Multiple sequence alignment - TraesCS3D01G350700

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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 TraesCS3D01G350700 chr3D 100.000 2935 0 0 1 2935 461950165 461953099 0.000000e+00 5421.0
1 TraesCS3D01G350700 chr3A 85.742 2048 94 84 2 1943 604324506 604326461 0.000000e+00 1982.0
2 TraesCS3D01G350700 chr3A 83.879 428 41 9 1942 2356 604326623 604327035 1.650000e-102 383.0
3 TraesCS3D01G350700 chr3B 89.679 1618 64 42 518 2091 612799188 612800746 0.000000e+00 1967.0
4 TraesCS3D01G350700 chr3B 82.270 423 53 18 2417 2831 612803507 612803915 2.170000e-91 346.0
5 TraesCS3D01G350700 chr3B 87.266 267 26 3 2094 2356 612802960 612803222 6.150000e-77 298.0
6 TraesCS3D01G350700 chr3B 87.081 209 16 8 299 501 612798922 612799125 2.940000e-55 226.0
7 TraesCS3D01G350700 chr2B 86.111 252 29 5 2359 2605 457345815 457346065 1.730000e-67 267.0
8 TraesCS3D01G350700 chr2A 86.056 251 30 4 2359 2605 522492935 522493184 6.240000e-67 265.0
9 TraesCS3D01G350700 chr2A 76.821 151 26 7 2673 2817 406661034 406661181 3.140000e-10 76.8
10 TraesCS3D01G350700 chr1A 83.186 226 35 3 2365 2589 388935904 388936127 1.380000e-48 204.0
11 TraesCS3D01G350700 chr1A 97.143 70 2 0 1383 1452 482964107 482964038 5.140000e-23 119.0
12 TraesCS3D01G350700 chr1A 86.585 82 9 2 1222 1302 22282864 22282784 4.030000e-14 89.8
13 TraesCS3D01G350700 chr6D 79.924 264 45 7 2361 2622 56906101 56905844 1.390000e-43 187.0
14 TraesCS3D01G350700 chr6B 82.432 222 30 8 2375 2589 85115471 85115252 5.000000e-43 185.0
15 TraesCS3D01G350700 chr4D 82.524 206 32 4 2369 2572 39352922 39353125 8.360000e-41 178.0
16 TraesCS3D01G350700 chr1D 81.614 223 34 6 2373 2591 78967054 78966835 8.360000e-41 178.0
17 TraesCS3D01G350700 chr1D 82.126 207 34 3 2401 2605 23245804 23246009 1.080000e-39 174.0
18 TraesCS3D01G350700 chr1D 97.143 70 2 0 1383 1452 383177970 383177901 5.140000e-23 119.0
19 TraesCS3D01G350700 chr1D 86.420 81 9 2 1223 1302 20061997 20062076 1.450000e-13 87.9
20 TraesCS3D01G350700 chr1D 86.250 80 9 2 1224 1302 20193515 20193593 5.210000e-13 86.1
21 TraesCS3D01G350700 chr1B 81.553 206 29 6 2401 2605 39590791 39590594 8.420000e-36 161.0
22 TraesCS3D01G350700 chr1B 79.736 227 19 15 1226 1452 513481425 513481226 3.940000e-29 139.0
23 TraesCS3D01G350700 chr1B 85.366 82 10 2 1222 1302 33857284 33857204 1.870000e-12 84.2
24 TraesCS3D01G350700 chr5B 74.632 272 53 15 1192 1451 659604746 659605013 4.000000e-19 106.0
25 TraesCS3D01G350700 chr5A 75.309 243 40 13 1217 1451 651755174 651755404 6.690000e-17 99.0
26 TraesCS3D01G350700 chr5D 75.309 243 39 17 1221 1451 525302710 525302943 2.410000e-16 97.1
27 TraesCS3D01G350700 chr5D 74.104 251 45 17 1213 1451 525250416 525250658 5.210000e-13 86.1


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 TraesCS3D01G350700 chr3D 461950165 461953099 2934 False 5421.00 5421 100.0000 1 2935 1 chr3D.!!$F1 2934
1 TraesCS3D01G350700 chr3A 604324506 604327035 2529 False 1182.50 1982 84.8105 2 2356 2 chr3A.!!$F1 2354
2 TraesCS3D01G350700 chr3B 612798922 612803915 4993 False 709.25 1967 86.5740 299 2831 4 chr3B.!!$F1 2532

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
40 41 0.036388 TTCCCGCTGGATCTTCACAC 60.036 55.0 0.00 0.0 41.40 3.82 F
1017 1172 0.250901 ATTTCAGTTCGCTGCTGGGT 60.251 50.0 7.52 0.0 44.62 4.51 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1622 1812 1.135660 CACAAGCAGATCAAGCAGCTG 60.136 52.381 10.11 10.11 37.41 4.24 R
2157 4730 0.266152 ACTAGCACCTCCTAGCCCAT 59.734 55.000 0.00 0.00 38.68 4.00 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
24 25 2.287849 GCCACAAAAGTCAAGAGCTTCC 60.288 50.000 0.00 0.00 0.00 3.46
39 40 0.250234 CTTCCCGCTGGATCTTCACA 59.750 55.000 0.00 0.00 41.40 3.58
40 41 0.036388 TTCCCGCTGGATCTTCACAC 60.036 55.000 0.00 0.00 41.40 3.82
41 42 1.450312 CCCGCTGGATCTTCACACC 60.450 63.158 0.00 0.00 0.00 4.16
58 59 4.680237 CCACACCAGCGAGCGGAA 62.680 66.667 11.61 0.00 0.00 4.30
59 60 3.114616 CACACCAGCGAGCGGAAG 61.115 66.667 11.61 7.08 0.00 3.46
119 128 3.112075 CGTCGCGCATCACACCTT 61.112 61.111 8.75 0.00 0.00 3.50
126 135 1.410737 CGCATCACACCTTACGTCCG 61.411 60.000 0.00 0.00 0.00 4.79
127 136 1.693083 GCATCACACCTTACGTCCGC 61.693 60.000 0.00 0.00 0.00 5.54
128 137 1.153901 ATCACACCTTACGTCCGCG 60.154 57.895 0.00 0.00 44.93 6.46
209 241 1.446792 CACACTTGGCTCGATCGCT 60.447 57.895 11.09 0.00 0.00 4.93
217 249 2.028190 CTCGATCGCTCGCCCAAT 59.972 61.111 11.09 0.00 44.65 3.16
220 252 1.592669 CGATCGCTCGCCCAATTCT 60.593 57.895 0.26 0.00 38.20 2.40
233 272 3.899981 AATTCTGCTGGCGCCGTCA 62.900 57.895 23.90 20.33 34.43 4.35
249 295 2.514592 CATCTGGCGTGCGGGAAT 60.515 61.111 0.00 0.00 0.00 3.01
262 308 3.512516 GGAATGGCCACTGCGCTC 61.513 66.667 8.16 0.00 38.85 5.03
274 320 1.275471 CTGCGCTCTTCGTTCGTCAA 61.275 55.000 9.73 0.00 41.07 3.18
317 367 5.569441 CGCACGGAATATACTAGTCAAGATG 59.431 44.000 0.00 0.00 0.00 2.90
352 402 1.067142 TGTGCACCGGAACAGATAGAC 60.067 52.381 15.69 0.00 0.00 2.59
354 404 1.621317 TGCACCGGAACAGATAGACAA 59.379 47.619 9.46 0.00 0.00 3.18
362 413 4.386049 CGGAACAGATAGACAAGTCACAAC 59.614 45.833 2.72 0.00 0.00 3.32
363 414 4.691216 GGAACAGATAGACAAGTCACAACC 59.309 45.833 2.72 0.00 0.00 3.77
369 420 1.691976 AGACAAGTCACAACCGGATCA 59.308 47.619 9.46 0.00 0.00 2.92
421 502 3.624300 CGAGAGCGCGCCATCTTG 61.624 66.667 30.33 23.91 0.00 3.02
507 591 3.681835 GCACCCGTCGACCACTCT 61.682 66.667 10.58 0.00 0.00 3.24
682 826 1.139734 GCCATCGCTCTCTCGTGAA 59.860 57.895 0.00 0.00 0.00 3.18
690 834 1.593551 GCTCTCTCGTGAACTCGATCG 60.594 57.143 9.36 9.36 39.12 3.69
711 855 3.277211 TTCTGGAACGACGAGGCGG 62.277 63.158 0.00 0.00 35.12 6.13
752 902 3.773860 TTTATTGCCTAACCATGTGCG 57.226 42.857 0.00 0.00 0.00 5.34
784 934 1.986575 GCCCATGCTTGAACGAGCTC 61.987 60.000 14.04 2.73 43.11 4.09
874 1024 3.903783 GCCATTGGCTACTTCGCA 58.096 55.556 20.66 0.00 46.69 5.10
926 1081 2.223971 TGACGTGAACAACTCTCCTTCC 60.224 50.000 0.00 0.00 0.00 3.46
975 1130 2.420022 ACCGGTCGTACGTATATATGCC 59.580 50.000 16.05 5.25 0.00 4.40
977 1132 2.679837 CGGTCGTACGTATATATGCCCT 59.320 50.000 16.05 0.00 0.00 5.19
979 1134 3.242543 GGTCGTACGTATATATGCCCTCG 60.243 52.174 16.05 0.00 0.00 4.63
1017 1172 0.250901 ATTTCAGTTCGCTGCTGGGT 60.251 50.000 7.52 0.00 44.62 4.51
1621 1811 4.923942 CGCAGCTCCGGGCATCAT 62.924 66.667 15.92 0.00 44.79 2.45
1622 1812 2.976903 GCAGCTCCGGGCATCATC 60.977 66.667 15.92 0.00 44.79 2.92
1623 1813 2.507452 CAGCTCCGGGCATCATCA 59.493 61.111 15.92 0.00 44.79 3.07
1698 1892 8.870116 ACTTGTATAGATAGGATGTGCATACAA 58.130 33.333 0.00 0.00 40.84 2.41
1699 1893 9.881649 CTTGTATAGATAGGATGTGCATACAAT 57.118 33.333 0.00 0.00 40.84 2.71
1789 1983 7.814264 ATTAAGACATGGATGGAGTTCAATC 57.186 36.000 0.00 0.00 0.00 2.67
1841 2037 8.542926 TGATTGAGTAATTTTCAGAGAGGATGA 58.457 33.333 0.00 0.00 0.00 2.92
1859 2055 7.673082 AGAGGATGATTGAGAAATTTTGGAACT 59.327 33.333 0.00 0.00 0.00 3.01
1884 2080 2.299013 TCCTTGACATGTCGTTAGCTGT 59.701 45.455 20.54 0.00 0.00 4.40
1902 2098 1.410517 TGTAGCCTGTAGATCAGCAGC 59.589 52.381 10.06 6.84 42.38 5.25
1932 2128 4.979197 TCCGAATTCCGATTGTTGTTTTTG 59.021 37.500 0.00 0.00 41.76 2.44
1937 2133 7.377397 CGAATTCCGATTGTTGTTTTTGTTCTA 59.623 33.333 0.00 0.00 41.76 2.10
1994 2353 6.753279 TGGTACTATTTATTTCCGAAGACACG 59.247 38.462 0.00 0.00 0.00 4.49
2015 2374 4.919754 ACGAACGGTGTCTAACTGAATTAC 59.080 41.667 0.00 0.00 38.65 1.89
2018 2377 6.468319 CGAACGGTGTCTAACTGAATTACTAG 59.532 42.308 0.00 0.00 38.65 2.57
2020 2379 7.224522 ACGGTGTCTAACTGAATTACTAGTT 57.775 36.000 0.00 7.22 38.65 2.24
2021 2380 7.311408 ACGGTGTCTAACTGAATTACTAGTTC 58.689 38.462 0.00 0.00 38.65 3.01
2022 2381 7.040201 ACGGTGTCTAACTGAATTACTAGTTCA 60.040 37.037 0.00 0.00 38.65 3.18
2023 2382 7.811236 CGGTGTCTAACTGAATTACTAGTTCAA 59.189 37.037 0.00 0.00 38.11 2.69
2024 2383 8.923683 GGTGTCTAACTGAATTACTAGTTCAAC 58.076 37.037 0.00 0.00 38.11 3.18
2025 2384 9.694137 GTGTCTAACTGAATTACTAGTTCAACT 57.306 33.333 0.00 0.00 38.11 3.16
2054 2413 5.643379 TGATGGTTGAGTAAAATTGGAGC 57.357 39.130 0.00 0.00 0.00 4.70
2056 2415 5.716228 TGATGGTTGAGTAAAATTGGAGCAT 59.284 36.000 0.00 0.00 0.00 3.79
2064 2423 6.040054 TGAGTAAAATTGGAGCATGATCATGG 59.960 38.462 31.62 16.72 39.16 3.66
2186 4763 5.041191 AGGAGGTGCTAGTATTTTCCATG 57.959 43.478 9.64 0.00 0.00 3.66
2189 4766 3.117512 AGGTGCTAGTATTTTCCATGGGG 60.118 47.826 13.02 0.00 0.00 4.96
2199 4776 3.065462 TCCATGGGGAAAACAAGCC 57.935 52.632 13.02 0.00 41.32 4.35
2231 4808 2.158081 ACCTTCTCCTCCCTCAAACTCT 60.158 50.000 0.00 0.00 0.00 3.24
2232 4809 2.499693 CCTTCTCCTCCCTCAAACTCTC 59.500 54.545 0.00 0.00 0.00 3.20
2233 4810 3.440127 CTTCTCCTCCCTCAAACTCTCT 58.560 50.000 0.00 0.00 0.00 3.10
2238 4815 2.370189 CCTCCCTCAAACTCTCTTGTGT 59.630 50.000 0.00 0.00 0.00 3.72
2252 4829 2.033424 TCTTGTGTCTCTCGTGTGAGTG 59.967 50.000 0.00 0.00 43.09 3.51
2257 4834 1.333931 GTCTCTCGTGTGAGTGTGTCA 59.666 52.381 0.00 0.00 43.09 3.58
2291 4868 6.185852 TGATGTGCATGTTCAAGATTGTAG 57.814 37.500 0.00 0.00 0.00 2.74
2292 4869 5.706833 TGATGTGCATGTTCAAGATTGTAGT 59.293 36.000 0.00 0.00 0.00 2.73
2293 4870 6.878389 TGATGTGCATGTTCAAGATTGTAGTA 59.122 34.615 0.00 0.00 0.00 1.82
2310 4887 5.626142 TGTAGTAATGAAAAAGCAGGTGGA 58.374 37.500 0.00 0.00 0.00 4.02
2325 4902 2.359169 TGGAGCGATCGCCCTCTTT 61.359 57.895 34.89 16.92 43.17 2.52
2365 5196 9.581099 AAGGATTATGGCTTGTAAAATTTTACG 57.419 29.630 27.51 18.81 44.52 3.18
2404 5235 9.991906 ATCTGATATCAAAATTTTTAGGCATGG 57.008 29.630 6.90 0.00 0.00 3.66
2405 5236 9.199645 TCTGATATCAAAATTTTTAGGCATGGA 57.800 29.630 6.90 0.00 0.00 3.41
2406 5237 9.820725 CTGATATCAAAATTTTTAGGCATGGAA 57.179 29.630 6.90 0.00 0.00 3.53
2411 5242 8.915057 TCAAAATTTTTAGGCATGGAAAATCA 57.085 26.923 0.00 0.00 33.26 2.57
2412 5243 9.347240 TCAAAATTTTTAGGCATGGAAAATCAA 57.653 25.926 0.00 0.00 33.26 2.57
2413 5244 9.962783 CAAAATTTTTAGGCATGGAAAATCAAA 57.037 25.926 0.00 0.00 33.26 2.69
2414 5245 9.964303 AAAATTTTTAGGCATGGAAAATCAAAC 57.036 25.926 0.00 0.00 33.26 2.93
2415 5246 6.777526 TTTTTAGGCATGGAAAATCAAACG 57.222 33.333 0.00 0.00 0.00 3.60
2416 5247 5.461032 TTTAGGCATGGAAAATCAAACGT 57.539 34.783 0.00 0.00 0.00 3.99
2448 5279 6.183360 GGCAATTTATGTTGACATGAGGATGA 60.183 38.462 0.00 0.00 37.08 2.92
2451 5282 8.410912 CAATTTATGTTGACATGAGGATGACAT 58.589 33.333 0.00 3.75 34.79 3.06
2465 5296 7.988737 TGAGGATGACATATTTAGTTTGCAAG 58.011 34.615 0.00 0.00 0.00 4.01
2469 5300 5.389778 TGACATATTTAGTTTGCAAGCACG 58.610 37.500 16.04 0.00 0.00 5.34
2470 5301 4.732784 ACATATTTAGTTTGCAAGCACGG 58.267 39.130 16.04 0.62 0.00 4.94
2471 5302 2.064573 ATTTAGTTTGCAAGCACGGC 57.935 45.000 16.04 0.00 0.00 5.68
2472 5303 0.741326 TTTAGTTTGCAAGCACGGCA 59.259 45.000 16.04 0.00 40.00 5.69
2488 5319 2.871633 ACGGCAATTTTCTGGCAAAAAG 59.128 40.909 11.31 0.67 41.82 2.27
2493 5324 6.198687 GGCAATTTTCTGGCAAAAAGTAAAC 58.801 36.000 11.31 4.82 41.38 2.01
2499 5330 6.959639 TTCTGGCAAAAAGTAAACTGAGAT 57.040 33.333 0.00 0.00 0.00 2.75
2500 5331 6.317789 TCTGGCAAAAAGTAAACTGAGATG 57.682 37.500 0.00 0.00 0.00 2.90
2501 5332 6.061441 TCTGGCAAAAAGTAAACTGAGATGA 58.939 36.000 0.00 0.00 0.00 2.92
2515 5346 3.358118 TGAGATGAATTTGCCATGCTCA 58.642 40.909 0.00 0.00 31.87 4.26
2516 5347 3.958147 TGAGATGAATTTGCCATGCTCAT 59.042 39.130 0.00 0.00 30.66 2.90
2520 5351 3.852286 TGAATTTGCCATGCTCATCAAC 58.148 40.909 0.00 0.00 0.00 3.18
2521 5352 3.512329 TGAATTTGCCATGCTCATCAACT 59.488 39.130 0.00 0.00 0.00 3.16
2525 5356 4.439305 TTGCCATGCTCATCAACTAAAC 57.561 40.909 0.00 0.00 0.00 2.01
2529 5360 4.418392 CCATGCTCATCAACTAAACTTGC 58.582 43.478 0.00 0.00 0.00 4.01
2537 5368 5.122239 TCATCAACTAAACTTGCCATCTTCG 59.878 40.000 0.00 0.00 0.00 3.79
2538 5369 3.751175 TCAACTAAACTTGCCATCTTCGG 59.249 43.478 0.00 0.00 0.00 4.30
2572 5404 8.592105 ATTTGTCATGAAAATGTTCGATTTGT 57.408 26.923 0.00 0.00 36.46 2.83
2576 5408 7.866898 TGTCATGAAAATGTTCGATTTGTCATT 59.133 29.630 0.00 2.12 36.46 2.57
2578 5410 7.541783 TCATGAAAATGTTCGATTTGTCATTCC 59.458 33.333 0.00 2.35 36.46 3.01
2579 5411 6.980593 TGAAAATGTTCGATTTGTCATTCCT 58.019 32.000 0.00 0.00 36.46 3.36
2584 5416 9.757227 AAATGTTCGATTTGTCATTCCTAAAAA 57.243 25.926 0.00 0.00 31.41 1.94
2585 5417 9.927668 AATGTTCGATTTGTCATTCCTAAAAAT 57.072 25.926 0.00 0.00 0.00 1.82
2586 5418 8.964420 TGTTCGATTTGTCATTCCTAAAAATC 57.036 30.769 0.00 0.00 35.08 2.17
2588 5420 9.065871 GTTCGATTTGTCATTCCTAAAAATCTG 57.934 33.333 0.00 0.00 35.87 2.90
2594 5426 9.912634 TTTGTCATTCCTAAAAATCTGACATTC 57.087 29.630 4.25 0.00 35.42 2.67
2595 5427 8.634335 TGTCATTCCTAAAAATCTGACATTCA 57.366 30.769 0.00 0.00 31.26 2.57
2596 5428 8.514594 TGTCATTCCTAAAAATCTGACATTCAC 58.485 33.333 0.00 0.00 31.26 3.18
2598 5430 8.733458 TCATTCCTAAAAATCTGACATTCACTG 58.267 33.333 0.00 0.00 0.00 3.66
2599 5431 7.452880 TTCCTAAAAATCTGACATTCACTGG 57.547 36.000 0.00 0.00 0.00 4.00
2600 5432 6.778821 TCCTAAAAATCTGACATTCACTGGA 58.221 36.000 0.00 0.00 0.00 3.86
2602 5434 8.548025 TCCTAAAAATCTGACATTCACTGGATA 58.452 33.333 0.00 0.00 0.00 2.59
2607 5439 7.488187 AATCTGACATTCACTGGATATTTCG 57.512 36.000 0.00 0.00 0.00 3.46
2608 5440 6.220726 TCTGACATTCACTGGATATTTCGA 57.779 37.500 0.00 0.00 0.00 3.71
2609 5441 6.820335 TCTGACATTCACTGGATATTTCGAT 58.180 36.000 0.00 0.00 0.00 3.59
2610 5442 6.925718 TCTGACATTCACTGGATATTTCGATC 59.074 38.462 0.00 0.00 0.00 3.69
2611 5443 6.820335 TGACATTCACTGGATATTTCGATCT 58.180 36.000 0.00 0.00 0.00 2.75
2647 5479 3.646162 TGTTTCAAGAGTAAGAGAGGCCA 59.354 43.478 5.01 0.00 0.00 5.36
2652 5484 4.020543 CAAGAGTAAGAGAGGCCACTACT 58.979 47.826 5.01 4.39 0.00 2.57
2653 5485 3.626930 AGAGTAAGAGAGGCCACTACTG 58.373 50.000 5.01 0.00 0.00 2.74
2698 5530 5.986135 CACACCCTATCACTATAAGCACTTC 59.014 44.000 0.00 0.00 0.00 3.01
2700 5532 4.281182 ACCCTATCACTATAAGCACTTCCG 59.719 45.833 0.00 0.00 0.00 4.30
2702 5534 5.010719 CCCTATCACTATAAGCACTTCCGAA 59.989 44.000 0.00 0.00 0.00 4.30
2705 5537 5.654603 TCACTATAAGCACTTCCGAAAGA 57.345 39.130 0.00 0.00 36.30 2.52
2706 5538 5.408356 TCACTATAAGCACTTCCGAAAGAC 58.592 41.667 0.00 0.00 36.30 3.01
2707 5539 5.185249 TCACTATAAGCACTTCCGAAAGACT 59.815 40.000 0.00 0.00 36.30 3.24
2710 5542 2.910688 AGCACTTCCGAAAGACTGAA 57.089 45.000 0.00 0.00 36.30 3.02
2712 5544 2.103263 AGCACTTCCGAAAGACTGAACT 59.897 45.455 0.00 0.00 36.30 3.01
2714 5546 3.675698 GCACTTCCGAAAGACTGAACTAG 59.324 47.826 0.00 0.00 36.30 2.57
2723 5555 6.970043 CCGAAAGACTGAACTAGTAGATCTTG 59.030 42.308 0.00 2.33 40.53 3.02
2738 5570 8.918961 AGTAGATCTTGAGATTAACAAAGTCG 57.081 34.615 0.00 0.00 34.37 4.18
2739 5571 6.654793 AGATCTTGAGATTAACAAAGTCGC 57.345 37.500 0.00 0.00 34.37 5.19
2740 5572 6.402222 AGATCTTGAGATTAACAAAGTCGCT 58.598 36.000 0.00 0.00 34.37 4.93
2751 5583 3.381949 ACAAAGTCGCTACAGACACTTC 58.618 45.455 0.00 0.00 43.24 3.01
2761 5593 4.559251 GCTACAGACACTTCATAGTTGACG 59.441 45.833 0.00 0.00 30.26 4.35
2762 5594 3.318017 ACAGACACTTCATAGTTGACGC 58.682 45.455 0.00 0.00 30.26 5.19
2810 5646 7.962995 AGTGTCAGAAAGTCTATAATCTGGA 57.037 36.000 0.00 0.00 39.74 3.86
2831 5667 4.586001 GGAAAATATGTCATCACCCATGCT 59.414 41.667 0.00 0.00 31.70 3.79
2832 5668 5.508489 GGAAAATATGTCATCACCCATGCTG 60.508 44.000 0.00 0.00 31.70 4.41
2833 5669 2.643995 TATGTCATCACCCATGCTGG 57.356 50.000 0.00 0.00 37.25 4.85
2842 5678 3.612251 CCATGCTGGGGCTTTGAG 58.388 61.111 0.00 0.00 39.59 3.02
2843 5679 1.000521 CCATGCTGGGGCTTTGAGA 60.001 57.895 0.00 0.00 39.59 3.27
2844 5680 0.612732 CCATGCTGGGGCTTTGAGAA 60.613 55.000 0.00 0.00 39.59 2.87
2845 5681 0.815734 CATGCTGGGGCTTTGAGAAG 59.184 55.000 0.00 0.00 39.59 2.85
2846 5682 0.324091 ATGCTGGGGCTTTGAGAAGG 60.324 55.000 0.00 0.00 39.59 3.46
2847 5683 1.380302 GCTGGGGCTTTGAGAAGGA 59.620 57.895 0.00 0.00 33.34 3.36
2848 5684 0.033699 GCTGGGGCTTTGAGAAGGAT 60.034 55.000 0.00 0.00 33.34 3.24
2849 5685 1.760192 CTGGGGCTTTGAGAAGGATG 58.240 55.000 0.00 0.00 33.34 3.51
2850 5686 0.332632 TGGGGCTTTGAGAAGGATGG 59.667 55.000 0.00 0.00 33.34 3.51
2851 5687 0.332972 GGGGCTTTGAGAAGGATGGT 59.667 55.000 0.00 0.00 33.34 3.55
2852 5688 1.272704 GGGGCTTTGAGAAGGATGGTT 60.273 52.381 0.00 0.00 33.34 3.67
2853 5689 1.821136 GGGCTTTGAGAAGGATGGTTG 59.179 52.381 0.00 0.00 33.34 3.77
2854 5690 2.555227 GGGCTTTGAGAAGGATGGTTGA 60.555 50.000 0.00 0.00 33.34 3.18
2855 5691 3.157087 GGCTTTGAGAAGGATGGTTGAA 58.843 45.455 0.00 0.00 33.34 2.69
2856 5692 3.192212 GGCTTTGAGAAGGATGGTTGAAG 59.808 47.826 0.00 0.00 33.34 3.02
2857 5693 3.366781 GCTTTGAGAAGGATGGTTGAAGC 60.367 47.826 0.00 0.00 33.34 3.86
2858 5694 3.507162 TTGAGAAGGATGGTTGAAGCA 57.493 42.857 0.00 0.00 0.00 3.91
2859 5695 3.507162 TGAGAAGGATGGTTGAAGCAA 57.493 42.857 0.00 0.00 0.00 3.91
2860 5696 3.831323 TGAGAAGGATGGTTGAAGCAAA 58.169 40.909 0.00 0.00 0.00 3.68
2861 5697 4.214310 TGAGAAGGATGGTTGAAGCAAAA 58.786 39.130 0.00 0.00 0.00 2.44
2862 5698 4.279169 TGAGAAGGATGGTTGAAGCAAAAG 59.721 41.667 0.00 0.00 0.00 2.27
2863 5699 4.473444 AGAAGGATGGTTGAAGCAAAAGA 58.527 39.130 0.00 0.00 0.00 2.52
2864 5700 4.279420 AGAAGGATGGTTGAAGCAAAAGAC 59.721 41.667 0.00 0.00 0.00 3.01
2865 5701 3.565307 AGGATGGTTGAAGCAAAAGACA 58.435 40.909 0.00 0.00 0.00 3.41
2866 5702 3.960102 AGGATGGTTGAAGCAAAAGACAA 59.040 39.130 0.00 0.00 0.00 3.18
2867 5703 4.590222 AGGATGGTTGAAGCAAAAGACAAT 59.410 37.500 0.00 0.00 0.00 2.71
2868 5704 5.774690 AGGATGGTTGAAGCAAAAGACAATA 59.225 36.000 0.00 0.00 0.00 1.90
2869 5705 6.438425 AGGATGGTTGAAGCAAAAGACAATAT 59.562 34.615 0.00 0.00 0.00 1.28
2870 5706 7.615365 AGGATGGTTGAAGCAAAAGACAATATA 59.385 33.333 0.00 0.00 0.00 0.86
2871 5707 8.416329 GGATGGTTGAAGCAAAAGACAATATAT 58.584 33.333 0.00 0.00 0.00 0.86
2872 5708 9.241317 GATGGTTGAAGCAAAAGACAATATATG 57.759 33.333 0.00 0.00 0.00 1.78
2874 5710 9.237187 TGGTTGAAGCAAAAGACAATATATGTA 57.763 29.630 0.00 0.00 44.12 2.29
2875 5711 9.503427 GGTTGAAGCAAAAGACAATATATGTAC 57.497 33.333 0.00 0.00 44.12 2.90
2878 5714 8.397906 TGAAGCAAAAGACAATATATGTACTGC 58.602 33.333 0.00 0.00 44.12 4.40
2879 5715 7.264373 AGCAAAAGACAATATATGTACTGCC 57.736 36.000 0.00 0.00 44.12 4.85
2880 5716 6.828273 AGCAAAAGACAATATATGTACTGCCA 59.172 34.615 0.00 0.00 44.12 4.92
2881 5717 7.012704 AGCAAAAGACAATATATGTACTGCCAG 59.987 37.037 0.00 0.00 44.12 4.85
2882 5718 7.642669 CAAAAGACAATATATGTACTGCCAGG 58.357 38.462 0.00 0.00 44.12 4.45
2883 5719 6.747414 AAGACAATATATGTACTGCCAGGA 57.253 37.500 0.00 0.00 44.12 3.86
2884 5720 6.352016 AGACAATATATGTACTGCCAGGAG 57.648 41.667 0.00 0.00 44.12 3.69
2885 5721 5.247110 AGACAATATATGTACTGCCAGGAGG 59.753 44.000 0.00 0.00 44.12 4.30
2886 5722 4.907875 ACAATATATGTACTGCCAGGAGGT 59.092 41.667 0.00 0.00 41.63 3.85
2887 5723 5.369699 ACAATATATGTACTGCCAGGAGGTT 59.630 40.000 0.00 0.00 41.63 3.50
2888 5724 3.845781 ATATGTACTGCCAGGAGGTTG 57.154 47.619 0.00 0.00 37.19 3.77
2889 5725 0.620556 ATGTACTGCCAGGAGGTTGG 59.379 55.000 0.00 0.00 41.35 3.77
2890 5726 1.299976 GTACTGCCAGGAGGTTGGG 59.700 63.158 0.00 0.00 38.72 4.12
2891 5727 1.923395 TACTGCCAGGAGGTTGGGG 60.923 63.158 0.00 0.00 38.72 4.96
2892 5728 4.052518 CTGCCAGGAGGTTGGGGG 62.053 72.222 0.00 0.00 38.72 5.40
2893 5729 4.608514 TGCCAGGAGGTTGGGGGA 62.609 66.667 0.00 0.00 38.72 4.81
2894 5730 3.732849 GCCAGGAGGTTGGGGGAG 61.733 72.222 0.00 0.00 38.72 4.30
2895 5731 3.017581 CCAGGAGGTTGGGGGAGG 61.018 72.222 0.00 0.00 34.46 4.30
2896 5732 3.017581 CAGGAGGTTGGGGGAGGG 61.018 72.222 0.00 0.00 0.00 4.30
2897 5733 4.371231 AGGAGGTTGGGGGAGGGG 62.371 72.222 0.00 0.00 0.00 4.79
2898 5734 4.695791 GGAGGTTGGGGGAGGGGT 62.696 72.222 0.00 0.00 0.00 4.95
2899 5735 3.339093 GAGGTTGGGGGAGGGGTG 61.339 72.222 0.00 0.00 0.00 4.61
2900 5736 4.217266 AGGTTGGGGGAGGGGTGT 62.217 66.667 0.00 0.00 0.00 4.16
2901 5737 2.204182 GGTTGGGGGAGGGGTGTA 60.204 66.667 0.00 0.00 0.00 2.90
2902 5738 1.853565 GGTTGGGGGAGGGGTGTAA 60.854 63.158 0.00 0.00 0.00 2.41
2903 5739 1.689412 GTTGGGGGAGGGGTGTAAG 59.311 63.158 0.00 0.00 0.00 2.34
2904 5740 1.542881 TTGGGGGAGGGGTGTAAGG 60.543 63.158 0.00 0.00 0.00 2.69
2905 5741 2.694992 GGGGGAGGGGTGTAAGGG 60.695 72.222 0.00 0.00 0.00 3.95
2906 5742 3.417779 GGGGAGGGGTGTAAGGGC 61.418 72.222 0.00 0.00 0.00 5.19
2907 5743 2.286197 GGGAGGGGTGTAAGGGCT 60.286 66.667 0.00 0.00 0.00 5.19
2908 5744 1.003835 GGGAGGGGTGTAAGGGCTA 59.996 63.158 0.00 0.00 0.00 3.93
2909 5745 0.401541 GGGAGGGGTGTAAGGGCTAT 60.402 60.000 0.00 0.00 0.00 2.97
2910 5746 1.057471 GGAGGGGTGTAAGGGCTATC 58.943 60.000 0.00 0.00 0.00 2.08
2911 5747 1.694693 GGAGGGGTGTAAGGGCTATCA 60.695 57.143 0.00 0.00 0.00 2.15
2912 5748 2.124411 GAGGGGTGTAAGGGCTATCAA 58.876 52.381 0.00 0.00 0.00 2.57
2913 5749 2.711547 GAGGGGTGTAAGGGCTATCAAT 59.288 50.000 0.00 0.00 0.00 2.57
2914 5750 3.131252 AGGGGTGTAAGGGCTATCAATT 58.869 45.455 0.00 0.00 0.00 2.32
2915 5751 4.312487 AGGGGTGTAAGGGCTATCAATTA 58.688 43.478 0.00 0.00 0.00 1.40
2916 5752 4.920129 AGGGGTGTAAGGGCTATCAATTAT 59.080 41.667 0.00 0.00 0.00 1.28
2917 5753 5.375655 AGGGGTGTAAGGGCTATCAATTATT 59.624 40.000 0.00 0.00 0.00 1.40
2918 5754 6.075315 GGGGTGTAAGGGCTATCAATTATTT 58.925 40.000 0.00 0.00 0.00 1.40
2919 5755 6.208797 GGGGTGTAAGGGCTATCAATTATTTC 59.791 42.308 0.00 0.00 0.00 2.17
2920 5756 7.004691 GGGTGTAAGGGCTATCAATTATTTCT 58.995 38.462 0.00 0.00 0.00 2.52
2921 5757 7.175119 GGGTGTAAGGGCTATCAATTATTTCTC 59.825 40.741 0.00 0.00 0.00 2.87
2922 5758 7.939588 GGTGTAAGGGCTATCAATTATTTCTCT 59.060 37.037 0.00 0.00 0.00 3.10
2923 5759 8.994170 GTGTAAGGGCTATCAATTATTTCTCTC 58.006 37.037 0.00 0.00 0.00 3.20
2924 5760 8.938883 TGTAAGGGCTATCAATTATTTCTCTCT 58.061 33.333 0.00 0.00 0.00 3.10
2927 5763 7.912719 AGGGCTATCAATTATTTCTCTCTACC 58.087 38.462 0.00 0.00 0.00 3.18
2928 5764 7.037945 AGGGCTATCAATTATTTCTCTCTACCC 60.038 40.741 0.00 0.00 0.00 3.69
2929 5765 7.106890 GGCTATCAATTATTTCTCTCTACCCC 58.893 42.308 0.00 0.00 0.00 4.95
2930 5766 7.106890 GCTATCAATTATTTCTCTCTACCCCC 58.893 42.308 0.00 0.00 0.00 5.40
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 1.871039 GCTCTTGACTTTTGTGGCGTA 59.129 47.619 0.00 0.00 0.00 4.42
4 5 2.294512 GGGAAGCTCTTGACTTTTGTGG 59.705 50.000 0.00 0.00 0.00 4.17
24 25 1.450312 GGGTGTGAAGATCCAGCGG 60.450 63.158 0.00 0.00 0.00 5.52
41 42 4.680237 TTCCGCTCGCTGGTGTGG 62.680 66.667 0.00 0.00 38.39 4.17
57 58 4.675029 CCGTTCCGTCACCCGCTT 62.675 66.667 0.00 0.00 34.38 4.68
59 60 4.974989 AACCGTTCCGTCACCCGC 62.975 66.667 0.00 0.00 34.38 6.13
60 61 2.735857 GAACCGTTCCGTCACCCG 60.736 66.667 0.00 0.00 0.00 5.28
61 62 2.357881 GGAACCGTTCCGTCACCC 60.358 66.667 14.56 0.00 40.59 4.61
103 104 1.708027 GTAAGGTGTGATGCGCGAC 59.292 57.895 12.10 0.88 0.00 5.19
166 198 4.228097 CATCTTTGCTCCGCGGCG 62.228 66.667 23.51 17.52 34.52 6.46
173 205 0.961019 TGTGGCCAACATCTTTGCTC 59.039 50.000 7.24 0.00 32.36 4.26
177 209 2.071778 AGTGTGTGGCCAACATCTTT 57.928 45.000 7.24 0.00 41.97 2.52
204 236 2.182842 GCAGAATTGGGCGAGCGAT 61.183 57.895 0.00 0.00 0.00 4.58
209 241 2.751436 GCCAGCAGAATTGGGCGA 60.751 61.111 0.00 0.00 36.58 5.54
233 272 2.514592 CATTCCCGCACGCCAGAT 60.515 61.111 0.00 0.00 0.00 2.90
262 308 3.301197 CGTGCATATCTTGACGAACGAAG 60.301 47.826 0.14 0.00 33.50 3.79
274 320 1.588932 CGCGTGGACGTGCATATCT 60.589 57.895 14.45 0.00 43.06 1.98
352 402 1.194547 CGTTGATCCGGTTGTGACTTG 59.805 52.381 0.00 0.00 0.00 3.16
354 404 0.677288 TCGTTGATCCGGTTGTGACT 59.323 50.000 0.00 0.00 0.00 3.41
362 413 2.080286 ACTTGTTCTCGTTGATCCGG 57.920 50.000 0.00 0.00 0.00 5.14
363 414 3.059044 CGTTACTTGTTCTCGTTGATCCG 59.941 47.826 0.00 0.00 0.00 4.18
369 420 6.803320 TCGATTATTCGTTACTTGTTCTCGTT 59.197 34.615 6.89 0.00 45.65 3.85
404 485 3.624300 CAAGATGGCGCGCTCTCG 61.624 66.667 32.29 12.82 39.07 4.04
421 502 3.551551 CGGTTCTCCACATTTTTCGAAC 58.448 45.455 0.00 0.00 0.00 3.95
507 591 3.120546 GCGTACGTGACTGTAGAGTTGTA 60.121 47.826 17.90 0.00 30.16 2.41
645 789 3.006537 TGGCGATGGTTAGCTACTAATCC 59.993 47.826 0.00 0.00 0.00 3.01
682 826 0.173708 GTTCCAGAAGCCGATCGAGT 59.826 55.000 18.66 0.00 0.00 4.18
690 834 1.446272 CCTCGTCGTTCCAGAAGCC 60.446 63.158 0.00 0.00 0.00 4.35
711 855 1.664649 GTTTGCTTGCTTTCCCGGC 60.665 57.895 0.00 0.00 0.00 6.13
712 856 0.389025 AAGTTTGCTTGCTTTCCCGG 59.611 50.000 0.00 0.00 32.92 5.73
868 1018 3.776849 TGTGCGTGCGATGCGAAG 61.777 61.111 0.00 0.00 31.36 3.79
898 1048 0.653636 GTTGTTCACGTCAAAGCCGA 59.346 50.000 0.00 0.00 0.00 5.54
926 1081 0.179073 CGGGTGGCTGATCTTGTAGG 60.179 60.000 0.00 0.00 0.00 3.18
1017 1172 7.387948 TCATCACGAGATCGATCTTTGTATCTA 59.612 37.037 27.90 15.08 43.02 1.98
1156 1340 3.396911 CTTGCTGATGCTGCCGCTG 62.397 63.158 0.70 0.00 40.48 5.18
1157 1341 3.132139 CTTGCTGATGCTGCCGCT 61.132 61.111 0.70 0.00 40.48 5.52
1158 1342 4.849329 GCTTGCTGATGCTGCCGC 62.849 66.667 0.00 0.00 40.48 6.53
1159 1343 4.189188 GGCTTGCTGATGCTGCCG 62.189 66.667 0.00 0.00 44.23 5.69
1161 1345 4.189188 CCGGCTTGCTGATGCTGC 62.189 66.667 2.59 0.00 40.48 5.25
1162 1346 2.749044 ACCGGCTTGCTGATGCTG 60.749 61.111 0.00 0.00 40.48 4.41
1163 1347 2.749044 CACCGGCTTGCTGATGCT 60.749 61.111 0.00 0.00 40.48 3.79
1164 1348 2.747460 TCACCGGCTTGCTGATGC 60.747 61.111 0.00 0.00 40.20 3.91
1165 1349 2.743752 CGTCACCGGCTTGCTGATG 61.744 63.158 0.00 0.00 0.00 3.07
1166 1350 2.434884 CGTCACCGGCTTGCTGAT 60.435 61.111 0.00 0.00 0.00 2.90
1582 1772 4.084888 GCCGACGTTTCTTGCCCG 62.085 66.667 0.00 0.00 0.00 6.13
1621 1811 1.271217 ACAAGCAGATCAAGCAGCTGA 60.271 47.619 20.43 0.00 37.41 4.26
1622 1812 1.135660 CACAAGCAGATCAAGCAGCTG 60.136 52.381 10.11 10.11 37.41 4.24
1623 1813 1.166129 CACAAGCAGATCAAGCAGCT 58.834 50.000 11.97 0.00 39.37 4.24
1699 1893 9.855021 CGGAATCATCATGTATGTATTGTACTA 57.145 33.333 0.00 0.00 36.89 1.82
1700 1894 8.367911 ACGGAATCATCATGTATGTATTGTACT 58.632 33.333 0.00 0.00 36.89 2.73
1701 1895 8.435430 CACGGAATCATCATGTATGTATTGTAC 58.565 37.037 0.00 0.00 36.89 2.90
1859 2055 5.580691 CAGCTAACGACATGTCAAGGATTAA 59.419 40.000 24.93 1.31 0.00 1.40
1902 2098 3.126831 CAATCGGAATTCGGAAGAGAGG 58.873 50.000 18.30 3.14 43.69 3.69
1968 2327 7.043590 CGTGTCTTCGGAAATAAATAGTACCAG 60.044 40.741 0.00 0.00 0.00 4.00
1969 2328 6.753279 CGTGTCTTCGGAAATAAATAGTACCA 59.247 38.462 0.00 0.00 0.00 3.25
1970 2329 6.974622 TCGTGTCTTCGGAAATAAATAGTACC 59.025 38.462 0.00 0.00 0.00 3.34
1971 2330 7.975866 TCGTGTCTTCGGAAATAAATAGTAC 57.024 36.000 0.00 0.00 0.00 2.73
1972 2331 7.218773 CGTTCGTGTCTTCGGAAATAAATAGTA 59.781 37.037 0.00 0.00 0.00 1.82
1973 2332 6.034256 CGTTCGTGTCTTCGGAAATAAATAGT 59.966 38.462 0.00 0.00 0.00 2.12
1994 2353 7.311408 ACTAGTAATTCAGTTAGACACCGTTC 58.689 38.462 0.00 0.00 0.00 3.95
2018 2377 6.874134 ACTCAACCATCATGTACTAGTTGAAC 59.126 38.462 0.00 0.00 41.98 3.18
2020 2379 6.605471 ACTCAACCATCATGTACTAGTTGA 57.395 37.500 0.00 0.00 40.76 3.18
2021 2380 8.771920 TTTACTCAACCATCATGTACTAGTTG 57.228 34.615 0.00 0.00 36.73 3.16
2022 2381 9.959721 ATTTTACTCAACCATCATGTACTAGTT 57.040 29.630 0.00 0.00 0.00 2.24
2023 2382 9.959721 AATTTTACTCAACCATCATGTACTAGT 57.040 29.630 0.00 0.00 0.00 2.57
2025 2384 9.173021 CCAATTTTACTCAACCATCATGTACTA 57.827 33.333 0.00 0.00 0.00 1.82
2026 2385 7.888021 TCCAATTTTACTCAACCATCATGTACT 59.112 33.333 0.00 0.00 0.00 2.73
2027 2386 8.050778 TCCAATTTTACTCAACCATCATGTAC 57.949 34.615 0.00 0.00 0.00 2.90
2031 2390 5.716228 TGCTCCAATTTTACTCAACCATCAT 59.284 36.000 0.00 0.00 0.00 2.45
2037 2396 6.855836 TGATCATGCTCCAATTTTACTCAAC 58.144 36.000 0.00 0.00 0.00 3.18
2054 2413 4.022329 ACTGTGCAATATGCCATGATCATG 60.022 41.667 25.97 25.97 44.23 3.07
2056 2415 3.558033 ACTGTGCAATATGCCATGATCA 58.442 40.909 0.00 0.00 44.23 2.92
2091 2453 9.791801 ACATCAAACCATATATGTGCAAGTATA 57.208 29.630 11.73 0.00 31.56 1.47
2092 2454 8.696043 ACATCAAACCATATATGTGCAAGTAT 57.304 30.769 11.73 0.00 31.56 2.12
2095 4668 7.259882 ACAACATCAAACCATATATGTGCAAG 58.740 34.615 11.73 0.00 33.04 4.01
2153 4726 1.150986 AGCACCTCCTAGCCCATAGAT 59.849 52.381 0.00 0.00 32.76 1.98
2157 4730 0.266152 ACTAGCACCTCCTAGCCCAT 59.734 55.000 0.00 0.00 38.68 4.00
2186 4763 3.691342 GCCGGGCTTGTTTTCCCC 61.691 66.667 12.87 0.00 39.39 4.81
2189 4766 0.524414 AATACGCCGGGCTTGTTTTC 59.476 50.000 18.34 0.00 0.00 2.29
2199 4776 0.529992 GGAGAAGGTCAATACGCCGG 60.530 60.000 0.00 0.00 0.00 6.13
2231 4808 2.033424 CACTCACACGAGAGACACAAGA 59.967 50.000 10.35 0.00 42.34 3.02
2232 4809 2.223595 ACACTCACACGAGAGACACAAG 60.224 50.000 10.35 0.00 42.34 3.16
2233 4810 1.749063 ACACTCACACGAGAGACACAA 59.251 47.619 10.35 0.00 42.34 3.33
2238 4815 1.675552 TGACACACTCACACGAGAGA 58.324 50.000 10.35 0.00 42.34 3.10
2252 4829 2.687935 ACATCAACCAAAGGTGTGACAC 59.312 45.455 7.29 7.29 35.34 3.67
2257 4834 1.774110 TGCACATCAACCAAAGGTGT 58.226 45.000 0.00 0.00 35.34 4.16
2291 4868 3.670627 CGCTCCACCTGCTTTTTCATTAC 60.671 47.826 0.00 0.00 0.00 1.89
2292 4869 2.487762 CGCTCCACCTGCTTTTTCATTA 59.512 45.455 0.00 0.00 0.00 1.90
2293 4870 1.270550 CGCTCCACCTGCTTTTTCATT 59.729 47.619 0.00 0.00 0.00 2.57
2310 4887 2.622064 AATAAAAGAGGGCGATCGCT 57.378 45.000 36.25 20.67 41.60 4.93
2325 4902 9.200817 AGCCATAATCCTTTTTGAGCTAAATAA 57.799 29.630 0.00 0.00 0.00 1.40
2387 5218 9.962783 TTTGATTTTCCATGCCTAAAAATTTTG 57.037 25.926 3.73 0.00 33.85 2.44
2388 5219 9.964303 GTTTGATTTTCCATGCCTAAAAATTTT 57.036 25.926 0.00 0.00 33.85 1.82
2389 5220 8.288913 CGTTTGATTTTCCATGCCTAAAAATTT 58.711 29.630 0.00 0.00 33.85 1.82
2390 5221 7.443879 ACGTTTGATTTTCCATGCCTAAAAATT 59.556 29.630 0.00 0.00 33.85 1.82
2391 5222 6.934083 ACGTTTGATTTTCCATGCCTAAAAAT 59.066 30.769 6.22 6.22 35.79 1.82
2392 5223 6.284459 ACGTTTGATTTTCCATGCCTAAAAA 58.716 32.000 0.00 0.00 0.00 1.94
2393 5224 5.848406 ACGTTTGATTTTCCATGCCTAAAA 58.152 33.333 0.00 0.00 0.00 1.52
2394 5225 5.461032 ACGTTTGATTTTCCATGCCTAAA 57.539 34.783 0.00 0.00 0.00 1.85
2395 5226 5.461032 AACGTTTGATTTTCCATGCCTAA 57.539 34.783 0.00 0.00 0.00 2.69
2396 5227 5.461032 AAACGTTTGATTTTCCATGCCTA 57.539 34.783 13.81 0.00 0.00 3.93
2397 5228 4.335400 AAACGTTTGATTTTCCATGCCT 57.665 36.364 13.81 0.00 0.00 4.75
2398 5229 4.509600 TGAAAACGTTTGATTTTCCATGCC 59.490 37.500 15.46 0.00 42.77 4.40
2399 5230 5.649602 TGAAAACGTTTGATTTTCCATGC 57.350 34.783 15.46 0.00 42.77 4.06
2400 5231 6.592166 CCATGAAAACGTTTGATTTTCCATG 58.408 36.000 15.46 16.34 42.77 3.66
2401 5232 5.179182 GCCATGAAAACGTTTGATTTTCCAT 59.821 36.000 15.46 6.91 42.77 3.41
2402 5233 4.509600 GCCATGAAAACGTTTGATTTTCCA 59.490 37.500 15.46 4.97 42.77 3.53
2403 5234 4.509600 TGCCATGAAAACGTTTGATTTTCC 59.490 37.500 15.46 1.92 42.77 3.13
2404 5235 5.649602 TGCCATGAAAACGTTTGATTTTC 57.350 34.783 15.46 8.47 43.41 2.29
2405 5236 6.616774 ATTGCCATGAAAACGTTTGATTTT 57.383 29.167 15.46 0.00 31.96 1.82
2406 5237 6.616774 AATTGCCATGAAAACGTTTGATTT 57.383 29.167 15.46 0.00 0.00 2.17
2407 5238 6.616774 AAATTGCCATGAAAACGTTTGATT 57.383 29.167 15.46 0.00 0.00 2.57
2408 5239 7.387397 ACATAAATTGCCATGAAAACGTTTGAT 59.613 29.630 15.46 7.13 0.00 2.57
2409 5240 6.703607 ACATAAATTGCCATGAAAACGTTTGA 59.296 30.769 15.46 4.82 0.00 2.69
2410 5241 6.886307 ACATAAATTGCCATGAAAACGTTTG 58.114 32.000 15.46 2.14 0.00 2.93
2411 5242 7.225538 TCAACATAAATTGCCATGAAAACGTTT 59.774 29.630 7.96 7.96 0.00 3.60
2412 5243 6.703607 TCAACATAAATTGCCATGAAAACGTT 59.296 30.769 0.00 0.00 0.00 3.99
2413 5244 6.145371 GTCAACATAAATTGCCATGAAAACGT 59.855 34.615 0.00 0.00 0.00 3.99
2414 5245 6.145209 TGTCAACATAAATTGCCATGAAAACG 59.855 34.615 0.00 0.00 0.00 3.60
2415 5246 7.418840 TGTCAACATAAATTGCCATGAAAAC 57.581 32.000 0.00 0.00 0.00 2.43
2416 5247 7.876582 TCATGTCAACATAAATTGCCATGAAAA 59.123 29.630 9.14 0.00 46.42 2.29
2440 5271 7.415541 GCTTGCAAACTAAATATGTCATCCTCA 60.416 37.037 0.00 0.00 0.00 3.86
2448 5279 4.732784 CCGTGCTTGCAAACTAAATATGT 58.267 39.130 0.00 0.00 0.00 2.29
2451 5282 2.554462 TGCCGTGCTTGCAAACTAAATA 59.446 40.909 0.00 0.00 35.40 1.40
2456 5287 3.205395 TTGCCGTGCTTGCAAACT 58.795 50.000 0.00 0.00 45.11 2.66
2465 5296 0.599728 TTGCCAGAAAATTGCCGTGC 60.600 50.000 0.00 0.00 0.00 5.34
2469 5300 6.038161 AGTTTACTTTTTGCCAGAAAATTGCC 59.962 34.615 0.00 0.00 0.00 4.52
2470 5301 6.906678 CAGTTTACTTTTTGCCAGAAAATTGC 59.093 34.615 0.00 0.00 0.00 3.56
2471 5302 8.195617 TCAGTTTACTTTTTGCCAGAAAATTG 57.804 30.769 0.00 0.00 0.00 2.32
2472 5303 8.257306 TCTCAGTTTACTTTTTGCCAGAAAATT 58.743 29.630 0.00 0.00 0.00 1.82
2488 5319 5.517770 GCATGGCAAATTCATCTCAGTTTAC 59.482 40.000 0.00 0.00 0.00 2.01
2493 5324 3.380320 TGAGCATGGCAAATTCATCTCAG 59.620 43.478 0.00 0.00 31.66 3.35
2499 5330 3.512329 AGTTGATGAGCATGGCAAATTCA 59.488 39.130 0.00 0.00 0.00 2.57
2500 5331 4.119442 AGTTGATGAGCATGGCAAATTC 57.881 40.909 0.00 0.00 0.00 2.17
2501 5332 5.664294 TTAGTTGATGAGCATGGCAAATT 57.336 34.783 0.00 0.00 0.00 1.82
2515 5346 4.396166 CCGAAGATGGCAAGTTTAGTTGAT 59.604 41.667 0.00 0.00 0.00 2.57
2516 5347 3.751175 CCGAAGATGGCAAGTTTAGTTGA 59.249 43.478 0.00 0.00 0.00 3.18
2529 5360 7.424803 TGACAAATTATATTTGCCGAAGATGG 58.575 34.615 11.05 0.00 32.93 3.51
2551 5382 7.801547 ATGACAAATCGAACATTTTCATGAC 57.198 32.000 0.00 0.00 34.11 3.06
2565 5397 8.236586 TGTCAGATTTTTAGGAATGACAAATCG 58.763 33.333 3.52 0.00 42.79 3.34
2572 5404 8.733458 CAGTGAATGTCAGATTTTTAGGAATGA 58.267 33.333 0.00 0.00 0.00 2.57
2576 5408 6.778821 TCCAGTGAATGTCAGATTTTTAGGA 58.221 36.000 0.00 0.00 0.00 2.94
2584 5416 6.820335 TCGAAATATCCAGTGAATGTCAGAT 58.180 36.000 0.00 0.00 0.00 2.90
2585 5417 6.220726 TCGAAATATCCAGTGAATGTCAGA 57.779 37.500 0.00 0.00 0.00 3.27
2586 5418 6.927936 AGATCGAAATATCCAGTGAATGTCAG 59.072 38.462 0.00 0.00 0.00 3.51
2588 5420 8.818141 TTAGATCGAAATATCCAGTGAATGTC 57.182 34.615 0.00 0.00 0.00 3.06
2631 5463 4.020543 CAGTAGTGGCCTCTCTTACTCTT 58.979 47.826 11.38 0.00 0.00 2.85
2637 5469 4.439253 AAAAACAGTAGTGGCCTCTCTT 57.561 40.909 11.38 0.00 0.00 2.85
2668 5500 4.778213 ATAGTGATAGGGTGTGCACATT 57.222 40.909 24.69 14.17 33.85 2.71
2669 5501 5.743130 GCTTATAGTGATAGGGTGTGCACAT 60.743 44.000 24.69 9.98 33.85 3.21
2670 5502 4.442893 GCTTATAGTGATAGGGTGTGCACA 60.443 45.833 17.42 17.42 33.85 4.57
2671 5503 4.058817 GCTTATAGTGATAGGGTGTGCAC 58.941 47.826 10.75 10.75 0.00 4.57
2698 5530 6.687081 AGATCTACTAGTTCAGTCTTTCGG 57.313 41.667 0.00 0.00 38.80 4.30
2700 5532 8.952278 TCTCAAGATCTACTAGTTCAGTCTTTC 58.048 37.037 0.00 0.00 38.80 2.62
2702 5534 9.474313 AATCTCAAGATCTACTAGTTCAGTCTT 57.526 33.333 0.00 3.86 34.55 3.01
2714 5546 7.489757 AGCGACTTTGTTAATCTCAAGATCTAC 59.510 37.037 0.00 0.00 32.75 2.59
2723 5555 5.862323 TGTCTGTAGCGACTTTGTTAATCTC 59.138 40.000 0.00 0.00 35.00 2.75
2737 5569 4.559251 GTCAACTATGAAGTGTCTGTAGCG 59.441 45.833 0.00 0.00 37.30 4.26
2738 5570 4.559251 CGTCAACTATGAAGTGTCTGTAGC 59.441 45.833 0.00 0.00 37.30 3.58
2739 5571 4.559251 GCGTCAACTATGAAGTGTCTGTAG 59.441 45.833 0.00 0.00 37.30 2.74
2740 5572 4.482386 GCGTCAACTATGAAGTGTCTGTA 58.518 43.478 0.00 0.00 37.30 2.74
2751 5583 0.998669 TGACATGCGCGTCAACTATG 59.001 50.000 14.62 7.75 42.82 2.23
2761 5593 3.621268 TCTTTTAGTGGTATGACATGCGC 59.379 43.478 0.00 0.00 0.00 6.09
2762 5594 5.794687 TTCTTTTAGTGGTATGACATGCG 57.205 39.130 0.00 0.00 0.00 4.73
2801 5633 8.226810 TGGGTGATGACATATTTTCCAGATTAT 58.773 33.333 0.00 0.00 0.00 1.28
2802 5634 7.581814 TGGGTGATGACATATTTTCCAGATTA 58.418 34.615 0.00 0.00 0.00 1.75
2808 5644 4.586001 AGCATGGGTGATGACATATTTTCC 59.414 41.667 0.00 0.00 33.31 3.13
2810 5646 5.524971 CAGCATGGGTGATGACATATTTT 57.475 39.130 0.00 0.00 44.34 1.82
2831 5667 0.332632 CCATCCTTCTCAAAGCCCCA 59.667 55.000 0.00 0.00 0.00 4.96
2832 5668 0.332972 ACCATCCTTCTCAAAGCCCC 59.667 55.000 0.00 0.00 0.00 5.80
2833 5669 1.821136 CAACCATCCTTCTCAAAGCCC 59.179 52.381 0.00 0.00 0.00 5.19
2834 5670 2.795329 TCAACCATCCTTCTCAAAGCC 58.205 47.619 0.00 0.00 0.00 4.35
2835 5671 3.366781 GCTTCAACCATCCTTCTCAAAGC 60.367 47.826 0.00 0.00 0.00 3.51
2836 5672 3.822735 TGCTTCAACCATCCTTCTCAAAG 59.177 43.478 0.00 0.00 0.00 2.77
2837 5673 3.831323 TGCTTCAACCATCCTTCTCAAA 58.169 40.909 0.00 0.00 0.00 2.69
2838 5674 3.507162 TGCTTCAACCATCCTTCTCAA 57.493 42.857 0.00 0.00 0.00 3.02
2839 5675 3.507162 TTGCTTCAACCATCCTTCTCA 57.493 42.857 0.00 0.00 0.00 3.27
2840 5676 4.520492 TCTTTTGCTTCAACCATCCTTCTC 59.480 41.667 0.00 0.00 0.00 2.87
2841 5677 4.279420 GTCTTTTGCTTCAACCATCCTTCT 59.721 41.667 0.00 0.00 0.00 2.85
2842 5678 4.037923 TGTCTTTTGCTTCAACCATCCTTC 59.962 41.667 0.00 0.00 0.00 3.46
2843 5679 3.960102 TGTCTTTTGCTTCAACCATCCTT 59.040 39.130 0.00 0.00 0.00 3.36
2844 5680 3.565307 TGTCTTTTGCTTCAACCATCCT 58.435 40.909 0.00 0.00 0.00 3.24
2845 5681 4.320608 TTGTCTTTTGCTTCAACCATCC 57.679 40.909 0.00 0.00 0.00 3.51
2846 5682 9.241317 CATATATTGTCTTTTGCTTCAACCATC 57.759 33.333 0.00 0.00 0.00 3.51
2847 5683 8.752187 ACATATATTGTCTTTTGCTTCAACCAT 58.248 29.630 0.00 0.00 30.89 3.55
2848 5684 8.121305 ACATATATTGTCTTTTGCTTCAACCA 57.879 30.769 0.00 0.00 30.89 3.67
2849 5685 9.503427 GTACATATATTGTCTTTTGCTTCAACC 57.497 33.333 0.00 0.00 39.87 3.77
2852 5688 8.397906 GCAGTACATATATTGTCTTTTGCTTCA 58.602 33.333 0.00 0.00 39.87 3.02
2853 5689 7.857885 GGCAGTACATATATTGTCTTTTGCTTC 59.142 37.037 0.00 0.00 39.87 3.86
2854 5690 7.339212 TGGCAGTACATATATTGTCTTTTGCTT 59.661 33.333 0.00 0.00 39.87 3.91
2855 5691 6.828273 TGGCAGTACATATATTGTCTTTTGCT 59.172 34.615 0.00 0.00 39.87 3.91
2856 5692 7.026631 TGGCAGTACATATATTGTCTTTTGC 57.973 36.000 0.00 0.00 39.87 3.68
2857 5693 7.498900 TCCTGGCAGTACATATATTGTCTTTTG 59.501 37.037 14.43 0.00 39.87 2.44
2858 5694 7.573710 TCCTGGCAGTACATATATTGTCTTTT 58.426 34.615 14.43 0.00 39.87 2.27
2859 5695 7.136822 TCCTGGCAGTACATATATTGTCTTT 57.863 36.000 14.43 0.00 39.87 2.52
2860 5696 6.239714 CCTCCTGGCAGTACATATATTGTCTT 60.240 42.308 14.43 0.00 39.87 3.01
2861 5697 5.247110 CCTCCTGGCAGTACATATATTGTCT 59.753 44.000 14.43 0.00 39.87 3.41
2862 5698 5.012148 ACCTCCTGGCAGTACATATATTGTC 59.988 44.000 14.43 0.00 36.95 3.18
2863 5699 4.907875 ACCTCCTGGCAGTACATATATTGT 59.092 41.667 14.43 0.00 38.51 2.71
2864 5700 5.489792 ACCTCCTGGCAGTACATATATTG 57.510 43.478 14.43 0.00 36.63 1.90
2865 5701 5.221925 CCAACCTCCTGGCAGTACATATATT 60.222 44.000 14.43 0.00 36.63 1.28
2866 5702 4.287067 CCAACCTCCTGGCAGTACATATAT 59.713 45.833 14.43 0.00 36.63 0.86
2867 5703 3.646162 CCAACCTCCTGGCAGTACATATA 59.354 47.826 14.43 0.00 36.63 0.86
2868 5704 2.439507 CCAACCTCCTGGCAGTACATAT 59.560 50.000 14.43 0.00 36.63 1.78
2869 5705 1.837439 CCAACCTCCTGGCAGTACATA 59.163 52.381 14.43 0.00 36.63 2.29
2870 5706 0.620556 CCAACCTCCTGGCAGTACAT 59.379 55.000 14.43 0.00 36.63 2.29
2871 5707 1.488705 CCCAACCTCCTGGCAGTACA 61.489 60.000 14.43 0.00 34.88 2.90
2872 5708 1.299976 CCCAACCTCCTGGCAGTAC 59.700 63.158 14.43 0.00 34.88 2.73
2873 5709 1.923395 CCCCAACCTCCTGGCAGTA 60.923 63.158 14.43 0.00 34.88 2.74
2874 5710 3.260100 CCCCAACCTCCTGGCAGT 61.260 66.667 14.43 0.00 34.88 4.40
2875 5711 4.052518 CCCCCAACCTCCTGGCAG 62.053 72.222 7.75 7.75 34.88 4.85
2876 5712 4.608514 TCCCCCAACCTCCTGGCA 62.609 66.667 0.00 0.00 34.88 4.92
2877 5713 3.732849 CTCCCCCAACCTCCTGGC 61.733 72.222 0.00 0.00 34.88 4.85
2878 5714 3.017581 CCTCCCCCAACCTCCTGG 61.018 72.222 0.00 0.00 39.83 4.45
2879 5715 3.017581 CCCTCCCCCAACCTCCTG 61.018 72.222 0.00 0.00 0.00 3.86
2880 5716 4.371231 CCCCTCCCCCAACCTCCT 62.371 72.222 0.00 0.00 0.00 3.69
2881 5717 4.695791 ACCCCTCCCCCAACCTCC 62.696 72.222 0.00 0.00 0.00 4.30
2882 5718 2.776053 TACACCCCTCCCCCAACCTC 62.776 65.000 0.00 0.00 0.00 3.85
2883 5719 2.364323 TTACACCCCTCCCCCAACCT 62.364 60.000 0.00 0.00 0.00 3.50
2884 5720 1.853565 TTACACCCCTCCCCCAACC 60.854 63.158 0.00 0.00 0.00 3.77
2885 5721 1.689412 CTTACACCCCTCCCCCAAC 59.311 63.158 0.00 0.00 0.00 3.77
2886 5722 1.542881 CCTTACACCCCTCCCCCAA 60.543 63.158 0.00 0.00 0.00 4.12
2887 5723 2.126372 CCTTACACCCCTCCCCCA 59.874 66.667 0.00 0.00 0.00 4.96
2888 5724 2.694992 CCCTTACACCCCTCCCCC 60.695 72.222 0.00 0.00 0.00 5.40
2889 5725 2.556608 TAGCCCTTACACCCCTCCCC 62.557 65.000 0.00 0.00 0.00 4.81
2890 5726 0.401541 ATAGCCCTTACACCCCTCCC 60.402 60.000 0.00 0.00 0.00 4.30
2891 5727 1.057471 GATAGCCCTTACACCCCTCC 58.943 60.000 0.00 0.00 0.00 4.30
2892 5728 1.802553 TGATAGCCCTTACACCCCTC 58.197 55.000 0.00 0.00 0.00 4.30
2893 5729 2.280308 TTGATAGCCCTTACACCCCT 57.720 50.000 0.00 0.00 0.00 4.79
2894 5730 3.595190 AATTGATAGCCCTTACACCCC 57.405 47.619 0.00 0.00 0.00 4.95
2895 5731 7.004691 AGAAATAATTGATAGCCCTTACACCC 58.995 38.462 0.00 0.00 0.00 4.61
2896 5732 7.939588 AGAGAAATAATTGATAGCCCTTACACC 59.060 37.037 0.00 0.00 0.00 4.16
2897 5733 8.910351 AGAGAAATAATTGATAGCCCTTACAC 57.090 34.615 0.00 0.00 0.00 2.90
2898 5734 8.938883 AGAGAGAAATAATTGATAGCCCTTACA 58.061 33.333 0.00 0.00 0.00 2.41
2901 5737 8.379331 GGTAGAGAGAAATAATTGATAGCCCTT 58.621 37.037 0.00 0.00 0.00 3.95
2902 5738 7.037945 GGGTAGAGAGAAATAATTGATAGCCCT 60.038 40.741 0.00 0.00 0.00 5.19
2903 5739 7.106890 GGGTAGAGAGAAATAATTGATAGCCC 58.893 42.308 0.00 0.00 0.00 5.19
2904 5740 7.106890 GGGGTAGAGAGAAATAATTGATAGCC 58.893 42.308 0.00 0.00 0.00 3.93
2905 5741 7.106890 GGGGGTAGAGAGAAATAATTGATAGC 58.893 42.308 0.00 0.00 0.00 2.97


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

AutoCloner maintained by Alex Coulton.