Multiple sequence alignment - TraesCS3B01G259900

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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 TraesCS3B01G259900 chr3B 100.000 5131 0 0 1 5131 417723544 417728674 0.000000e+00 9476.0
1 TraesCS3B01G259900 chr3B 89.474 418 32 4 16 422 213717008 213716592 7.620000e-143 518.0
2 TraesCS3B01G259900 chr3A 94.110 2462 83 27 2338 4751 430788302 430790749 0.000000e+00 3687.0
3 TraesCS3B01G259900 chr3A 90.538 1395 77 19 780 2131 430786836 430788218 0.000000e+00 1794.0
4 TraesCS3B01G259900 chr3A 94.961 258 8 4 4877 5131 430791077 430791332 2.880000e-107 399.0
5 TraesCS3B01G259900 chr3A 93.694 111 7 0 2139 2249 430788192 430788302 3.180000e-37 167.0
6 TraesCS3B01G259900 chr3A 83.333 102 13 4 4739 4838 688195263 688195164 1.970000e-14 91.6
7 TraesCS3B01G259900 chr3A 83.333 102 13 4 4739 4838 688228013 688227914 1.970000e-14 91.6
8 TraesCS3B01G259900 chr3D 92.632 2565 93 28 2337 4866 303585856 303583353 0.000000e+00 3602.0
9 TraesCS3B01G259900 chr3D 91.293 1493 77 18 776 2227 303587823 303586343 0.000000e+00 1988.0
10 TraesCS3B01G259900 chr3D 94.022 184 10 1 4948 5131 303583247 303583065 1.410000e-70 278.0
11 TraesCS3B01G259900 chr3D 83.465 127 17 4 4740 4863 104031401 104031526 1.170000e-21 115.0
12 TraesCS3B01G259900 chr3D 86.022 93 11 2 4755 4845 37995214 37995122 1.180000e-16 99.0
13 TraesCS3B01G259900 chr3D 95.745 47 2 0 4880 4926 303583296 303583250 5.510000e-10 76.8
14 TraesCS3B01G259900 chr1D 81.920 802 105 26 5 775 414929368 414928576 4.330000e-180 641.0
15 TraesCS3B01G259900 chr1D 87.075 441 33 10 5 422 205110962 205110523 1.290000e-130 477.0
16 TraesCS3B01G259900 chr1D 76.871 147 28 6 634 776 355479021 355479165 1.530000e-10 78.7
17 TraesCS3B01G259900 chr4A 81.931 808 98 32 5 770 535888905 535889706 1.560000e-179 640.0
18 TraesCS3B01G259900 chr7B 82.447 752 71 32 5 718 604293160 604293888 7.350000e-168 601.0
19 TraesCS3B01G259900 chr7B 95.000 40 0 2 544 582 591295889 591295927 1.540000e-05 62.1
20 TraesCS3B01G259900 chr2B 80.760 816 97 37 6 775 140497841 140498642 2.660000e-162 582.0
21 TraesCS3B01G259900 chr2B 82.400 125 18 4 4744 4865 196255458 196255581 7.030000e-19 106.0
22 TraesCS3B01G259900 chr7A 89.277 429 35 3 5 422 65968803 65969231 1.270000e-145 527.0
23 TraesCS3B01G259900 chr7A 82.258 124 18 4 4740 4860 27883469 27883591 2.530000e-18 104.0
24 TraesCS3B01G259900 chr7A 96.774 31 1 0 1380 1410 21353834 21353804 9.000000e-03 52.8
25 TraesCS3B01G259900 chr1B 87.755 441 31 10 5 422 452720729 452721169 1.280000e-135 494.0
26 TraesCS3B01G259900 chr1B 83.036 112 15 4 4757 4865 427773165 427773055 1.180000e-16 99.0
27 TraesCS3B01G259900 chr6B 78.649 829 111 36 7 776 148919968 148919147 1.660000e-134 490.0
28 TraesCS3B01G259900 chr5D 83.784 518 55 20 98 588 522790264 522790779 1.010000e-126 464.0
29 TraesCS3B01G259900 chr2D 85.000 120 16 2 4746 4863 643786313 643786194 2.510000e-23 121.0
30 TraesCS3B01G259900 chr5A 82.787 122 18 3 4746 4865 169291301 169291181 7.030000e-19 106.0
31 TraesCS3B01G259900 chr5B 100.000 28 0 0 556 583 310058223 310058250 9.000000e-03 52.8
32 TraesCS3B01G259900 chr1A 100.000 28 0 0 555 582 528436404 528436431 9.000000e-03 52.8


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 TraesCS3B01G259900 chr3B 417723544 417728674 5130 False 9476.00 9476 100.00000 1 5131 1 chr3B.!!$F1 5130
1 TraesCS3B01G259900 chr3A 430786836 430791332 4496 False 1511.75 3687 93.32575 780 5131 4 chr3A.!!$F1 4351
2 TraesCS3B01G259900 chr3D 303583065 303587823 4758 True 1486.20 3602 93.42300 776 5131 4 chr3D.!!$R2 4355
3 TraesCS3B01G259900 chr1D 414928576 414929368 792 True 641.00 641 81.92000 5 775 1 chr1D.!!$R2 770
4 TraesCS3B01G259900 chr4A 535888905 535889706 801 False 640.00 640 81.93100 5 770 1 chr4A.!!$F1 765
5 TraesCS3B01G259900 chr7B 604293160 604293888 728 False 601.00 601 82.44700 5 718 1 chr7B.!!$F2 713
6 TraesCS3B01G259900 chr2B 140497841 140498642 801 False 582.00 582 80.76000 6 775 1 chr2B.!!$F1 769
7 TraesCS3B01G259900 chr6B 148919147 148919968 821 True 490.00 490 78.64900 7 776 1 chr6B.!!$R1 769
8 TraesCS3B01G259900 chr5D 522790264 522790779 515 False 464.00 464 83.78400 98 588 1 chr5D.!!$F1 490

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
525 608 0.253160 ATCCACCCCAGAAGCCTACA 60.253 55.0 0.00 0.0 0.00 2.74 F
1979 2117 0.031449 CCCGCTGCTAGAGCTACTTC 59.969 60.0 2.72 0.0 46.64 3.01 F
2295 2433 0.617820 TACCTGAACAGAGGGAGCCC 60.618 60.0 3.19 0.0 37.45 5.19 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2320 2458 0.105607 TAAAAACACCACCCCACCCC 60.106 55.0 0.0 0.0 0.00 4.95 R
3718 4262 2.770164 ACTATGTTCTTGCCGAAGCT 57.230 45.0 0.0 0.0 40.80 3.74 R
4287 4854 1.263356 AGATCCCCGAGTTTTCGTCA 58.737 50.0 0.0 0.0 45.28 4.35 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
29 30 6.015095 CCAGACTCATAGCTACAATGTCCATA 60.015 42.308 0.00 0.00 0.00 2.74
31 32 6.015010 AGACTCATAGCTACAATGTCCATACC 60.015 42.308 0.00 0.00 0.00 2.73
83 88 7.961325 ACAAAATAAATCAAATGGACCACAC 57.039 32.000 0.00 0.00 0.00 3.82
225 249 8.856103 ACATAATACATAAGCAAACATAACCCC 58.144 33.333 0.00 0.00 0.00 4.95
280 304 6.209391 ACCAAAATGATGAACTAGGGTTTGAG 59.791 38.462 0.00 0.00 35.58 3.02
282 306 7.362401 CCAAAATGATGAACTAGGGTTTGAGAG 60.362 40.741 0.00 0.00 35.58 3.20
283 307 4.826274 TGATGAACTAGGGTTTGAGAGG 57.174 45.455 0.00 0.00 35.58 3.69
284 308 4.168101 TGATGAACTAGGGTTTGAGAGGT 58.832 43.478 0.00 0.00 35.58 3.85
285 309 4.597507 TGATGAACTAGGGTTTGAGAGGTT 59.402 41.667 0.00 0.00 35.58 3.50
298 322 3.982475 TGAGAGGTTATGAGCTAATGCG 58.018 45.455 0.00 0.00 45.42 4.73
355 381 3.432378 GAACTGAGAGAGGTACCTTGGA 58.568 50.000 17.53 0.00 0.00 3.53
378 404 4.183865 TGATGAAAGTGCTACGAATCCAG 58.816 43.478 0.00 0.00 0.00 3.86
464 526 1.214175 TGGGGTGTGTTGAATGAGTGT 59.786 47.619 0.00 0.00 0.00 3.55
472 534 2.297701 GTTGAATGAGTGTGTGTGGGT 58.702 47.619 0.00 0.00 0.00 4.51
476 538 1.352622 ATGAGTGTGTGTGGGTGGGT 61.353 55.000 0.00 0.00 0.00 4.51
479 541 3.814906 TGTGTGTGGGTGGGTGGG 61.815 66.667 0.00 0.00 0.00 4.61
480 542 4.596585 GTGTGTGGGTGGGTGGGG 62.597 72.222 0.00 0.00 0.00 4.96
517 581 1.295020 CCAACCTTATCCACCCCAGA 58.705 55.000 0.00 0.00 0.00 3.86
525 608 0.253160 ATCCACCCCAGAAGCCTACA 60.253 55.000 0.00 0.00 0.00 2.74
526 609 0.474854 TCCACCCCAGAAGCCTACAA 60.475 55.000 0.00 0.00 0.00 2.41
527 610 0.625849 CCACCCCAGAAGCCTACAAT 59.374 55.000 0.00 0.00 0.00 2.71
532 615 1.839994 CCCAGAAGCCTACAATCAGGA 59.160 52.381 0.00 0.00 38.00 3.86
599 686 0.822121 GGCCCCTTTTTCACGTCAGT 60.822 55.000 0.00 0.00 0.00 3.41
607 694 4.299155 CTTTTTCACGTCAGTCAGAGCTA 58.701 43.478 0.00 0.00 0.00 3.32
749 842 7.265599 TGGGTCAGATCCTTAAATAAGACAA 57.734 36.000 0.07 0.00 35.33 3.18
776 872 5.897050 AGTCAAAACACGAAATTTTGCCTA 58.103 33.333 5.27 1.40 43.62 3.93
777 873 6.512297 AGTCAAAACACGAAATTTTGCCTAT 58.488 32.000 5.27 0.00 43.62 2.57
778 874 6.983890 AGTCAAAACACGAAATTTTGCCTATT 59.016 30.769 5.27 0.00 43.62 1.73
828 924 2.265904 GGGGCAAGGTTGGTTCGAC 61.266 63.158 0.00 0.00 0.00 4.20
1266 1362 2.945668 CTGCCATAGCCTCAAGGTAAAC 59.054 50.000 0.00 0.00 38.69 2.01
1297 1393 1.604593 GCTCCTTCCTTTGCTGGCA 60.605 57.895 0.00 0.00 0.00 4.92
1318 1414 4.371786 CATTACGTGCTGTACCATCAGAT 58.628 43.478 0.00 0.00 37.61 2.90
1339 1435 7.516557 TCAGATTAGTGATACTCCTAGGTCCTA 59.483 40.741 9.08 0.00 0.00 2.94
1342 1438 3.074836 AGTGATACTCCTAGGTCCTAGCC 59.925 52.174 19.30 5.39 33.12 3.93
1346 1442 3.200958 ACTCCTAGGTCCTAGCCAAAA 57.799 47.619 19.30 2.56 33.12 2.44
1347 1443 3.108376 ACTCCTAGGTCCTAGCCAAAAG 58.892 50.000 19.30 12.58 33.12 2.27
1348 1444 3.246021 ACTCCTAGGTCCTAGCCAAAAGA 60.246 47.826 19.30 9.64 33.12 2.52
1349 1445 3.375699 TCCTAGGTCCTAGCCAAAAGAG 58.624 50.000 19.30 4.58 33.12 2.85
1350 1446 3.108376 CCTAGGTCCTAGCCAAAAGAGT 58.892 50.000 19.30 0.00 33.12 3.24
1352 1448 4.902448 CCTAGGTCCTAGCCAAAAGAGTAT 59.098 45.833 19.30 0.00 33.12 2.12
1353 1449 6.075984 CCTAGGTCCTAGCCAAAAGAGTATA 58.924 44.000 19.30 0.00 33.12 1.47
1354 1450 5.873146 AGGTCCTAGCCAAAAGAGTATAC 57.127 43.478 0.00 0.00 0.00 1.47
1355 1451 4.654724 AGGTCCTAGCCAAAAGAGTATACC 59.345 45.833 0.00 0.00 0.00 2.73
1356 1452 4.654724 GGTCCTAGCCAAAAGAGTATACCT 59.345 45.833 0.00 0.00 0.00 3.08
1413 1509 1.008995 CGGGGAGCACACAAAAACG 60.009 57.895 0.00 0.00 0.00 3.60
1437 1533 2.903357 GATCCGAGCAGGGCTTCA 59.097 61.111 0.00 0.00 39.88 3.02
1447 1543 4.015084 GAGCAGGGCTTCATATATGCAAT 58.985 43.478 7.92 0.00 39.88 3.56
1527 1623 7.776933 CTGCTCAGCTAACAATGTCTAATAA 57.223 36.000 0.00 0.00 0.00 1.40
1528 1624 7.776933 TGCTCAGCTAACAATGTCTAATAAG 57.223 36.000 0.00 0.00 0.00 1.73
1529 1625 7.331026 TGCTCAGCTAACAATGTCTAATAAGT 58.669 34.615 0.00 0.00 0.00 2.24
1592 1688 2.131709 CATGCCTTCATGCCCCCAG 61.132 63.158 0.00 0.00 43.00 4.45
1593 1689 2.318966 ATGCCTTCATGCCCCCAGA 61.319 57.895 0.00 0.00 0.00 3.86
1641 1752 8.132362 ACTACATAAAAGCTCTCAATAGTCGAG 58.868 37.037 0.00 0.00 0.00 4.04
1762 1898 0.401738 CCTCCCTTGGTGAGCTGAAA 59.598 55.000 0.00 0.00 0.00 2.69
1835 1973 1.603842 CAGCTATCTGCCACCACCA 59.396 57.895 0.00 0.00 44.23 4.17
1850 1988 2.997315 CCAGAGCTCCGTCCACCA 60.997 66.667 10.93 0.00 0.00 4.17
1897 2035 1.455849 CCTGTTTCTCCAGGGTGCA 59.544 57.895 0.00 0.00 46.89 4.57
1938 2076 1.759299 AGCCACCGCCTATCCGTAA 60.759 57.895 0.00 0.00 34.57 3.18
1969 2107 4.082523 GTCCTGTGCCCGCTGCTA 62.083 66.667 0.00 0.00 42.00 3.49
1979 2117 0.031449 CCCGCTGCTAGAGCTACTTC 59.969 60.000 2.72 0.00 46.64 3.01
1980 2118 0.741326 CCGCTGCTAGAGCTACTTCA 59.259 55.000 2.72 0.00 46.64 3.02
1987 2125 3.954258 TGCTAGAGCTACTTCATGTGCTA 59.046 43.478 2.72 0.00 42.66 3.49
1988 2126 4.586421 TGCTAGAGCTACTTCATGTGCTAT 59.414 41.667 2.72 0.00 42.66 2.97
1989 2127 5.069648 TGCTAGAGCTACTTCATGTGCTATT 59.930 40.000 2.72 0.00 42.66 1.73
1999 2137 2.981784 TCATGTGCTATTATGGCTCCCT 59.018 45.455 1.70 0.00 0.00 4.20
2007 2145 1.279025 TTATGGCTCCCTGTCCCCAC 61.279 60.000 0.00 0.00 0.00 4.61
2022 2160 3.636231 CACGTTGCCTCCCCTCCA 61.636 66.667 0.00 0.00 0.00 3.86
2088 2226 2.885676 CTGCAGCGCTGTTGAACGT 61.886 57.895 35.80 0.00 0.00 3.99
2117 2255 0.918983 CATCCCAAAGGTAGGGCAGA 59.081 55.000 0.00 0.00 46.36 4.26
2187 2325 9.416284 TGGAGTGGGTAGGAAAAATAATAATTC 57.584 33.333 0.00 0.00 0.00 2.17
2188 2326 9.416284 GGAGTGGGTAGGAAAAATAATAATTCA 57.584 33.333 0.00 0.00 0.00 2.57
2192 2330 7.565768 TGGGTAGGAAAAATAATAATTCACCCC 59.434 37.037 0.00 0.00 37.99 4.95
2248 2386 6.385176 GGGTGGGTTTTATTAGGTACTAGTCT 59.615 42.308 0.00 0.00 44.25 3.24
2249 2387 7.270779 GGTGGGTTTTATTAGGTACTAGTCTG 58.729 42.308 0.00 0.00 44.25 3.51
2250 2388 7.093156 GGTGGGTTTTATTAGGTACTAGTCTGT 60.093 40.741 0.00 0.00 44.25 3.41
2251 2389 8.316946 GTGGGTTTTATTAGGTACTAGTCTGTT 58.683 37.037 0.00 0.00 44.25 3.16
2252 2390 8.534496 TGGGTTTTATTAGGTACTAGTCTGTTC 58.466 37.037 0.00 0.00 44.25 3.18
2253 2391 7.704047 GGGTTTTATTAGGTACTAGTCTGTTCG 59.296 40.741 0.00 0.00 44.25 3.95
2254 2392 8.462016 GGTTTTATTAGGTACTAGTCTGTTCGA 58.538 37.037 0.00 0.00 44.25 3.71
2255 2393 9.500864 GTTTTATTAGGTACTAGTCTGTTCGAG 57.499 37.037 0.00 0.00 44.25 4.04
2256 2394 7.798596 TTATTAGGTACTAGTCTGTTCGAGG 57.201 40.000 0.00 0.00 44.25 4.63
2257 2395 3.996921 AGGTACTAGTCTGTTCGAGGA 57.003 47.619 0.00 0.00 36.02 3.71
2258 2396 3.876341 AGGTACTAGTCTGTTCGAGGAG 58.124 50.000 0.00 0.00 36.02 3.69
2259 2397 3.518705 AGGTACTAGTCTGTTCGAGGAGA 59.481 47.826 0.00 0.00 36.02 3.71
2260 2398 4.164604 AGGTACTAGTCTGTTCGAGGAGAT 59.835 45.833 0.00 0.00 36.02 2.75
2261 2399 4.273969 GGTACTAGTCTGTTCGAGGAGATG 59.726 50.000 0.00 0.00 0.00 2.90
2262 2400 2.685897 ACTAGTCTGTTCGAGGAGATGC 59.314 50.000 0.00 0.00 0.00 3.91
2263 2401 1.550327 AGTCTGTTCGAGGAGATGCA 58.450 50.000 0.00 0.00 0.00 3.96
2264 2402 1.203523 AGTCTGTTCGAGGAGATGCAC 59.796 52.381 0.00 0.00 0.00 4.57
2265 2403 1.067565 GTCTGTTCGAGGAGATGCACA 60.068 52.381 0.00 0.00 0.00 4.57
2266 2404 1.618343 TCTGTTCGAGGAGATGCACAA 59.382 47.619 0.00 0.00 0.00 3.33
2267 2405 2.037121 TCTGTTCGAGGAGATGCACAAA 59.963 45.455 0.00 0.00 0.00 2.83
2268 2406 2.807967 CTGTTCGAGGAGATGCACAAAA 59.192 45.455 0.00 0.00 0.00 2.44
2269 2407 3.210227 TGTTCGAGGAGATGCACAAAAA 58.790 40.909 0.00 0.00 0.00 1.94
2290 2428 2.115343 GGCTTTACCTGAACAGAGGG 57.885 55.000 3.19 0.00 37.45 4.30
2291 2429 1.628846 GGCTTTACCTGAACAGAGGGA 59.371 52.381 3.19 0.00 37.45 4.20
2292 2430 2.355209 GGCTTTACCTGAACAGAGGGAG 60.355 54.545 3.19 0.00 37.45 4.30
2293 2431 2.937433 GCTTTACCTGAACAGAGGGAGC 60.937 54.545 3.19 4.44 37.45 4.70
2294 2432 1.276622 TTACCTGAACAGAGGGAGCC 58.723 55.000 3.19 0.00 37.45 4.70
2295 2433 0.617820 TACCTGAACAGAGGGAGCCC 60.618 60.000 3.19 0.00 37.45 5.19
2296 2434 2.674220 CCTGAACAGAGGGAGCCCC 61.674 68.421 0.91 2.16 45.90 5.80
2306 2444 3.381388 GGGAGCCCCAAAGTGAATT 57.619 52.632 5.45 0.00 44.65 2.17
2307 2445 1.644509 GGGAGCCCCAAAGTGAATTT 58.355 50.000 5.45 0.00 44.65 1.82
2308 2446 1.977854 GGGAGCCCCAAAGTGAATTTT 59.022 47.619 5.45 0.00 44.65 1.82
2309 2447 2.371841 GGGAGCCCCAAAGTGAATTTTT 59.628 45.455 5.45 0.00 44.65 1.94
2310 2448 3.580895 GGGAGCCCCAAAGTGAATTTTTA 59.419 43.478 5.45 0.00 44.65 1.52
2311 2449 4.322725 GGGAGCCCCAAAGTGAATTTTTAG 60.323 45.833 5.45 0.00 44.65 1.85
2312 2450 4.526650 GGAGCCCCAAAGTGAATTTTTAGA 59.473 41.667 0.00 0.00 0.00 2.10
2313 2451 5.011635 GGAGCCCCAAAGTGAATTTTTAGAA 59.988 40.000 0.00 0.00 0.00 2.10
2314 2452 6.463755 GGAGCCCCAAAGTGAATTTTTAGAAA 60.464 38.462 0.00 0.00 0.00 2.52
2315 2453 6.524734 AGCCCCAAAGTGAATTTTTAGAAAG 58.475 36.000 0.00 0.00 0.00 2.62
2316 2454 5.700832 GCCCCAAAGTGAATTTTTAGAAAGG 59.299 40.000 0.00 0.00 0.00 3.11
2317 2455 6.230472 CCCCAAAGTGAATTTTTAGAAAGGG 58.770 40.000 0.00 0.00 0.00 3.95
2318 2456 6.230472 CCCAAAGTGAATTTTTAGAAAGGGG 58.770 40.000 0.00 0.00 0.00 4.79
2319 2457 6.183361 CCCAAAGTGAATTTTTAGAAAGGGGT 60.183 38.462 0.00 0.00 0.00 4.95
2320 2458 6.705825 CCAAAGTGAATTTTTAGAAAGGGGTG 59.294 38.462 0.00 0.00 0.00 4.61
2321 2459 6.419484 AAGTGAATTTTTAGAAAGGGGTGG 57.581 37.500 0.00 0.00 0.00 4.61
2322 2460 4.838423 AGTGAATTTTTAGAAAGGGGTGGG 59.162 41.667 0.00 0.00 0.00 4.61
2323 2461 4.020573 GTGAATTTTTAGAAAGGGGTGGGG 60.021 45.833 0.00 0.00 0.00 4.96
2324 2462 3.935240 ATTTTTAGAAAGGGGTGGGGT 57.065 42.857 0.00 0.00 0.00 4.95
2325 2463 2.687003 TTTTAGAAAGGGGTGGGGTG 57.313 50.000 0.00 0.00 0.00 4.61
2326 2464 0.781278 TTTAGAAAGGGGTGGGGTGG 59.219 55.000 0.00 0.00 0.00 4.61
2327 2465 1.143970 TTAGAAAGGGGTGGGGTGGG 61.144 60.000 0.00 0.00 0.00 4.61
2328 2466 3.992641 GAAAGGGGTGGGGTGGGG 61.993 72.222 0.00 0.00 0.00 4.96
2329 2467 4.895675 AAAGGGGTGGGGTGGGGT 62.896 66.667 0.00 0.00 0.00 4.95
2335 2473 3.828023 GTGGGGTGGGGTGGTGTT 61.828 66.667 0.00 0.00 0.00 3.32
2404 2919 4.956085 AGGTTTATTTGGTTGTTCCTTGC 58.044 39.130 0.00 0.00 37.07 4.01
2407 2922 5.221441 GGTTTATTTGGTTGTTCCTTGCTCT 60.221 40.000 0.00 0.00 37.07 4.09
2568 3083 6.014647 AGGTTAAGTTTTCTATGTTTCCCCC 58.985 40.000 0.00 0.00 0.00 5.40
2577 3092 9.865321 GTTTTCTATGTTTCCCCCTTTTAATAC 57.135 33.333 0.00 0.00 0.00 1.89
2868 3383 1.069823 GGCGACATCACTCCATCTGAT 59.930 52.381 0.00 0.00 0.00 2.90
3105 3625 3.596214 TGAAGCCAATCTCGTAAAGGAC 58.404 45.455 0.00 0.00 0.00 3.85
3145 3665 7.765819 GCCTGCCATTATTTTCTTAACTTCATT 59.234 33.333 0.00 0.00 0.00 2.57
3187 3707 3.537580 TCTGCTTTCCTTTACACGTGTT 58.462 40.909 28.55 11.17 0.00 3.32
3188 3708 3.311322 TCTGCTTTCCTTTACACGTGTTG 59.689 43.478 28.55 16.60 0.00 3.33
3296 3822 6.855914 CGAAGCACTTGAAAGCATTTAAGTTA 59.144 34.615 8.89 0.00 39.27 2.24
3297 3823 7.538678 CGAAGCACTTGAAAGCATTTAAGTTAT 59.461 33.333 8.89 0.00 39.27 1.89
3327 3861 6.198966 CGGATTTTCTCCAAAAGTTTTGTCTG 59.801 38.462 23.29 14.60 45.24 3.51
3388 3931 6.476380 TCTGATGCACATTCTGTTTTGTTTTC 59.524 34.615 0.00 0.00 0.00 2.29
3389 3932 6.339730 TGATGCACATTCTGTTTTGTTTTCT 58.660 32.000 0.00 0.00 0.00 2.52
3390 3933 6.817641 TGATGCACATTCTGTTTTGTTTTCTT 59.182 30.769 0.00 0.00 0.00 2.52
3391 3934 7.333921 TGATGCACATTCTGTTTTGTTTTCTTT 59.666 29.630 0.00 0.00 0.00 2.52
3392 3935 6.829703 TGCACATTCTGTTTTGTTTTCTTTG 58.170 32.000 0.00 0.00 0.00 2.77
3393 3936 6.426328 TGCACATTCTGTTTTGTTTTCTTTGT 59.574 30.769 0.00 0.00 0.00 2.83
3394 3937 7.041508 TGCACATTCTGTTTTGTTTTCTTTGTT 60.042 29.630 0.00 0.00 0.00 2.83
3395 3938 7.802720 GCACATTCTGTTTTGTTTTCTTTGTTT 59.197 29.630 0.00 0.00 0.00 2.83
3396 3939 9.662545 CACATTCTGTTTTGTTTTCTTTGTTTT 57.337 25.926 0.00 0.00 0.00 2.43
3418 3961 2.435372 TGTTCTGTTTGGTCCAGCTT 57.565 45.000 0.00 0.00 0.00 3.74
3425 3968 5.324409 TCTGTTTGGTCCAGCTTATTTCAT 58.676 37.500 0.00 0.00 0.00 2.57
3598 4142 2.330254 CACGGTGTGCATTGGTTCT 58.670 52.632 0.00 0.00 0.00 3.01
3718 4262 9.863650 AAGTCTAGCTAAACTCATGTATACCTA 57.136 33.333 0.00 0.00 0.00 3.08
3739 4283 3.003480 AGCTTCGGCAAGAACATAGTTC 58.997 45.455 1.77 1.77 44.74 3.01
3866 4410 1.742268 GTTGCCATCTTCCTCTTCTGC 59.258 52.381 0.00 0.00 0.00 4.26
3867 4411 0.986527 TGCCATCTTCCTCTTCTGCA 59.013 50.000 0.00 0.00 0.00 4.41
3868 4412 1.339438 TGCCATCTTCCTCTTCTGCAC 60.339 52.381 0.00 0.00 0.00 4.57
3869 4413 1.339438 GCCATCTTCCTCTTCTGCACA 60.339 52.381 0.00 0.00 0.00 4.57
3870 4414 2.683152 GCCATCTTCCTCTTCTGCACAT 60.683 50.000 0.00 0.00 0.00 3.21
3871 4415 3.432749 GCCATCTTCCTCTTCTGCACATA 60.433 47.826 0.00 0.00 0.00 2.29
3872 4416 4.746089 GCCATCTTCCTCTTCTGCACATAT 60.746 45.833 0.00 0.00 0.00 1.78
3873 4417 4.755629 CCATCTTCCTCTTCTGCACATATG 59.244 45.833 0.00 0.00 0.00 1.78
3874 4418 5.366460 CATCTTCCTCTTCTGCACATATGT 58.634 41.667 1.41 1.41 0.00 2.29
3875 4419 6.463472 CCATCTTCCTCTTCTGCACATATGTA 60.463 42.308 8.32 0.00 0.00 2.29
3876 4420 6.544928 TCTTCCTCTTCTGCACATATGTAA 57.455 37.500 8.32 0.00 0.00 2.41
3877 4421 7.129457 TCTTCCTCTTCTGCACATATGTAAT 57.871 36.000 8.32 0.00 0.00 1.89
3878 4422 6.988580 TCTTCCTCTTCTGCACATATGTAATG 59.011 38.462 8.32 0.00 0.00 1.90
3879 4423 6.239217 TCCTCTTCTGCACATATGTAATGT 57.761 37.500 8.32 0.00 0.00 2.71
3880 4424 7.360113 TCCTCTTCTGCACATATGTAATGTA 57.640 36.000 8.32 0.00 0.00 2.29
3881 4425 7.210174 TCCTCTTCTGCACATATGTAATGTAC 58.790 38.462 8.32 0.00 0.00 2.90
3882 4426 7.069950 TCCTCTTCTGCACATATGTAATGTACT 59.930 37.037 8.32 0.00 0.00 2.73
3883 4427 7.170489 CCTCTTCTGCACATATGTAATGTACTG 59.830 40.741 8.32 0.00 0.00 2.74
3884 4428 7.781056 TCTTCTGCACATATGTAATGTACTGA 58.219 34.615 8.32 1.74 0.00 3.41
3885 4429 8.424133 TCTTCTGCACATATGTAATGTACTGAT 58.576 33.333 8.32 0.00 0.00 2.90
3886 4430 8.593492 TTCTGCACATATGTAATGTACTGATC 57.407 34.615 8.32 0.00 0.00 2.92
3957 4522 5.034152 GTGCTAGATGAGTTCTTTCTCTCG 58.966 45.833 0.00 0.00 35.79 4.04
3984 4549 4.398988 GCTGGTAATGTGATTGATCAACCA 59.601 41.667 11.07 3.74 40.04 3.67
4007 4572 8.943002 ACCATATAGACCGTAAAAAGTTGAAAG 58.057 33.333 0.00 0.00 0.00 2.62
4013 4578 5.716094 ACCGTAAAAAGTTGAAAGTGCTTT 58.284 33.333 0.00 0.00 34.35 3.51
4161 4726 5.529581 TGATGTTTGGTGCTCGATATAGA 57.470 39.130 0.00 0.00 0.00 1.98
4192 4759 1.139498 TCATGATGGGGTGGTGTGGT 61.139 55.000 0.00 0.00 0.00 4.16
4225 4792 1.089920 CAGATTCAAGCCCACTTCGG 58.910 55.000 0.00 0.00 32.29 4.30
4257 4824 3.700538 ACCAATTTGCCTCAGCTATCAA 58.299 40.909 0.00 0.00 40.80 2.57
4285 4852 3.054287 TGGTAAGGAATAACGGAATGGCA 60.054 43.478 0.00 0.00 0.00 4.92
4287 4854 4.583073 GGTAAGGAATAACGGAATGGCATT 59.417 41.667 13.54 13.54 0.00 3.56
4291 4858 3.548014 GGAATAACGGAATGGCATTGACG 60.548 47.826 19.07 22.14 0.00 4.35
4370 4942 9.979578 GAGACTAGTAGTATGTAGTAAGCAGTA 57.020 37.037 1.27 0.00 29.34 2.74
4407 4979 4.955335 TGGTTAGGAACTTAGATCCAGGA 58.045 43.478 11.11 0.00 41.75 3.86
4447 5022 3.173151 CAGGAAATAAAAAGGCTGGGGT 58.827 45.455 0.00 0.00 0.00 4.95
4454 5029 0.185175 AAAAGGCTGGGGTCGTTCTT 59.815 50.000 0.00 0.00 0.00 2.52
4457 5032 1.201429 AGGCTGGGGTCGTTCTTGAT 61.201 55.000 0.00 0.00 0.00 2.57
4476 5051 2.046217 GCCACCTTCCTTCGGTCC 60.046 66.667 0.00 0.00 30.82 4.46
4479 5054 0.109723 CCACCTTCCTTCGGTCCAAA 59.890 55.000 0.00 0.00 30.82 3.28
4494 5069 6.516718 TCGGTCCAAATTGATCTCTCTTATC 58.483 40.000 0.00 0.00 0.00 1.75
4501 5076 4.844998 TTGATCTCTCTTATCGCTCTGG 57.155 45.455 0.00 0.00 0.00 3.86
4502 5077 2.556189 TGATCTCTCTTATCGCTCTGGC 59.444 50.000 0.00 0.00 0.00 4.85
4504 5079 1.035923 CTCTCTTATCGCTCTGGCCA 58.964 55.000 4.71 4.71 34.44 5.36
4519 5098 3.582647 TCTGGCCAAGTCATTTCACTCTA 59.417 43.478 7.01 0.00 0.00 2.43
4529 5108 9.573133 CAAGTCATTTCACTCTAAACTTTTTGT 57.427 29.630 0.00 0.00 0.00 2.83
4530 5109 9.573133 AAGTCATTTCACTCTAAACTTTTTGTG 57.427 29.630 0.00 0.00 0.00 3.33
4534 5113 9.520204 CATTTCACTCTAAACTTTTTGTGTGAT 57.480 29.630 16.29 5.73 41.83 3.06
4605 5198 7.118723 ACCAATACAAGCTCATGAAAGGAATA 58.881 34.615 0.00 0.00 0.00 1.75
4729 5328 7.435192 AGAAATTCCAACTCAAAAACGAATGAC 59.565 33.333 0.00 0.00 0.00 3.06
4734 5333 6.033341 CCAACTCAAAAACGAATGACTTTGA 58.967 36.000 0.00 0.00 36.59 2.69
4751 5350 3.857157 TTGACTAAAAGCTCCCACAGT 57.143 42.857 0.00 0.00 0.00 3.55
4765 5364 1.471676 CCACAGTCGCCTTCATAGTCC 60.472 57.143 0.00 0.00 0.00 3.85
4768 5367 1.204704 CAGTCGCCTTCATAGTCCACA 59.795 52.381 0.00 0.00 0.00 4.17
4770 5369 0.824109 TCGCCTTCATAGTCCACAGG 59.176 55.000 0.00 0.00 0.00 4.00
4808 5581 0.392998 ATGCACATCACGGAAGGACC 60.393 55.000 0.00 0.00 0.00 4.46
4867 5640 6.257586 AGTCTAGGACTTGAACTCTGGTAAT 58.742 40.000 0.00 0.00 40.28 1.89
4868 5641 6.378848 AGTCTAGGACTTGAACTCTGGTAATC 59.621 42.308 0.00 0.00 40.28 1.75
4869 5642 6.153000 GTCTAGGACTTGAACTCTGGTAATCA 59.847 42.308 0.00 0.00 0.00 2.57
4870 5643 5.153950 AGGACTTGAACTCTGGTAATCAC 57.846 43.478 0.00 0.00 0.00 3.06
4873 5646 5.279506 GGACTTGAACTCTGGTAATCACAGA 60.280 44.000 0.00 0.00 42.31 3.41
4875 5648 6.773638 ACTTGAACTCTGGTAATCACAGATT 58.226 36.000 0.00 0.00 43.43 2.40
4877 5650 5.491070 TGAACTCTGGTAATCACAGATTGG 58.509 41.667 2.65 0.00 43.43 3.16
4878 5651 5.013079 TGAACTCTGGTAATCACAGATTGGT 59.987 40.000 2.65 0.00 43.43 3.67
4889 5705 5.598416 TCACAGATTGGTCATAGTGTAGG 57.402 43.478 0.00 0.00 0.00 3.18
4933 5749 7.116376 ACAAGAGATGAATTACACAACAGTACG 59.884 37.037 0.00 0.00 0.00 3.67
4960 5776 1.401931 CCGCTTTTCACTTCATGCCAG 60.402 52.381 0.00 0.00 0.00 4.85
5006 5822 5.970317 TGACTAAGTTCTACAATCACGGA 57.030 39.130 0.00 0.00 0.00 4.69
5011 5827 7.889469 ACTAAGTTCTACAATCACGGAGTAAA 58.111 34.615 0.00 0.00 41.61 2.01
5059 5875 4.179298 GCTATCATCAGCTCAATATCGCA 58.821 43.478 0.00 0.00 38.57 5.10
5097 5915 1.878088 CAAGTCACTCACAAGCTGCAT 59.122 47.619 1.02 0.00 0.00 3.96
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 3.101643 TGTAGCTATGAGTCTGGGTGT 57.898 47.619 0.00 0.00 0.00 4.16
1 2 4.141846 ACATTGTAGCTATGAGTCTGGGTG 60.142 45.833 0.00 0.00 0.00 4.61
2 3 4.033709 ACATTGTAGCTATGAGTCTGGGT 58.966 43.478 0.00 0.00 0.00 4.51
3 4 4.502259 GGACATTGTAGCTATGAGTCTGGG 60.502 50.000 0.00 0.00 0.00 4.45
18 19 7.591821 ACCCTTATATTTGGTATGGACATTGT 58.408 34.615 0.00 0.00 0.00 2.71
29 30 9.762381 TTGTCATCTTAAACCCTTATATTTGGT 57.238 29.630 0.00 0.00 0.00 3.67
39 44 7.595819 TTTGTTGATTGTCATCTTAAACCCT 57.404 32.000 0.00 0.00 0.00 4.34
83 88 7.565680 AGATCACCTTAATAGTAACCAAGTGG 58.434 38.462 0.00 0.00 42.17 4.00
194 211 6.794374 TGTTTGCTTATGTATTATGTGCCTG 58.206 36.000 0.00 0.00 0.00 4.85
280 304 2.221981 GTGCGCATTAGCTCATAACCTC 59.778 50.000 15.91 0.00 37.85 3.85
282 306 1.939934 TGTGCGCATTAGCTCATAACC 59.060 47.619 15.91 0.00 37.85 2.85
283 307 3.673746 TTGTGCGCATTAGCTCATAAC 57.326 42.857 15.91 0.00 37.85 1.89
284 308 4.411327 GTTTTGTGCGCATTAGCTCATAA 58.589 39.130 15.91 4.19 37.85 1.90
285 309 3.181501 GGTTTTGTGCGCATTAGCTCATA 60.182 43.478 15.91 0.00 37.85 2.15
298 322 6.670077 TTGGTTAAAATCTTGGTTTTGTGC 57.330 33.333 2.22 0.00 33.62 4.57
355 381 4.769688 TGGATTCGTAGCACTTTCATCAT 58.230 39.130 0.00 0.00 0.00 2.45
378 404 3.057596 TCATTTGGTTGACATTTCTCCGC 60.058 43.478 0.00 0.00 0.00 5.54
422 448 0.900647 CCTCACCTCTCCACCGAGTT 60.901 60.000 0.00 0.00 37.40 3.01
424 450 1.304547 ACCTCACCTCTCCACCGAG 60.305 63.158 0.00 0.00 37.48 4.63
428 454 1.674057 CCACACCTCACCTCTCCAC 59.326 63.158 0.00 0.00 0.00 4.02
429 455 1.536418 CCCACACCTCACCTCTCCA 60.536 63.158 0.00 0.00 0.00 3.86
493 557 1.591768 GGTGGATAAGGTTGGGAGGA 58.408 55.000 0.00 0.00 0.00 3.71
517 581 1.561542 CAGGGTCCTGATTGTAGGCTT 59.438 52.381 11.39 0.00 46.30 4.35
532 615 3.377253 TCTAACACCTATCGTCAGGGT 57.623 47.619 9.38 2.87 40.29 4.34
538 624 3.635836 GGTAGGCTTCTAACACCTATCGT 59.364 47.826 0.00 0.00 38.30 3.73
563 649 2.281091 CTACCGCCAGGGACCCTA 59.719 66.667 14.38 0.00 43.47 3.53
599 686 2.570365 TAACGGCCGTTAGCTCTGA 58.430 52.632 39.67 23.11 43.05 3.27
724 817 7.451731 TGTCTTATTTAAGGATCTGACCCAT 57.548 36.000 0.00 0.00 34.14 4.00
749 842 6.799441 GGCAAAATTTCGTGTTTTGACTTTTT 59.201 30.769 19.19 0.00 46.24 1.94
776 872 1.938016 GCCGTCCGTGTTGTCACTAAT 60.938 52.381 0.00 0.00 41.89 1.73
777 873 0.598158 GCCGTCCGTGTTGTCACTAA 60.598 55.000 0.00 0.00 41.89 2.24
778 874 1.007038 GCCGTCCGTGTTGTCACTA 60.007 57.895 0.00 0.00 41.89 2.74
1266 1362 3.818787 GGAGCAAGCATGGCGTGG 61.819 66.667 9.08 0.00 42.81 4.94
1305 1401 7.450014 AGGAGTATCACTAATCTGATGGTACAG 59.550 40.741 0.00 0.00 38.84 2.74
1318 1414 5.222089 GGCTAGGACCTAGGAGTATCACTAA 60.222 48.000 26.58 0.00 36.25 2.24
1352 1448 9.914834 AGCAAAGGTGTATCAAAATTATAGGTA 57.085 29.630 0.00 0.00 0.00 3.08
1353 1449 8.823220 AGCAAAGGTGTATCAAAATTATAGGT 57.177 30.769 0.00 0.00 0.00 3.08
1369 1465 5.689383 TTTAGCTCAAGTTAGCAAAGGTG 57.311 39.130 0.00 0.00 45.30 4.00
1371 1467 6.456988 CGGTATTTAGCTCAAGTTAGCAAAGG 60.457 42.308 0.00 0.00 45.30 3.11
1526 1622 8.860088 TCATGCACTACACATCATATACTACTT 58.140 33.333 0.00 0.00 0.00 2.24
1527 1623 8.409358 TCATGCACTACACATCATATACTACT 57.591 34.615 0.00 0.00 0.00 2.57
1528 1624 8.916654 GTTCATGCACTACACATCATATACTAC 58.083 37.037 0.00 0.00 0.00 2.73
1529 1625 8.637986 TGTTCATGCACTACACATCATATACTA 58.362 33.333 0.00 0.00 0.00 1.82
1593 1689 3.172339 GGATAGGTGATCTGCTGGAGAT 58.828 50.000 11.72 11.72 44.78 2.75
1641 1752 5.126779 GGGATCTGTTGGAGGAAGAAATAC 58.873 45.833 0.00 0.00 0.00 1.89
1694 1805 1.290955 GGTTTTTAGTTGGCCGCCC 59.709 57.895 7.03 0.00 0.00 6.13
1822 1960 1.908340 GAGCTCTGGTGGTGGCAGAT 61.908 60.000 6.43 0.00 0.00 2.90
1835 1973 2.118513 AGTGGTGGACGGAGCTCT 59.881 61.111 14.64 0.00 0.00 4.09
1850 1988 1.997874 GAGGAGGGGATGGTGCAGT 60.998 63.158 0.00 0.00 0.00 4.40
1892 2030 3.050275 GACAGAAGGCGGTGCACC 61.050 66.667 26.78 26.78 0.00 5.01
1894 2032 4.329545 GGGACAGAAGGCGGTGCA 62.330 66.667 0.00 0.00 32.52 4.57
1897 2035 3.003763 GAGGGGACAGAAGGCGGT 61.004 66.667 0.00 0.00 0.00 5.68
1927 2065 0.859232 CGCACACATTACGGATAGGC 59.141 55.000 0.00 0.00 0.00 3.93
1969 2107 6.462500 CCATAATAGCACATGAAGTAGCTCT 58.538 40.000 0.00 0.00 36.47 4.09
1979 2117 3.079578 CAGGGAGCCATAATAGCACATG 58.920 50.000 0.00 0.00 0.00 3.21
1980 2118 2.713167 ACAGGGAGCCATAATAGCACAT 59.287 45.455 0.00 0.00 0.00 3.21
1987 2125 0.328450 TGGGGACAGGGAGCCATAAT 60.328 55.000 0.00 0.00 35.01 1.28
1988 2126 1.083895 TGGGGACAGGGAGCCATAA 59.916 57.895 0.00 0.00 35.01 1.90
1989 2127 1.692749 GTGGGGACAGGGAGCCATA 60.693 63.158 0.00 0.00 44.46 2.74
1999 2137 3.948719 GGAGGCAACGTGGGGACA 61.949 66.667 0.00 0.00 46.39 4.02
2007 2145 4.760047 CGTGGAGGGGAGGCAACG 62.760 72.222 0.00 0.00 46.39 4.10
2117 2255 1.675641 GGTTGTCCATCGCCTTGCT 60.676 57.895 0.00 0.00 0.00 3.91
2155 2293 2.561209 TCCTACCCACTCCATTAGCA 57.439 50.000 0.00 0.00 0.00 3.49
2159 2297 9.951866 ATTATTATTTTTCCTACCCACTCCATT 57.048 29.630 0.00 0.00 0.00 3.16
2187 2325 1.351017 ACACTTACATGTCAGGGGGTG 59.649 52.381 13.71 11.22 0.00 4.61
2188 2326 1.351017 CACACTTACATGTCAGGGGGT 59.649 52.381 13.71 5.10 0.00 4.95
2248 2386 2.542020 TTTGTGCATCTCCTCGAACA 57.458 45.000 0.00 0.00 0.00 3.18
2249 2387 3.896648 TTTTTGTGCATCTCCTCGAAC 57.103 42.857 0.00 0.00 0.00 3.95
2271 2409 1.628846 TCCCTCTGTTCAGGTAAAGCC 59.371 52.381 0.00 0.00 37.58 4.35
2272 2410 2.937433 GCTCCCTCTGTTCAGGTAAAGC 60.937 54.545 0.00 2.27 0.00 3.51
2273 2411 2.355209 GGCTCCCTCTGTTCAGGTAAAG 60.355 54.545 0.00 0.00 0.00 1.85
2274 2412 1.628846 GGCTCCCTCTGTTCAGGTAAA 59.371 52.381 0.00 0.00 0.00 2.01
2275 2413 1.276622 GGCTCCCTCTGTTCAGGTAA 58.723 55.000 0.00 0.00 0.00 2.85
2276 2414 0.617820 GGGCTCCCTCTGTTCAGGTA 60.618 60.000 0.00 0.00 0.00 3.08
2277 2415 1.920835 GGGCTCCCTCTGTTCAGGT 60.921 63.158 0.00 0.00 0.00 4.00
2278 2416 2.674220 GGGGCTCCCTCTGTTCAGG 61.674 68.421 4.74 0.00 41.34 3.86
2279 2417 1.492133 TTGGGGCTCCCTCTGTTCAG 61.492 60.000 0.00 0.00 45.70 3.02
2280 2418 1.065410 TTTGGGGCTCCCTCTGTTCA 61.065 55.000 0.00 0.00 45.70 3.18
2281 2419 0.322906 CTTTGGGGCTCCCTCTGTTC 60.323 60.000 0.00 0.00 45.70 3.18
2282 2420 1.068352 ACTTTGGGGCTCCCTCTGTT 61.068 55.000 0.00 0.00 45.70 3.16
2283 2421 1.464198 ACTTTGGGGCTCCCTCTGT 60.464 57.895 0.00 0.00 45.70 3.41
2284 2422 1.001641 CACTTTGGGGCTCCCTCTG 60.002 63.158 0.00 0.00 45.70 3.35
2285 2423 0.772124 TTCACTTTGGGGCTCCCTCT 60.772 55.000 0.00 0.00 45.70 3.69
2286 2424 0.332972 ATTCACTTTGGGGCTCCCTC 59.667 55.000 0.00 0.00 45.70 4.30
2287 2425 0.786435 AATTCACTTTGGGGCTCCCT 59.214 50.000 0.00 0.00 45.70 4.20
2288 2426 1.644509 AAATTCACTTTGGGGCTCCC 58.355 50.000 0.00 0.72 45.71 4.30
2289 2427 3.769739 AAAAATTCACTTTGGGGCTCC 57.230 42.857 0.00 0.00 0.00 4.70
2290 2428 5.722021 TCTAAAAATTCACTTTGGGGCTC 57.278 39.130 0.00 0.00 0.00 4.70
2291 2429 6.464322 CCTTTCTAAAAATTCACTTTGGGGCT 60.464 38.462 0.00 0.00 0.00 5.19
2292 2430 5.700832 CCTTTCTAAAAATTCACTTTGGGGC 59.299 40.000 0.00 0.00 0.00 5.80
2293 2431 6.230472 CCCTTTCTAAAAATTCACTTTGGGG 58.770 40.000 0.00 0.00 0.00 4.96
2294 2432 6.183361 ACCCCTTTCTAAAAATTCACTTTGGG 60.183 38.462 0.00 0.00 0.00 4.12
2295 2433 6.705825 CACCCCTTTCTAAAAATTCACTTTGG 59.294 38.462 0.00 0.00 0.00 3.28
2296 2434 6.705825 CCACCCCTTTCTAAAAATTCACTTTG 59.294 38.462 0.00 0.00 0.00 2.77
2297 2435 6.183361 CCCACCCCTTTCTAAAAATTCACTTT 60.183 38.462 0.00 0.00 0.00 2.66
2298 2436 5.306937 CCCACCCCTTTCTAAAAATTCACTT 59.693 40.000 0.00 0.00 0.00 3.16
2299 2437 4.838423 CCCACCCCTTTCTAAAAATTCACT 59.162 41.667 0.00 0.00 0.00 3.41
2300 2438 4.020573 CCCCACCCCTTTCTAAAAATTCAC 60.021 45.833 0.00 0.00 0.00 3.18
2301 2439 4.164204 CCCCACCCCTTTCTAAAAATTCA 58.836 43.478 0.00 0.00 0.00 2.57
2302 2440 4.020573 CACCCCACCCCTTTCTAAAAATTC 60.021 45.833 0.00 0.00 0.00 2.17
2303 2441 3.907474 CACCCCACCCCTTTCTAAAAATT 59.093 43.478 0.00 0.00 0.00 1.82
2304 2442 3.516586 CACCCCACCCCTTTCTAAAAAT 58.483 45.455 0.00 0.00 0.00 1.82
2305 2443 2.426561 CCACCCCACCCCTTTCTAAAAA 60.427 50.000 0.00 0.00 0.00 1.94
2306 2444 1.148236 CCACCCCACCCCTTTCTAAAA 59.852 52.381 0.00 0.00 0.00 1.52
2307 2445 0.781278 CCACCCCACCCCTTTCTAAA 59.219 55.000 0.00 0.00 0.00 1.85
2308 2446 1.143970 CCCACCCCACCCCTTTCTAA 61.144 60.000 0.00 0.00 0.00 2.10
2309 2447 1.542881 CCCACCCCACCCCTTTCTA 60.543 63.158 0.00 0.00 0.00 2.10
2310 2448 2.863988 CCCACCCCACCCCTTTCT 60.864 66.667 0.00 0.00 0.00 2.52
2311 2449 3.992641 CCCCACCCCACCCCTTTC 61.993 72.222 0.00 0.00 0.00 2.62
2312 2450 4.895675 ACCCCACCCCACCCCTTT 62.896 66.667 0.00 0.00 0.00 3.11
2318 2456 2.882403 AAAACACCACCCCACCCCAC 62.882 60.000 0.00 0.00 0.00 4.61
2319 2457 2.182858 AAAAACACCACCCCACCCCA 62.183 55.000 0.00 0.00 0.00 4.96
2320 2458 0.105607 TAAAAACACCACCCCACCCC 60.106 55.000 0.00 0.00 0.00 4.95
2321 2459 1.334160 CTAAAAACACCACCCCACCC 58.666 55.000 0.00 0.00 0.00 4.61
2322 2460 1.334160 CCTAAAAACACCACCCCACC 58.666 55.000 0.00 0.00 0.00 4.61
2323 2461 1.133419 TCCCTAAAAACACCACCCCAC 60.133 52.381 0.00 0.00 0.00 4.61
2324 2462 1.232909 TCCCTAAAAACACCACCCCA 58.767 50.000 0.00 0.00 0.00 4.96
2325 2463 2.042569 AGATCCCTAAAAACACCACCCC 59.957 50.000 0.00 0.00 0.00 4.95
2326 2464 3.089284 CAGATCCCTAAAAACACCACCC 58.911 50.000 0.00 0.00 0.00 4.61
2327 2465 2.492088 GCAGATCCCTAAAAACACCACC 59.508 50.000 0.00 0.00 0.00 4.61
2328 2466 3.191371 CAGCAGATCCCTAAAAACACCAC 59.809 47.826 0.00 0.00 0.00 4.16
2329 2467 3.420893 CAGCAGATCCCTAAAAACACCA 58.579 45.455 0.00 0.00 0.00 4.17
2330 2468 2.755103 CCAGCAGATCCCTAAAAACACC 59.245 50.000 0.00 0.00 0.00 4.16
2331 2469 3.686016 TCCAGCAGATCCCTAAAAACAC 58.314 45.455 0.00 0.00 0.00 3.32
2332 2470 3.587061 TCTCCAGCAGATCCCTAAAAACA 59.413 43.478 0.00 0.00 0.00 2.83
2333 2471 4.222124 TCTCCAGCAGATCCCTAAAAAC 57.778 45.455 0.00 0.00 0.00 2.43
2334 2472 4.385643 CCATCTCCAGCAGATCCCTAAAAA 60.386 45.833 0.00 0.00 40.20 1.94
2335 2473 3.137176 CCATCTCCAGCAGATCCCTAAAA 59.863 47.826 0.00 0.00 40.20 1.52
2404 2919 1.895798 TGGTCTGTGGTAAGAGCAGAG 59.104 52.381 2.16 0.00 46.77 3.35
2901 3416 6.307318 CACACATTTCATTTAGAGCTTCTTGC 59.693 38.462 0.00 0.00 43.29 4.01
3015 3530 6.984474 CCTCAGCTAGAAAACGGTCAATTATA 59.016 38.462 0.00 0.00 0.00 0.98
3024 3539 6.183360 CCTTAATTTCCTCAGCTAGAAAACGG 60.183 42.308 9.12 5.13 35.72 4.44
3025 3540 6.183360 CCCTTAATTTCCTCAGCTAGAAAACG 60.183 42.308 9.12 0.00 35.72 3.60
3105 3625 5.841957 ATGGCAGGCTTACTTTATCAAAG 57.158 39.130 0.00 0.00 44.10 2.77
3308 3834 5.126869 TGCATCAGACAAAACTTTTGGAGAA 59.873 36.000 16.79 2.70 0.00 2.87
3309 3835 4.644234 TGCATCAGACAAAACTTTTGGAGA 59.356 37.500 16.79 11.71 0.00 3.71
3388 3931 7.547370 TGGACCAAACAGAACATAAAAACAAAG 59.453 33.333 0.00 0.00 0.00 2.77
3389 3932 7.386851 TGGACCAAACAGAACATAAAAACAAA 58.613 30.769 0.00 0.00 0.00 2.83
3390 3933 6.936279 TGGACCAAACAGAACATAAAAACAA 58.064 32.000 0.00 0.00 0.00 2.83
3391 3934 6.531503 TGGACCAAACAGAACATAAAAACA 57.468 33.333 0.00 0.00 0.00 2.83
3392 3935 5.462068 GCTGGACCAAACAGAACATAAAAAC 59.538 40.000 0.00 0.00 38.20 2.43
3393 3936 5.362430 AGCTGGACCAAACAGAACATAAAAA 59.638 36.000 0.00 0.00 38.20 1.94
3394 3937 4.892934 AGCTGGACCAAACAGAACATAAAA 59.107 37.500 0.00 0.00 38.20 1.52
3395 3938 4.469657 AGCTGGACCAAACAGAACATAAA 58.530 39.130 0.00 0.00 38.20 1.40
3396 3939 4.098914 AGCTGGACCAAACAGAACATAA 57.901 40.909 0.00 0.00 38.20 1.90
3559 4103 4.219944 GTGCCAGAGTTCGTATATATGGGA 59.780 45.833 2.10 0.00 0.00 4.37
3563 4107 3.825014 ACCGTGCCAGAGTTCGTATATAT 59.175 43.478 0.00 0.00 0.00 0.86
3564 4108 3.004002 CACCGTGCCAGAGTTCGTATATA 59.996 47.826 0.00 0.00 0.00 0.86
3598 4142 4.479158 AGGGCAGGTTGTTTCAGAATAAA 58.521 39.130 0.00 0.00 0.00 1.40
3701 4245 6.516194 GCCGAAGCTAGGTATACATGAGTTTA 60.516 42.308 5.01 0.00 35.50 2.01
3718 4262 2.770164 ACTATGTTCTTGCCGAAGCT 57.230 45.000 0.00 0.00 40.80 3.74
3739 4283 3.745975 TCAACAAGGTAGCAACAGATTCG 59.254 43.478 0.00 0.00 0.00 3.34
3871 4415 9.006839 CAGCATAAATGGATCAGTACATTACAT 57.993 33.333 0.00 0.00 37.93 2.29
3872 4416 8.210265 TCAGCATAAATGGATCAGTACATTACA 58.790 33.333 0.00 0.00 37.93 2.41
3873 4417 8.499162 GTCAGCATAAATGGATCAGTACATTAC 58.501 37.037 0.00 0.00 37.93 1.89
3874 4418 8.432013 AGTCAGCATAAATGGATCAGTACATTA 58.568 33.333 0.00 0.00 37.93 1.90
3875 4419 7.285566 AGTCAGCATAAATGGATCAGTACATT 58.714 34.615 0.00 0.00 40.70 2.71
3876 4420 6.835174 AGTCAGCATAAATGGATCAGTACAT 58.165 36.000 0.00 0.00 0.00 2.29
3877 4421 6.098838 AGAGTCAGCATAAATGGATCAGTACA 59.901 38.462 0.00 0.00 0.00 2.90
3878 4422 6.423302 CAGAGTCAGCATAAATGGATCAGTAC 59.577 42.308 0.00 0.00 0.00 2.73
3879 4423 6.519382 CAGAGTCAGCATAAATGGATCAGTA 58.481 40.000 0.00 0.00 0.00 2.74
3880 4424 5.366460 CAGAGTCAGCATAAATGGATCAGT 58.634 41.667 0.00 0.00 0.00 3.41
3881 4425 4.213694 GCAGAGTCAGCATAAATGGATCAG 59.786 45.833 2.12 0.00 0.00 2.90
3882 4426 4.132336 GCAGAGTCAGCATAAATGGATCA 58.868 43.478 2.12 0.00 0.00 2.92
3883 4427 4.024218 GTGCAGAGTCAGCATAAATGGATC 60.024 45.833 13.75 0.00 44.79 3.36
3884 4428 3.881688 GTGCAGAGTCAGCATAAATGGAT 59.118 43.478 13.75 0.00 44.79 3.41
3885 4429 3.273434 GTGCAGAGTCAGCATAAATGGA 58.727 45.455 13.75 0.00 44.79 3.41
3886 4430 3.011818 TGTGCAGAGTCAGCATAAATGG 58.988 45.455 13.75 0.00 44.79 3.16
3957 4522 4.877823 TGATCAATCACATTACCAGCAGTC 59.122 41.667 0.00 0.00 0.00 3.51
3984 4549 8.448615 GCACTTTCAACTTTTTACGGTCTATAT 58.551 33.333 0.00 0.00 0.00 0.86
4257 4824 3.583966 TCCGTTATTCCTTACCAACACCT 59.416 43.478 0.00 0.00 0.00 4.00
4285 4852 2.236395 AGATCCCCGAGTTTTCGTCAAT 59.764 45.455 0.00 0.00 45.28 2.57
4287 4854 1.263356 AGATCCCCGAGTTTTCGTCA 58.737 50.000 0.00 0.00 45.28 4.35
4291 4858 5.417894 ACCAAATTTAGATCCCCGAGTTTTC 59.582 40.000 0.00 0.00 0.00 2.29
4370 4942 7.834181 AGTTCCTAACCAACAGCATACATAAAT 59.166 33.333 0.00 0.00 0.00 1.40
4407 4979 4.216687 TCCTGACTCAACAAAAACGTGTTT 59.783 37.500 0.00 0.00 39.73 2.83
4447 5022 2.151202 GAAGGTGGCAATCAAGAACGA 58.849 47.619 0.00 0.00 0.00 3.85
4454 5029 3.248043 CGAAGGAAGGTGGCAATCA 57.752 52.632 0.00 0.00 0.00 2.57
4476 5051 6.145858 CCAGAGCGATAAGAGAGATCAATTTG 59.854 42.308 0.00 0.00 0.00 2.32
4479 5054 4.321899 GCCAGAGCGATAAGAGAGATCAAT 60.322 45.833 0.00 0.00 0.00 2.57
4494 5069 0.449388 GAAATGACTTGGCCAGAGCG 59.551 55.000 5.11 0.00 41.24 5.03
4501 5076 5.948992 AGTTTAGAGTGAAATGACTTGGC 57.051 39.130 0.00 0.00 0.00 4.52
4502 5077 9.023967 CAAAAAGTTTAGAGTGAAATGACTTGG 57.976 33.333 0.00 0.00 0.00 3.61
4504 5079 9.573133 CACAAAAAGTTTAGAGTGAAATGACTT 57.427 29.630 8.51 0.00 0.00 3.01
4519 5098 4.050553 CGCATCCATCACACAAAAAGTTT 58.949 39.130 0.00 0.00 0.00 2.66
4529 5108 1.473788 CCATCAGACGCATCCATCACA 60.474 52.381 0.00 0.00 0.00 3.58
4530 5109 1.202568 TCCATCAGACGCATCCATCAC 60.203 52.381 0.00 0.00 0.00 3.06
4534 5113 0.176449 CACTCCATCAGACGCATCCA 59.824 55.000 0.00 0.00 0.00 3.41
4605 5198 3.118884 GCCCACTTCTGCAAATCATGATT 60.119 43.478 15.36 15.36 0.00 2.57
4703 5302 7.435192 GTCATTCGTTTTTGAGTTGGAATTTCT 59.565 33.333 0.00 0.00 0.00 2.52
4722 5321 5.390991 GGGAGCTTTTAGTCAAAGTCATTCG 60.391 44.000 0.00 0.00 43.62 3.34
4729 5328 4.137543 ACTGTGGGAGCTTTTAGTCAAAG 58.862 43.478 0.00 0.00 44.44 2.77
4734 5333 1.608283 GCGACTGTGGGAGCTTTTAGT 60.608 52.381 0.00 0.00 0.00 2.24
4745 5344 1.471676 GGACTATGAAGGCGACTGTGG 60.472 57.143 0.00 0.00 42.68 4.17
4751 5350 0.824109 CCTGTGGACTATGAAGGCGA 59.176 55.000 0.00 0.00 0.00 5.54
4770 5369 0.966920 TTCAGTGGGAGGAGACGTTC 59.033 55.000 0.00 0.00 0.00 3.95
4863 5636 7.653713 CCTACACTATGACCAATCTGTGATTAC 59.346 40.741 0.00 0.00 0.00 1.89
4867 5640 5.023452 ACCTACACTATGACCAATCTGTGA 58.977 41.667 0.00 0.00 0.00 3.58
4868 5641 5.105351 TCACCTACACTATGACCAATCTGTG 60.105 44.000 0.00 0.00 0.00 3.66
4869 5642 5.023452 TCACCTACACTATGACCAATCTGT 58.977 41.667 0.00 0.00 0.00 3.41
4870 5643 5.598416 TCACCTACACTATGACCAATCTG 57.402 43.478 0.00 0.00 0.00 2.90
4873 5646 7.676683 AGTATTCACCTACACTATGACCAAT 57.323 36.000 0.00 0.00 0.00 3.16
4875 5648 8.638873 CAATAGTATTCACCTACACTATGACCA 58.361 37.037 0.00 0.00 35.06 4.02
4877 5650 8.639761 ACCAATAGTATTCACCTACACTATGAC 58.360 37.037 0.00 0.00 35.06 3.06
4878 5651 8.777578 ACCAATAGTATTCACCTACACTATGA 57.222 34.615 0.00 0.00 35.06 2.15
4889 5705 7.103641 TCTCTTGTGGAACCAATAGTATTCAC 58.896 38.462 0.00 0.00 34.36 3.18
4933 5749 2.612212 TGAAGTGAAAAGCGGAAGTGAC 59.388 45.455 0.00 0.00 0.00 3.67
5097 5915 9.956720 CAAGAGATTTCTTTTTCTTAGCAAAGA 57.043 29.630 0.00 3.34 41.71 2.52


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

AutoCloner maintained by Alex Coulton.