2165 2615 1.742761 CCGCAGTTGGTCTCATTGAT 58.257 50.000 0.00 0.00 0.00 2.57
2166 2616 2.086869 CCGCAGTTGGTCTCATTGATT 58.913 47.619 0.00 0.00 0.00 2.57
2167 2617 3.270027 CCGCAGTTGGTCTCATTGATTA 58.730 45.455 0.00 0.00 0.00 1.75
2168 2618 3.689161 CCGCAGTTGGTCTCATTGATTAA 59.311 43.478 0.00 0.00 0.00 1.40
2169 2619 4.155826 CCGCAGTTGGTCTCATTGATTAAA 59.844 41.667 0.00 0.00 0.00 1.52
2170 2620 5.163622 CCGCAGTTGGTCTCATTGATTAAAT 60.164 40.000 0.00 0.00 0.00 1.40
2171 2621 6.324819 CGCAGTTGGTCTCATTGATTAAATT 58.675 36.000 0.00 0.00 0.00 1.82
2172 2622 6.808212 CGCAGTTGGTCTCATTGATTAAATTT 59.192 34.615 0.00 0.00 0.00 1.82
2173 2623 7.967854 CGCAGTTGGTCTCATTGATTAAATTTA 59.032 33.333 0.00 0.00 0.00 1.40
2174 2624 9.807649 GCAGTTGGTCTCATTGATTAAATTTAT 57.192 29.630 0.00 0.00 0.00 1.40
2193 2643 6.658188 TTTATGGTTAAAGTTGGACCTTGG 57.342 37.500 8.80 0.00 34.52 3.61
2194 2644 2.952116 TGGTTAAAGTTGGACCTTGGG 58.048 47.619 8.80 0.00 34.52 4.12
2195 2645 2.514582 TGGTTAAAGTTGGACCTTGGGA 59.485 45.455 8.80 0.00 34.52 4.37
2196 2646 3.052793 TGGTTAAAGTTGGACCTTGGGAA 60.053 43.478 8.80 0.00 34.52 3.97
2197 2647 3.572682 GGTTAAAGTTGGACCTTGGGAAG 59.427 47.826 0.00 0.00 0.00 3.46
2198 2648 1.704641 AAAGTTGGACCTTGGGAAGC 58.295 50.000 0.00 0.00 0.00 3.86
2199 2649 0.537371 AAGTTGGACCTTGGGAAGCG 60.537 55.000 0.00 0.00 0.00 4.68
2200 2650 2.282180 TTGGACCTTGGGAAGCGC 60.282 61.111 0.00 0.00 0.00 5.92
2201 2651 4.697756 TGGACCTTGGGAAGCGCG 62.698 66.667 0.00 0.00 0.00 6.86
2215 2665 3.637714 CGCGGGCGCACTATATTT 58.362 55.556 8.62 0.00 42.06 1.40
2216 2666 1.938861 CGCGGGCGCACTATATTTT 59.061 52.632 8.62 0.00 42.06 1.82
2217 2667 0.384230 CGCGGGCGCACTATATTTTG 60.384 55.000 8.62 0.00 42.06 2.44
2218 2668 0.941542 GCGGGCGCACTATATTTTGA 59.058 50.000 8.62 0.00 41.49 2.69
2219 2669 1.332375 GCGGGCGCACTATATTTTGAA 59.668 47.619 8.62 0.00 41.49 2.69
2220 2670 2.223386 GCGGGCGCACTATATTTTGAAA 60.223 45.455 8.62 0.00 41.49 2.69
2221 2671 3.550030 GCGGGCGCACTATATTTTGAAAT 60.550 43.478 8.62 0.00 41.49 2.17
2222 2672 3.974401 CGGGCGCACTATATTTTGAAATG 59.026 43.478 8.62 0.00 0.00 2.32
2223 2673 4.298332 GGGCGCACTATATTTTGAAATGG 58.702 43.478 10.83 0.00 0.00 3.16
2224 2674 4.037446 GGGCGCACTATATTTTGAAATGGA 59.963 41.667 10.83 0.00 0.00 3.41
2225 2675 5.215160 GGCGCACTATATTTTGAAATGGAG 58.785 41.667 10.83 0.06 0.00 3.86
2226 2676 5.215160 GCGCACTATATTTTGAAATGGAGG 58.785 41.667 0.30 0.00 0.00 4.30
2227 2677 5.762045 CGCACTATATTTTGAAATGGAGGG 58.238 41.667 0.00 0.00 0.00 4.30
2228 2678 5.530915 CGCACTATATTTTGAAATGGAGGGA 59.469 40.000 0.00 0.00 0.00 4.20
2229 2679 6.293626 CGCACTATATTTTGAAATGGAGGGAG 60.294 42.308 0.00 0.00 0.00 4.30
2230 2680 6.547510 GCACTATATTTTGAAATGGAGGGAGT 59.452 38.462 0.00 0.00 0.00 3.85
2231 2681 7.719633 GCACTATATTTTGAAATGGAGGGAGTA 59.280 37.037 0.00 0.00 0.00 2.59
2232 2682 9.627123 CACTATATTTTGAAATGGAGGGAGTAA 57.373 33.333 0.00 0.00 0.00 2.24
2233 2683 9.628500 ACTATATTTTGAAATGGAGGGAGTAAC 57.372 33.333 0.00 0.00 0.00 2.50
2234 2684 5.897377 ATTTTGAAATGGAGGGAGTAACG 57.103 39.130 0.00 0.00 0.00 3.18
2235 2685 4.360951 TTTGAAATGGAGGGAGTAACGT 57.639 40.909 0.00 0.00 0.00 3.99
2236 2686 4.360951 TTGAAATGGAGGGAGTAACGTT 57.639 40.909 5.88 5.88 0.00 3.99
2237 2687 4.360951 TGAAATGGAGGGAGTAACGTTT 57.639 40.909 5.91 0.00 0.00 3.60
2238 2688 4.721132 TGAAATGGAGGGAGTAACGTTTT 58.279 39.130 5.91 0.00 0.00 2.43
2239 2689 5.134661 TGAAATGGAGGGAGTAACGTTTTT 58.865 37.500 5.91 0.00 0.00 1.94
2240 2690 5.009210 TGAAATGGAGGGAGTAACGTTTTTG 59.991 40.000 5.91 0.00 0.00 2.44
2241 2691 3.842007 TGGAGGGAGTAACGTTTTTGA 57.158 42.857 5.91 0.00 0.00 2.69
2242 2692 3.469739 TGGAGGGAGTAACGTTTTTGAC 58.530 45.455 5.91 0.00 0.00 3.18
2243 2693 3.118334 TGGAGGGAGTAACGTTTTTGACA 60.118 43.478 5.91 0.00 0.00 3.58
2244 2694 3.249320 GGAGGGAGTAACGTTTTTGACAC 59.751 47.826 5.91 0.00 0.00 3.67
2245 2695 4.124970 GAGGGAGTAACGTTTTTGACACT 58.875 43.478 5.91 1.78 0.00 3.55
2246 2696 5.280654 AGGGAGTAACGTTTTTGACACTA 57.719 39.130 5.91 0.00 0.00 2.74
2247 2697 5.295152 AGGGAGTAACGTTTTTGACACTAG 58.705 41.667 5.91 0.00 0.00 2.57
2248 2698 5.052481 GGGAGTAACGTTTTTGACACTAGT 58.948 41.667 5.91 0.00 0.00 2.57
2249 2699 5.050567 GGGAGTAACGTTTTTGACACTAGTG 60.051 44.000 21.44 21.44 0.00 2.74
2251 2701 6.697019 GGAGTAACGTTTTTGACACTAGTGTA 59.303 38.462 27.98 11.50 45.05 2.90
2252 2702 7.096312 GGAGTAACGTTTTTGACACTAGTGTAG 60.096 40.741 27.98 14.79 45.05 2.74
2253 2703 7.260603 AGTAACGTTTTTGACACTAGTGTAGT 58.739 34.615 27.98 15.35 45.05 2.73
2266 2716 6.579491 ACTAGTGTAGTGTGAAAAACGTTC 57.421 37.500 0.00 0.00 37.69 3.95
2267 2717 6.335777 ACTAGTGTAGTGTGAAAAACGTTCT 58.664 36.000 0.00 0.00 37.69 3.01
2268 2718 6.815142 ACTAGTGTAGTGTGAAAAACGTTCTT 59.185 34.615 0.00 0.00 37.69 2.52
2269 2719 7.975616 ACTAGTGTAGTGTGAAAAACGTTCTTA 59.024 33.333 0.00 0.00 37.69 2.10
2270 2720 7.781548 AGTGTAGTGTGAAAAACGTTCTTAT 57.218 32.000 0.00 0.00 0.00 1.73
2271 2721 8.876275 AGTGTAGTGTGAAAAACGTTCTTATA 57.124 30.769 0.00 0.00 0.00 0.98
2272 2722 9.485206 AGTGTAGTGTGAAAAACGTTCTTATAT 57.515 29.630 0.00 0.00 0.00 0.86
2277 2727 9.458374 AGTGTGAAAAACGTTCTTATATTTTGG 57.542 29.630 0.00 0.00 0.00 3.28
2278 2728 8.696175 GTGTGAAAAACGTTCTTATATTTTGGG 58.304 33.333 0.00 0.00 0.00 4.12
2279 2729 8.630917 TGTGAAAAACGTTCTTATATTTTGGGA 58.369 29.630 0.00 0.00 0.00 4.37
2280 2730 8.908678 GTGAAAAACGTTCTTATATTTTGGGAC 58.091 33.333 0.00 0.00 0.00 4.46
2281 2731 8.630917 TGAAAAACGTTCTTATATTTTGGGACA 58.369 29.630 0.00 0.00 0.00 4.02
2282 2732 9.124807 GAAAAACGTTCTTATATTTTGGGACAG 57.875 33.333 0.00 0.00 42.39 3.51
2283 2733 7.989416 AAACGTTCTTATATTTTGGGACAGA 57.011 32.000 0.00 0.00 42.39 3.41
2284 2734 7.611213 AACGTTCTTATATTTTGGGACAGAG 57.389 36.000 0.00 0.00 42.39 3.35
2285 2735 6.113411 ACGTTCTTATATTTTGGGACAGAGG 58.887 40.000 0.00 0.00 42.39 3.69
2286 2736 5.527582 CGTTCTTATATTTTGGGACAGAGGG 59.472 44.000 0.00 0.00 42.39 4.30
2287 2737 6.631766 CGTTCTTATATTTTGGGACAGAGGGA 60.632 42.308 0.00 0.00 42.39 4.20
2288 2738 6.500589 TCTTATATTTTGGGACAGAGGGAG 57.499 41.667 0.00 0.00 42.39 4.30
2289 2739 5.970640 TCTTATATTTTGGGACAGAGGGAGT 59.029 40.000 0.00 0.00 42.39 3.85
2290 2740 7.136885 TCTTATATTTTGGGACAGAGGGAGTA 58.863 38.462 0.00 0.00 42.39 2.59
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
6 7 6.727824 AACGAGATTTCTTGTGTCCATAAG 57.272 37.500 1.21 0.00 40.35 1.73
72 73 7.964559 TCATTTGCTAATTTTGATGAAGACGAG 59.035 33.333 0.00 0.00 0.00 4.18
132 133 7.487189 CGCTTTGCTGAAAGATCTAATCAATTT 59.513 33.333 11.15 0.00 41.12 1.82
139 140 5.689383 AAACGCTTTGCTGAAAGATCTAA 57.311 34.783 0.00 0.00 41.12 2.10
211 213 2.159599 CCGAGGTCGTTCACTACTACAC 60.160 54.545 0.00 0.00 37.74 2.90
218 220 1.203994 CAATACCCGAGGTCGTTCACT 59.796 52.381 0.00 0.00 37.09 3.41
223 597 1.106285 GGTACAATACCCGAGGTCGT 58.894 55.000 0.00 0.00 43.18 4.34
224 598 3.953201 GGTACAATACCCGAGGTCG 57.047 57.895 0.00 0.00 43.18 4.79
316 731 9.467258 CAGAAACTTCAAGATGCAAGATAAAAA 57.533 29.630 0.00 0.00 0.00 1.94
351 766 0.982704 TGCAATGGGTTTGATTGGGG 59.017 50.000 0.00 0.00 37.53 4.96
463 879 8.413309 TGATTCCTCTGATCAAAAGTTTTGAT 57.587 30.769 33.62 33.62 41.43 2.57
611 1029 5.106869 CCAACTAAAAATAGTACTGCACGCA 60.107 40.000 5.39 0.00 0.00 5.24
742 1160 2.051334 TAGTTGTGTTGGTTGCAGCT 57.949 45.000 0.00 0.00 0.00 4.24
775 1193 6.579666 ACCGTAAATTAAATGTTTGCTTCGAC 59.420 34.615 0.00 0.00 0.00 4.20
850 1268 7.174946 TGGTGAAAACAGAGATAAATTCTGGTC 59.825 37.037 7.13 2.74 41.59 4.02
984 1402 1.914764 CATTTTGGGGCAGCAGGGT 60.915 57.895 0.00 0.00 0.00 4.34
1055 1473 4.730949 ATTTGATGCAAGTTCCAGATGG 57.269 40.909 0.00 0.00 0.00 3.51
1162 1580 3.057734 CTCTTTCGCGTGTTCCTTAAGT 58.942 45.455 5.77 0.00 0.00 2.24
1163 1581 2.412089 CCTCTTTCGCGTGTTCCTTAAG 59.588 50.000 5.77 0.00 0.00 1.85
1195 1613 5.766590 TCCTTCTTGTCCTTCTTTTCCTTT 58.233 37.500 0.00 0.00 0.00 3.11
1249 1667 3.119280 CCTCTCCGACCTTCTCTTTCTTC 60.119 52.174 0.00 0.00 0.00 2.87
1272 1690 0.583438 CAGCTTGACCGTGTCAGTTG 59.417 55.000 6.79 6.46 43.69 3.16
1284 1702 0.692476 TAGCTTTGCCCTCAGCTTGA 59.308 50.000 0.00 0.00 44.28 3.02
1327 1745 0.036858 GCTTCTTCGCCTTCAGGTCT 60.037 55.000 0.00 0.00 37.57 3.85
1375 1793 1.524482 CTCTGCTGCCTTACCCTCC 59.476 63.158 0.00 0.00 0.00 4.30
1408 1826 1.293924 CATCGAAATCTCAGCCGCTT 58.706 50.000 0.00 0.00 0.00 4.68
1419 1837 1.923356 AGGCAACAACCCATCGAAAT 58.077 45.000 0.00 0.00 41.41 2.17
1436 1854 5.702349 AAGCTGTTTCATTCTTCTCAAGG 57.298 39.130 0.00 0.00 0.00 3.61
1513 1932 7.545265 GCACAATAATATGCCAGTCAAAAGAAA 59.455 33.333 0.00 0.00 35.73 2.52
1520 1939 7.637631 TTAAAGCACAATAATATGCCAGTCA 57.362 32.000 0.00 0.00 43.12 3.41
1585 2006 5.536161 ACTTGTGTGCACCAAAATCTAGATT 59.464 36.000 15.69 12.37 0.00 2.40
1615 2038 6.001460 AGTTTCCCACGAATTTGATACAAGA 58.999 36.000 0.00 0.00 0.00 3.02
1628 2051 1.414550 TCATGTCACAGTTTCCCACGA 59.585 47.619 0.00 0.00 0.00 4.35
1634 2057 5.934625 AGAGGTACATTCATGTCACAGTTTC 59.065 40.000 0.00 0.00 41.97 2.78
1680 2103 5.694995 ACTCCAGATTTCAAGAAAGGTCAA 58.305 37.500 1.48 0.00 33.32 3.18
1681 2104 5.310409 ACTCCAGATTTCAAGAAAGGTCA 57.690 39.130 1.48 0.00 33.32 4.02
1760 2183 1.906990 ATGCTCTATGCTGAATGGCC 58.093 50.000 0.00 0.00 43.37 5.36
1784 2207 1.229975 TTGTCATGTGAGCCGCAGTG 61.230 55.000 0.00 0.00 0.00 3.66
1785 2208 0.321919 ATTGTCATGTGAGCCGCAGT 60.322 50.000 0.00 0.00 0.00 4.40
1894 2344 6.407979 GGAGATTGTTCTGAAGCTCTTCCTAT 60.408 42.308 7.12 0.00 38.25 2.57
1896 2346 4.323409 GGAGATTGTTCTGAAGCTCTTCCT 60.323 45.833 7.12 0.00 38.25 3.36
1900 2350 4.630644 TTGGAGATTGTTCTGAAGCTCT 57.369 40.909 0.00 0.00 38.25 4.09
1969 2419 6.839657 AGTATTATATTATGGGACGGAGGGAG 59.160 42.308 0.00 0.00 0.00 4.30
1970 2420 6.748969 AGTATTATATTATGGGACGGAGGGA 58.251 40.000 0.00 0.00 0.00 4.20
1971 2421 7.418712 GGAAGTATTATATTATGGGACGGAGGG 60.419 44.444 0.00 0.00 0.00 4.30
1972 2422 7.344871 AGGAAGTATTATATTATGGGACGGAGG 59.655 40.741 0.00 0.00 0.00 4.30
1973 2423 8.307582 AGGAAGTATTATATTATGGGACGGAG 57.692 38.462 0.00 0.00 0.00 4.63
1974 2424 7.343833 GGAGGAAGTATTATATTATGGGACGGA 59.656 40.741 0.00 0.00 0.00 4.69
1975 2425 7.125204 TGGAGGAAGTATTATATTATGGGACGG 59.875 40.741 0.00 0.00 0.00 4.79
1976 2426 8.074613 TGGAGGAAGTATTATATTATGGGACG 57.925 38.462 0.00 0.00 0.00 4.79
1979 2429 9.853177 GGAATGGAGGAAGTATTATATTATGGG 57.147 37.037 0.00 0.00 0.00 4.00
1985 2435 9.745018 CATTGTGGAATGGAGGAAGTATTATAT 57.255 33.333 0.00 0.00 36.12 0.86
1986 2436 8.723365 ACATTGTGGAATGGAGGAAGTATTATA 58.277 33.333 0.00 0.00 43.00 0.98
1987 2437 7.586349 ACATTGTGGAATGGAGGAAGTATTAT 58.414 34.615 0.00 0.00 43.00 1.28
1988 2438 6.969043 ACATTGTGGAATGGAGGAAGTATTA 58.031 36.000 0.00 0.00 43.00 0.98
1989 2439 5.831103 ACATTGTGGAATGGAGGAAGTATT 58.169 37.500 0.00 0.00 43.00 1.89
1990 2440 5.456921 ACATTGTGGAATGGAGGAAGTAT 57.543 39.130 0.00 0.00 43.00 2.12
1991 2441 4.927267 ACATTGTGGAATGGAGGAAGTA 57.073 40.909 0.00 0.00 43.00 2.24
1992 2442 3.814504 ACATTGTGGAATGGAGGAAGT 57.185 42.857 0.00 0.00 43.00 3.01
1998 2448 3.719268 AGCACTACATTGTGGAATGGA 57.281 42.857 7.20 0.00 43.00 3.41
1999 2449 3.129287 GGAAGCACTACATTGTGGAATGG 59.871 47.826 7.20 0.00 43.00 3.16
2000 2450 4.012374 AGGAAGCACTACATTGTGGAATG 58.988 43.478 7.20 0.00 44.11 2.67
2001 2451 4.018960 AGAGGAAGCACTACATTGTGGAAT 60.019 41.667 7.20 0.00 38.31 3.01
2002 2452 3.327757 AGAGGAAGCACTACATTGTGGAA 59.672 43.478 7.20 0.00 38.31 3.53
2003 2453 2.906389 AGAGGAAGCACTACATTGTGGA 59.094 45.455 7.20 0.00 38.31 4.02
2004 2454 3.340814 AGAGGAAGCACTACATTGTGG 57.659 47.619 0.00 0.00 38.31 4.17
2005 2455 5.525378 GGAATAGAGGAAGCACTACATTGTG 59.475 44.000 0.00 0.00 40.62 3.33
2006 2456 5.396884 GGGAATAGAGGAAGCACTACATTGT 60.397 44.000 0.00 0.00 0.00 2.71
2007 2457 5.059833 GGGAATAGAGGAAGCACTACATTG 58.940 45.833 0.00 0.00 0.00 2.82
2008 2458 4.202264 CGGGAATAGAGGAAGCACTACATT 60.202 45.833 0.00 0.00 0.00 2.71
2009 2459 3.322254 CGGGAATAGAGGAAGCACTACAT 59.678 47.826 0.00 0.00 0.00 2.29
2010 2460 2.693591 CGGGAATAGAGGAAGCACTACA 59.306 50.000 0.00 0.00 0.00 2.74
2011 2461 2.694109 ACGGGAATAGAGGAAGCACTAC 59.306 50.000 0.00 0.00 0.00 2.73
2012 2462 2.693591 CACGGGAATAGAGGAAGCACTA 59.306 50.000 0.00 0.00 0.00 2.74
2013 2463 1.482593 CACGGGAATAGAGGAAGCACT 59.517 52.381 0.00 0.00 0.00 4.40
2014 2464 1.941325 CACGGGAATAGAGGAAGCAC 58.059 55.000 0.00 0.00 0.00 4.40
2015 2465 0.178068 GCACGGGAATAGAGGAAGCA 59.822 55.000 0.00 0.00 0.00 3.91
2016 2466 0.466124 AGCACGGGAATAGAGGAAGC 59.534 55.000 0.00 0.00 0.00 3.86
2017 2467 2.168521 TGAAGCACGGGAATAGAGGAAG 59.831 50.000 0.00 0.00 0.00 3.46
2018 2468 2.184533 TGAAGCACGGGAATAGAGGAA 58.815 47.619 0.00 0.00 0.00 3.36
2019 2469 1.860641 TGAAGCACGGGAATAGAGGA 58.139 50.000 0.00 0.00 0.00 3.71
2020 2470 2.093447 AGTTGAAGCACGGGAATAGAGG 60.093 50.000 0.00 0.00 0.00 3.69
2021 2471 3.252974 AGTTGAAGCACGGGAATAGAG 57.747 47.619 0.00 0.00 0.00 2.43
2022 2472 3.695830 AAGTTGAAGCACGGGAATAGA 57.304 42.857 0.00 0.00 0.00 1.98
2023 2473 3.751175 TCAAAGTTGAAGCACGGGAATAG 59.249 43.478 0.00 0.00 33.55 1.73
2024 2474 3.500680 GTCAAAGTTGAAGCACGGGAATA 59.499 43.478 0.00 0.00 39.21 1.75
2025 2475 2.293399 GTCAAAGTTGAAGCACGGGAAT 59.707 45.455 0.00 0.00 39.21 3.01
2026 2476 1.673920 GTCAAAGTTGAAGCACGGGAA 59.326 47.619 0.00 0.00 39.21 3.97
2027 2477 1.305201 GTCAAAGTTGAAGCACGGGA 58.695 50.000 0.00 0.00 39.21 5.14
2028 2478 0.310854 GGTCAAAGTTGAAGCACGGG 59.689 55.000 0.00 0.00 39.21 5.28
2029 2479 0.041312 CGGTCAAAGTTGAAGCACGG 60.041 55.000 0.00 0.00 39.21 4.94
2030 2480 0.655733 ACGGTCAAAGTTGAAGCACG 59.344 50.000 0.00 2.00 39.21 5.34
2031 2481 3.955771 TTACGGTCAAAGTTGAAGCAC 57.044 42.857 0.00 0.00 39.21 4.40
2032 2482 5.508200 AATTTACGGTCAAAGTTGAAGCA 57.492 34.783 0.00 0.00 39.21 3.91
2033 2483 7.646526 AGTTAAATTTACGGTCAAAGTTGAAGC 59.353 33.333 0.00 0.00 39.21 3.86
2042 2492 9.896263 GGTTTTGATAGTTAAATTTACGGTCAA 57.104 29.630 0.00 4.35 0.00 3.18
2043 2493 8.229137 CGGTTTTGATAGTTAAATTTACGGTCA 58.771 33.333 0.00 0.00 0.00 4.02
2044 2494 8.442384 TCGGTTTTGATAGTTAAATTTACGGTC 58.558 33.333 0.00 0.00 0.00 4.79
2045 2495 8.321650 TCGGTTTTGATAGTTAAATTTACGGT 57.678 30.769 0.00 0.00 0.00 4.83
2046 2496 9.777575 AATCGGTTTTGATAGTTAAATTTACGG 57.222 29.630 0.00 0.00 0.00 4.02
2049 2499 9.279904 CGCAATCGGTTTTGATAGTTAAATTTA 57.720 29.630 0.00 0.00 0.00 1.40
2050 2500 8.168681 CGCAATCGGTTTTGATAGTTAAATTT 57.831 30.769 0.00 0.00 0.00 1.82
2051 2501 7.734538 CGCAATCGGTTTTGATAGTTAAATT 57.265 32.000 0.00 0.00 0.00 1.82
2069 2519 2.485188 TTTTTGCTCCCGCCGCAATC 62.485 55.000 5.33 0.00 45.67 2.67
2070 2520 1.887344 ATTTTTGCTCCCGCCGCAAT 61.887 50.000 5.33 0.00 45.67 3.56
2071 2521 2.093537 AATTTTTGCTCCCGCCGCAA 62.094 50.000 0.00 0.00 44.83 4.85
2072 2522 1.244697 TAATTTTTGCTCCCGCCGCA 61.245 50.000 0.00 0.00 35.22 5.69
2073 2523 0.102300 ATAATTTTTGCTCCCGCCGC 59.898 50.000 0.00 0.00 34.43 6.53
2074 2524 3.252215 TGATATAATTTTTGCTCCCGCCG 59.748 43.478 0.00 0.00 34.43 6.46
2075 2525 4.278419 ACTGATATAATTTTTGCTCCCGCC 59.722 41.667 0.00 0.00 34.43 6.13
2076 2526 5.008613 TCACTGATATAATTTTTGCTCCCGC 59.991 40.000 0.00 0.00 0.00 6.13
2077 2527 6.618287 TCACTGATATAATTTTTGCTCCCG 57.382 37.500 0.00 0.00 0.00 5.14
2078 2528 9.468532 GAATTCACTGATATAATTTTTGCTCCC 57.531 33.333 0.00 0.00 0.00 4.30
2079 2529 9.173939 CGAATTCACTGATATAATTTTTGCTCC 57.826 33.333 6.22 0.00 0.00 4.70
2080 2530 9.722056 ACGAATTCACTGATATAATTTTTGCTC 57.278 29.630 6.22 0.00 0.00 4.26
2135 2585 0.589223 CAACTGCGGCGGTAGAAAAA 59.411 50.000 15.95 0.00 0.00 1.94
2136 2586 1.231958 CCAACTGCGGCGGTAGAAAA 61.232 55.000 15.95 0.00 0.00 2.29
2137 2587 1.669760 CCAACTGCGGCGGTAGAAA 60.670 57.895 15.95 0.00 0.00 2.52
2138 2588 2.047655 CCAACTGCGGCGGTAGAA 60.048 61.111 15.95 0.00 0.00 2.10
2139 2589 3.291101 GACCAACTGCGGCGGTAGA 62.291 63.158 15.95 0.00 31.63 2.59
2140 2590 2.813908 GACCAACTGCGGCGGTAG 60.814 66.667 15.95 12.26 31.63 3.18
2141 2591 3.291101 GAGACCAACTGCGGCGGTA 62.291 63.158 15.95 0.00 31.63 4.02
2142 2592 4.681978 GAGACCAACTGCGGCGGT 62.682 66.667 9.04 9.04 35.12 5.68
2143 2593 3.958147 ATGAGACCAACTGCGGCGG 62.958 63.158 9.78 7.39 0.00 6.13
2144 2594 2.034879 AATGAGACCAACTGCGGCG 61.035 57.895 0.51 0.51 0.00 6.46
2145 2595 0.955428 TCAATGAGACCAACTGCGGC 60.955 55.000 0.00 0.00 0.00 6.53
2146 2596 1.742761 ATCAATGAGACCAACTGCGG 58.257 50.000 0.00 0.00 0.00 5.69
2147 2597 4.944962 TTAATCAATGAGACCAACTGCG 57.055 40.909 0.00 0.00 0.00 5.18
2148 2598 9.807649 ATAAATTTAATCAATGAGACCAACTGC 57.192 29.630 1.21 0.00 0.00 4.40
2167 2617 8.154203 CCAAGGTCCAACTTTAACCATAAATTT 58.846 33.333 0.00 0.00 35.43 1.82
2168 2618 7.256511 CCCAAGGTCCAACTTTAACCATAAATT 60.257 37.037 0.00 0.00 35.43 1.82
2169 2619 6.212589 CCCAAGGTCCAACTTTAACCATAAAT 59.787 38.462 0.00 0.00 35.43 1.40
2170 2620 5.540719 CCCAAGGTCCAACTTTAACCATAAA 59.459 40.000 0.00 0.00 35.43 1.40
2171 2621 5.081032 CCCAAGGTCCAACTTTAACCATAA 58.919 41.667 0.00 0.00 35.43 1.90
2172 2622 4.354387 TCCCAAGGTCCAACTTTAACCATA 59.646 41.667 0.00 0.00 35.43 2.74
2173 2623 3.141272 TCCCAAGGTCCAACTTTAACCAT 59.859 43.478 0.00 0.00 35.43 3.55
2174 2624 2.514582 TCCCAAGGTCCAACTTTAACCA 59.485 45.455 0.00 0.00 35.43 3.67
2175 2625 3.232720 TCCCAAGGTCCAACTTTAACC 57.767 47.619 0.00 0.00 0.00 2.85
2176 2626 3.005472 GCTTCCCAAGGTCCAACTTTAAC 59.995 47.826 0.00 0.00 0.00 2.01
2177 2627 3.227614 GCTTCCCAAGGTCCAACTTTAA 58.772 45.455 0.00 0.00 0.00 1.52
2178 2628 2.812613 CGCTTCCCAAGGTCCAACTTTA 60.813 50.000 0.00 0.00 0.00 1.85
2179 2629 1.704641 GCTTCCCAAGGTCCAACTTT 58.295 50.000 0.00 0.00 0.00 2.66
2180 2630 0.537371 CGCTTCCCAAGGTCCAACTT 60.537 55.000 0.00 0.00 0.00 2.66
2181 2631 1.073199 CGCTTCCCAAGGTCCAACT 59.927 57.895 0.00 0.00 0.00 3.16
2182 2632 2.626780 GCGCTTCCCAAGGTCCAAC 61.627 63.158 0.00 0.00 0.00 3.77
2183 2633 2.282180 GCGCTTCCCAAGGTCCAA 60.282 61.111 0.00 0.00 0.00 3.53
2184 2634 4.697756 CGCGCTTCCCAAGGTCCA 62.698 66.667 5.56 0.00 0.00 4.02
2198 2648 0.384230 CAAAATATAGTGCGCCCGCG 60.384 55.000 4.18 4.36 45.51 6.46
2199 2649 0.941542 TCAAAATATAGTGCGCCCGC 59.058 50.000 4.18 5.60 42.35 6.13
2200 2650 3.684103 TTTCAAAATATAGTGCGCCCG 57.316 42.857 4.18 0.00 0.00 6.13
2201 2651 4.037446 TCCATTTCAAAATATAGTGCGCCC 59.963 41.667 4.18 0.00 0.00 6.13
2202 2652 5.181690 TCCATTTCAAAATATAGTGCGCC 57.818 39.130 4.18 0.00 0.00 6.53
2203 2653 5.215160 CCTCCATTTCAAAATATAGTGCGC 58.785 41.667 0.00 0.00 0.00 6.09
2204 2654 5.530915 TCCCTCCATTTCAAAATATAGTGCG 59.469 40.000 0.00 0.00 0.00 5.34
2205 2655 6.547510 ACTCCCTCCATTTCAAAATATAGTGC 59.452 38.462 0.00 0.00 0.00 4.40
2206 2656 9.627123 TTACTCCCTCCATTTCAAAATATAGTG 57.373 33.333 0.00 0.00 0.00 2.74
2207 2657 9.628500 GTTACTCCCTCCATTTCAAAATATAGT 57.372 33.333 0.00 0.00 0.00 2.12
2208 2658 8.774586 CGTTACTCCCTCCATTTCAAAATATAG 58.225 37.037 0.00 0.00 0.00 1.31
2209 2659 8.269317 ACGTTACTCCCTCCATTTCAAAATATA 58.731 33.333 0.00 0.00 0.00 0.86
2210 2660 7.116736 ACGTTACTCCCTCCATTTCAAAATAT 58.883 34.615 0.00 0.00 0.00 1.28
2211 2661 6.478129 ACGTTACTCCCTCCATTTCAAAATA 58.522 36.000 0.00 0.00 0.00 1.40
2212 2662 5.321927 ACGTTACTCCCTCCATTTCAAAAT 58.678 37.500 0.00 0.00 0.00 1.82
2213 2663 4.721132 ACGTTACTCCCTCCATTTCAAAA 58.279 39.130 0.00 0.00 0.00 2.44
2214 2664 4.360951 ACGTTACTCCCTCCATTTCAAA 57.639 40.909 0.00 0.00 0.00 2.69
2215 2665 4.360951 AACGTTACTCCCTCCATTTCAA 57.639 40.909 0.00 0.00 0.00 2.69
2216 2666 4.360951 AAACGTTACTCCCTCCATTTCA 57.639 40.909 0.00 0.00 0.00 2.69
2217 2667 5.239963 TCAAAAACGTTACTCCCTCCATTTC 59.760 40.000 0.00 0.00 0.00 2.17
2218 2668 5.009310 GTCAAAAACGTTACTCCCTCCATTT 59.991 40.000 0.00 0.00 0.00 2.32
2219 2669 4.517832 GTCAAAAACGTTACTCCCTCCATT 59.482 41.667 0.00 0.00 0.00 3.16
2220 2670 4.070009 GTCAAAAACGTTACTCCCTCCAT 58.930 43.478 0.00 0.00 0.00 3.41
2221 2671 3.118334 TGTCAAAAACGTTACTCCCTCCA 60.118 43.478 0.00 0.00 0.00 3.86
2222 2672 3.249320 GTGTCAAAAACGTTACTCCCTCC 59.751 47.826 0.00 0.00 0.00 4.30
2223 2673 4.124970 AGTGTCAAAAACGTTACTCCCTC 58.875 43.478 0.00 0.00 0.00 4.30
2224 2674 4.146745 AGTGTCAAAAACGTTACTCCCT 57.853 40.909 0.00 0.00 0.00 4.20
2225 2675 5.050567 CACTAGTGTCAAAAACGTTACTCCC 60.051 44.000 15.06 0.00 0.00 4.30
2226 2676 5.521372 ACACTAGTGTCAAAAACGTTACTCC 59.479 40.000 22.95 0.00 40.24 3.85
2227 2677 6.579491 ACACTAGTGTCAAAAACGTTACTC 57.421 37.500 22.95 0.00 40.24 2.59
2228 2678 7.260603 ACTACACTAGTGTCAAAAACGTTACT 58.739 34.615 31.11 2.47 43.74 2.24
2229 2679 7.455331 ACTACACTAGTGTCAAAAACGTTAC 57.545 36.000 31.11 0.00 43.74 2.50
2243 2693 6.335777 AGAACGTTTTTCACACTACACTAGT 58.664 36.000 0.46 0.00 40.28 2.57
2244 2694 6.823678 AGAACGTTTTTCACACTACACTAG 57.176 37.500 0.46 0.00 0.00 2.57
2245 2695 8.876275 ATAAGAACGTTTTTCACACTACACTA 57.124 30.769 7.42 0.00 0.00 2.74
2246 2696 7.781548 ATAAGAACGTTTTTCACACTACACT 57.218 32.000 7.42 0.00 0.00 3.55
2251 2701 9.458374 CCAAAATATAAGAACGTTTTTCACACT 57.542 29.630 7.42 0.00 0.00 3.55
2252 2702 8.696175 CCCAAAATATAAGAACGTTTTTCACAC 58.304 33.333 7.42 0.00 0.00 3.82
2253 2703 8.630917 TCCCAAAATATAAGAACGTTTTTCACA 58.369 29.630 7.42 0.00 0.00 3.58
2254 2704 8.908678 GTCCCAAAATATAAGAACGTTTTTCAC 58.091 33.333 7.42 0.00 0.00 3.18
2255 2705 8.630917 TGTCCCAAAATATAAGAACGTTTTTCA 58.369 29.630 7.42 0.00 0.00 2.69
2256 2706 9.124807 CTGTCCCAAAATATAAGAACGTTTTTC 57.875 33.333 7.42 0.00 0.00 2.29
2257 2707 8.852135 TCTGTCCCAAAATATAAGAACGTTTTT 58.148 29.630 9.22 9.22 0.00 1.94
2258 2708 8.398878 TCTGTCCCAAAATATAAGAACGTTTT 57.601 30.769 0.46 0.00 0.00 2.43
2259 2709 7.120726 CCTCTGTCCCAAAATATAAGAACGTTT 59.879 37.037 0.46 0.00 0.00 3.60
2260 2710 6.598064 CCTCTGTCCCAAAATATAAGAACGTT 59.402 38.462 0.00 0.00 0.00 3.99
2261 2711 6.113411 CCTCTGTCCCAAAATATAAGAACGT 58.887 40.000 0.00 0.00 0.00 3.99
2262 2712 5.527582 CCCTCTGTCCCAAAATATAAGAACG 59.472 44.000 0.00 0.00 0.00 3.95
2263 2713 6.659824 TCCCTCTGTCCCAAAATATAAGAAC 58.340 40.000 0.00 0.00 0.00 3.01
2264 2714 6.447084 ACTCCCTCTGTCCCAAAATATAAGAA 59.553 38.462 0.00 0.00 0.00 2.52
2265 2715 5.970640 ACTCCCTCTGTCCCAAAATATAAGA 59.029 40.000 0.00 0.00 0.00 2.10
2266 2716 6.253946 ACTCCCTCTGTCCCAAAATATAAG 57.746 41.667 0.00 0.00 0.00 1.73
2267 2717 7.136885 TCTACTCCCTCTGTCCCAAAATATAA 58.863 38.462 0.00 0.00 0.00 0.98
2268 2718 6.689561 TCTACTCCCTCTGTCCCAAAATATA 58.310 40.000 0.00 0.00 0.00 0.86
2269 2719 5.538877 TCTACTCCCTCTGTCCCAAAATAT 58.461 41.667 0.00 0.00 0.00 1.28
2270 2720 4.955335 TCTACTCCCTCTGTCCCAAAATA 58.045 43.478 0.00 0.00 0.00 1.40
2271 2721 3.803340 TCTACTCCCTCTGTCCCAAAAT 58.197 45.455 0.00 0.00 0.00 1.82
2272 2722 3.269592 TCTACTCCCTCTGTCCCAAAA 57.730 47.619 0.00 0.00 0.00 2.44
2273 2723 3.269592 TTCTACTCCCTCTGTCCCAAA 57.730 47.619 0.00 0.00 0.00 3.28
2274 2724 3.269592 TTTCTACTCCCTCTGTCCCAA 57.730 47.619 0.00 0.00 0.00 4.12
2275 2725 3.491766 ATTTCTACTCCCTCTGTCCCA 57.508 47.619 0.00 0.00 0.00 4.37
2276 2726 6.783482 ACTATAATTTCTACTCCCTCTGTCCC 59.217 42.308 0.00 0.00 0.00 4.46
2277 2727 7.842887 ACTATAATTTCTACTCCCTCTGTCC 57.157 40.000 0.00 0.00 0.00 4.02
2337 2787 2.217750 TGTGTTCGCAGCTATTTGTGT 58.782 42.857 0.00 0.00 0.00 3.72
2347 2797 1.391485 GTGCTATCACTGTGTTCGCAG 59.609 52.381 15.63 11.17 40.03 5.18
2394 2844 1.681264 AGTACTTGCTTTGGTTGTGCC 59.319 47.619 0.00 0.00 37.90 5.01


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

AutoCloner maintained by Alex Coulton.