Multiple sequence alignment - TraesCS5B01G490300

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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 TraesCS5B01G490300 chr5B 100.000 2489 0 0 1 2489 659550497 659548009 0.000000e+00 4597.0
1 TraesCS5B01G490300 chr5B 90.710 775 53 8 774 1534 659523444 659522675 0.000000e+00 1014.0
2 TraesCS5B01G490300 chr5B 90.444 743 60 3 828 1563 659506330 659505592 0.000000e+00 968.0
3 TraesCS5B01G490300 chr5B 80.299 670 53 37 139 763 659532474 659531839 1.370000e-117 433.0
4 TraesCS5B01G490300 chr5B 82.150 493 62 20 37 521 659507361 659506887 1.390000e-107 399.0
5 TraesCS5B01G490300 chr5B 92.607 257 8 4 556 807 659506884 659506634 2.350000e-95 359.0
6 TraesCS5B01G490300 chr5B 82.045 401 49 13 1138 1534 659471590 659471209 1.110000e-83 320.0
7 TraesCS5B01G490300 chr5B 79.481 424 63 17 1000 1417 659704430 659704835 1.890000e-71 279.0
8 TraesCS5B01G490300 chr5B 85.876 177 17 5 2270 2442 659521849 659521677 5.470000e-42 182.0
9 TraesCS5B01G490300 chr5B 91.379 58 3 2 2005 2062 659521992 659521937 7.380000e-11 78.7
10 TraesCS5B01G490300 chr5A 91.130 1567 88 23 111 1657 651541587 651540052 0.000000e+00 2076.0
11 TraesCS5B01G490300 chr5A 85.675 1445 102 44 267 1674 651529109 651527733 0.000000e+00 1424.0
12 TraesCS5B01G490300 chr5A 84.821 112 8 6 2218 2328 651539462 651539359 1.220000e-18 104.0
13 TraesCS5B01G490300 chr5D 90.594 1297 72 17 289 1568 525127273 525126010 0.000000e+00 1674.0
14 TraesCS5B01G490300 chr5D 85.846 1519 109 55 38 1534 525178431 525176997 0.000000e+00 1517.0
15 TraesCS5B01G490300 chr5D 82.090 402 47 15 1138 1534 525086305 525085924 1.110000e-83 320.0
16 TraesCS5B01G490300 chr5D 86.139 101 8 3 2227 2327 525123449 525123355 1.220000e-18 104.0
17 TraesCS5B01G490300 chr5D 82.540 126 15 6 1800 1921 525176848 525176726 1.220000e-18 104.0
18 TraesCS5B01G490300 chr5D 95.833 48 2 0 2442 2489 525176437 525176390 7.380000e-11 78.7


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 TraesCS5B01G490300 chr5B 659548009 659550497 2488 True 4597.000000 4597 100.000000 1 2489 1 chr5B.!!$R3 2488
1 TraesCS5B01G490300 chr5B 659505592 659507361 1769 True 575.333333 968 88.400333 37 1563 3 chr5B.!!$R4 1526
2 TraesCS5B01G490300 chr5B 659531839 659532474 635 True 433.000000 433 80.299000 139 763 1 chr5B.!!$R2 624
3 TraesCS5B01G490300 chr5B 659521677 659523444 1767 True 424.900000 1014 89.321667 774 2442 3 chr5B.!!$R5 1668
4 TraesCS5B01G490300 chr5A 651527733 651529109 1376 True 1424.000000 1424 85.675000 267 1674 1 chr5A.!!$R1 1407
5 TraesCS5B01G490300 chr5A 651539359 651541587 2228 True 1090.000000 2076 87.975500 111 2328 2 chr5A.!!$R2 2217
6 TraesCS5B01G490300 chr5D 525123355 525127273 3918 True 889.000000 1674 88.366500 289 2327 2 chr5D.!!$R2 2038
7 TraesCS5B01G490300 chr5D 525176390 525178431 2041 True 566.566667 1517 88.073000 38 2489 3 chr5D.!!$R3 2451

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
68 69 0.250513 GAACGTGATCTCAAGGCCCT 59.749 55.0 0.0 0.0 0.0 5.19 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1682 3488 1.13379 CACCCCTACACTAGTGCGTAC 59.866 57.143 22.9 0.0 0.0 3.67 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 7.765695 GAATGGATGTATGTGGGTTCATTAT 57.234 36.000 0.00 0.00 0.00 1.28
25 26 8.862325 GAATGGATGTATGTGGGTTCATTATA 57.138 34.615 0.00 0.00 0.00 0.98
26 27 9.295825 GAATGGATGTATGTGGGTTCATTATAA 57.704 33.333 0.00 0.00 0.00 0.98
27 28 8.868522 ATGGATGTATGTGGGTTCATTATAAG 57.131 34.615 0.00 0.00 0.00 1.73
28 29 7.230747 TGGATGTATGTGGGTTCATTATAAGG 58.769 38.462 0.00 0.00 0.00 2.69
29 30 7.147213 TGGATGTATGTGGGTTCATTATAAGGT 60.147 37.037 0.00 0.00 0.00 3.50
30 31 7.174946 GGATGTATGTGGGTTCATTATAAGGTG 59.825 40.741 0.00 0.00 0.00 4.00
31 32 6.964464 TGTATGTGGGTTCATTATAAGGTGT 58.036 36.000 0.00 0.00 0.00 4.16
32 33 8.091952 TGTATGTGGGTTCATTATAAGGTGTA 57.908 34.615 0.00 0.00 0.00 2.90
33 34 8.208224 TGTATGTGGGTTCATTATAAGGTGTAG 58.792 37.037 0.00 0.00 0.00 2.74
34 35 6.630203 TGTGGGTTCATTATAAGGTGTAGT 57.370 37.500 0.00 0.00 0.00 2.73
35 36 7.736881 TGTGGGTTCATTATAAGGTGTAGTA 57.263 36.000 0.00 0.00 0.00 1.82
49 50 4.397417 AGGTGTAGTAGTACGCTTTACCTG 59.603 45.833 18.34 0.00 39.30 4.00
66 67 1.363744 CTGAACGTGATCTCAAGGCC 58.636 55.000 0.00 0.00 0.00 5.19
68 69 0.250513 GAACGTGATCTCAAGGCCCT 59.749 55.000 0.00 0.00 0.00 5.19
78 79 0.905357 TCAAGGCCCTAAGCTGAGAC 59.095 55.000 0.00 0.00 43.05 3.36
86 87 2.104451 CCCTAAGCTGAGACATGCTGAT 59.896 50.000 0.00 0.00 39.71 2.90
117 118 8.593945 TGCCTCAGGATTTGATTTTAGTTTAT 57.406 30.769 0.00 0.00 34.68 1.40
180 182 1.154727 CACGACTTGCCGCGTTAAC 60.155 57.895 4.92 0.00 38.92 2.01
197 199 6.475727 CGCGTTAACTACTACTACTACCACTA 59.524 42.308 3.71 0.00 0.00 2.74
225 227 2.644992 CACCTTGCAAGCCCGAAC 59.355 61.111 21.43 0.00 0.00 3.95
284 311 4.142600 GCATCTACTTGTGTCCCAAATGTC 60.143 45.833 0.00 0.00 31.20 3.06
341 370 2.290960 ACAAGTTTCCCTATGTCCTGGC 60.291 50.000 0.00 0.00 0.00 4.85
398 434 7.976826 ACGATGTCTCTTTCCGACTATATATC 58.023 38.462 0.00 0.00 32.70 1.63
400 436 8.332464 CGATGTCTCTTTCCGACTATATATCTC 58.668 40.741 0.00 0.00 32.70 2.75
402 438 8.780846 TGTCTCTTTCCGACTATATATCTCTC 57.219 38.462 0.00 0.00 32.70 3.20
403 439 7.546316 TGTCTCTTTCCGACTATATATCTCTCG 59.454 40.741 0.00 0.00 32.70 4.04
404 440 7.760794 GTCTCTTTCCGACTATATATCTCTCGA 59.239 40.741 7.75 0.00 0.00 4.04
405 441 7.977293 TCTCTTTCCGACTATATATCTCTCGAG 59.023 40.741 5.93 5.93 0.00 4.04
409 445 7.172868 TCCGACTATATATCTCTCGAGTCTT 57.827 40.000 13.13 0.72 32.86 3.01
489 547 9.261180 AGTTATTAAGTTATCGACATGTCCATG 57.739 33.333 20.03 6.58 44.15 3.66
547 606 7.693132 AGTACATCTTCACCCATGCATATATT 58.307 34.615 0.00 0.00 0.00 1.28
552 614 9.404848 CATCTTCACCCATGCATATATTAATCT 57.595 33.333 0.00 0.00 0.00 2.40
631 704 1.695893 CTCACGCGGCAAGGTGTATG 61.696 60.000 12.47 0.00 35.67 2.39
679 762 7.601508 CACGGTTGAGACCTTATTAGTTTACTT 59.398 37.037 0.00 0.00 44.20 2.24
966 1391 2.763448 ACCAAGCTAGCTGGAAGTCTAG 59.237 50.000 28.87 12.33 40.94 2.43
982 1410 6.295916 GGAAGTCTAGAAAGGACAGGAAATCA 60.296 42.308 0.00 0.00 36.29 2.57
998 1426 7.092712 ACAGGAAATCAGAGGATCATCAAACTA 60.093 37.037 10.44 0.00 37.82 2.24
1022 1450 3.077556 AGCGGGGATGAAGCGAGT 61.078 61.111 0.00 0.00 35.78 4.18
1085 1513 0.377554 GACTCATCGACGTCGTCCAT 59.622 55.000 34.40 20.01 40.80 3.41
1133 1561 2.556287 CAAGAAAGCACGGCGACC 59.444 61.111 16.62 3.25 0.00 4.79
1362 1790 2.038329 ATGGGGTTCGAGACGGGA 59.962 61.111 0.00 0.00 0.00 5.14
1395 1823 2.048222 CACATGAGGCGTCACCGT 60.048 61.111 11.97 9.26 46.52 4.83
1534 1968 0.995728 GCTCAAGCTGTTCGTCTAGC 59.004 55.000 0.00 0.00 40.18 3.42
1535 1969 1.634702 CTCAAGCTGTTCGTCTAGCC 58.365 55.000 0.00 0.00 40.76 3.93
1565 3167 2.070028 GCTGGAAAGAAGGAAGACGAC 58.930 52.381 0.00 0.00 0.00 4.34
1567 3169 3.728845 CTGGAAAGAAGGAAGACGACAA 58.271 45.455 0.00 0.00 0.00 3.18
1569 3171 3.067833 GGAAAGAAGGAAGACGACAAGG 58.932 50.000 0.00 0.00 0.00 3.61
1573 3175 3.467803 AGAAGGAAGACGACAAGGTTTG 58.532 45.455 0.00 0.00 0.00 2.93
1575 3177 1.489230 AGGAAGACGACAAGGTTTGGT 59.511 47.619 0.00 0.00 34.12 3.67
1576 3178 1.871676 GGAAGACGACAAGGTTTGGTC 59.128 52.381 0.00 0.00 34.12 4.02
1577 3179 2.484947 GGAAGACGACAAGGTTTGGTCT 60.485 50.000 0.00 0.00 39.50 3.85
1578 3180 2.528041 AGACGACAAGGTTTGGTCTC 57.472 50.000 0.00 0.00 32.86 3.36
1579 3181 1.070289 AGACGACAAGGTTTGGTCTCC 59.930 52.381 0.00 0.00 32.86 3.71
1580 3182 1.070289 GACGACAAGGTTTGGTCTCCT 59.930 52.381 0.00 0.00 35.34 3.69
1584 3186 3.243068 CGACAAGGTTTGGTCTCCTTTTG 60.243 47.826 0.00 0.00 41.44 2.44
1588 3190 5.109210 CAAGGTTTGGTCTCCTTTTGTTTC 58.891 41.667 0.00 0.00 41.44 2.78
1601 3236 4.358851 CTTTTGTTTCTTGATGCGTGGAA 58.641 39.130 0.00 0.00 0.00 3.53
1690 3496 9.193133 GAAATTCATATGTATGTAGTACGCACT 57.807 33.333 1.90 0.00 36.01 4.40
1695 3501 7.443272 TCATATGTATGTAGTACGCACTAGTGT 59.557 37.037 23.44 7.94 37.94 3.55
1699 3505 3.273434 TGTAGTACGCACTAGTGTAGGG 58.727 50.000 23.44 12.93 41.09 3.53
1700 3506 1.760192 AGTACGCACTAGTGTAGGGG 58.240 55.000 23.44 8.89 41.09 4.79
1711 3529 6.281405 CACTAGTGTAGGGGTGAATATTGAC 58.719 44.000 15.06 0.00 32.12 3.18
1715 3533 4.809426 GTGTAGGGGTGAATATTGACGAAG 59.191 45.833 0.00 0.00 0.00 3.79
1755 3573 1.900245 TTTTGAACCTTACCCGCCTC 58.100 50.000 0.00 0.00 0.00 4.70
1756 3574 0.320946 TTTGAACCTTACCCGCCTCG 60.321 55.000 0.00 0.00 0.00 4.63
1774 4069 4.501071 CCTCGGAGGAAAATTCGTTTCTA 58.499 43.478 19.57 0.00 44.43 2.10
1779 4074 6.428771 TCGGAGGAAAATTCGTTTCTACATTT 59.571 34.615 0.00 0.00 44.43 2.32
1787 4082 7.581011 AATTCGTTTCTACATTTGGCAATTC 57.419 32.000 0.00 0.00 0.00 2.17
1847 4151 4.150451 CGAATATGATTGATGTACGCAGCA 59.850 41.667 0.00 0.00 39.48 4.41
1850 4154 4.997905 ATGATTGATGTACGCAGCATAC 57.002 40.909 0.00 0.00 40.97 2.39
1923 4373 6.820656 CCATCTATGTTTCCATAGCTGATACC 59.179 42.308 12.66 0.00 44.79 2.73
1928 4378 1.244816 TCCATAGCTGATACCGACCG 58.755 55.000 0.00 0.00 0.00 4.79
1971 4421 3.397405 TGTTCAAACACGTGTGATGTG 57.603 42.857 24.16 17.30 40.80 3.21
1976 4627 0.463654 AACACGTGTGATGTGCCTGT 60.464 50.000 24.16 0.00 38.65 4.00
1978 4629 1.202592 ACACGTGTGATGTGCCTGTTA 60.203 47.619 22.71 0.00 38.65 2.41
1979 4630 2.076100 CACGTGTGATGTGCCTGTTAT 58.924 47.619 7.58 0.00 0.00 1.89
1982 4633 3.932710 ACGTGTGATGTGCCTGTTATAAG 59.067 43.478 0.00 0.00 0.00 1.73
1994 4645 4.747931 GCCTGTTATAAGATGCATGGAGGT 60.748 45.833 2.46 0.00 0.00 3.85
2011 4662 1.498145 AGGTGGAGTATACCCTAGCGT 59.502 52.381 0.00 0.00 39.05 5.07
2012 4663 2.713167 AGGTGGAGTATACCCTAGCGTA 59.287 50.000 0.00 0.00 39.05 4.42
2014 4709 3.254411 GGTGGAGTATACCCTAGCGTAAC 59.746 52.174 0.00 0.00 31.89 2.50
2019 4714 4.714632 AGTATACCCTAGCGTAACCGTTA 58.285 43.478 0.00 0.00 36.15 3.18
2020 4715 5.316987 AGTATACCCTAGCGTAACCGTTAT 58.683 41.667 0.00 0.00 36.15 1.89
2067 4762 0.736325 CTTACGCCTTGACTGGGACG 60.736 60.000 0.00 0.00 0.00 4.79
2082 4777 0.179124 GGACGAGATGCTGACAGACC 60.179 60.000 6.65 0.00 0.00 3.85
2086 4781 1.476085 CGAGATGCTGACAGACCTTCT 59.524 52.381 6.65 2.60 0.00 2.85
2100 4795 4.681942 CAGACCTTCTACTTCAGTTTCGTG 59.318 45.833 0.00 0.00 0.00 4.35
2137 4880 1.337260 CCAAAGCCGCGATCTAGCTAT 60.337 52.381 8.23 0.00 35.30 2.97
2161 4904 2.143925 GGCCGCCACTATACTTGAATC 58.856 52.381 3.91 0.00 0.00 2.52
2176 4919 1.067213 TGAATCGAACGCTGGACATGA 60.067 47.619 0.00 0.00 0.00 3.07
2177 4920 1.590238 GAATCGAACGCTGGACATGAG 59.410 52.381 0.00 0.00 0.00 2.90
2178 4921 0.817654 ATCGAACGCTGGACATGAGA 59.182 50.000 0.00 0.00 0.00 3.27
2179 4922 0.601057 TCGAACGCTGGACATGAGAA 59.399 50.000 0.00 0.00 0.00 2.87
2180 4923 1.204704 TCGAACGCTGGACATGAGAAT 59.795 47.619 0.00 0.00 0.00 2.40
2181 4924 1.325640 CGAACGCTGGACATGAGAATG 59.674 52.381 0.00 0.00 0.00 2.67
2182 4925 2.621338 GAACGCTGGACATGAGAATGA 58.379 47.619 0.00 0.00 0.00 2.57
2197 4940 9.846689 ACATGAGAATGATGAGATGAGCCCATC 62.847 44.444 0.00 0.00 40.29 3.51
2205 4948 0.894184 GATGAGCCCATCTGCCCATG 60.894 60.000 0.13 0.00 44.42 3.66
2215 4958 3.750155 TGCCCATGCATGCACACG 61.750 61.111 25.37 14.44 44.23 4.49
2216 4959 3.751246 GCCCATGCATGCACACGT 61.751 61.111 25.37 3.57 37.47 4.49
2238 4981 0.527565 GATGTCATGGCACCAACACC 59.472 55.000 0.00 0.00 0.00 4.16
2242 4985 3.294493 ATGGCACCAACACCGCAC 61.294 61.111 0.00 0.00 0.00 5.34
2256 4999 2.751436 GCACGTCACCATGGCCAT 60.751 61.111 14.09 14.09 0.00 4.40
2257 5000 3.055080 GCACGTCACCATGGCCATG 62.055 63.158 34.82 34.82 38.51 3.66
2262 5005 1.474855 CGTCACCATGGCCATGTATGA 60.475 52.381 37.30 34.17 37.11 2.15
2267 5010 1.964933 CCATGGCCATGTATGAATGCA 59.035 47.619 37.30 0.00 37.11 3.96
2278 5021 3.622612 TGTATGAATGCACATGTTCGAGG 59.377 43.478 0.00 0.00 0.00 4.63
2287 5030 3.799420 GCACATGTTCGAGGAATCTACTC 59.201 47.826 0.00 0.00 0.00 2.59
2334 5081 5.409826 ACGCGTGTACTACTAGTTAGTTCTT 59.590 40.000 12.93 0.00 41.60 2.52
2356 5103 2.354259 GATATATGCTGGACTGCAGGC 58.646 52.381 19.93 16.59 46.71 4.85
2358 5105 0.549950 ATATGCTGGACTGCAGGCTT 59.450 50.000 21.42 12.38 46.71 4.35
2361 5108 2.752358 CTGGACTGCAGGCTTGGA 59.248 61.111 21.42 0.00 0.00 3.53
2370 5117 2.036217 CTGCAGGCTTGGACAAATTTCA 59.964 45.455 5.57 0.00 0.00 2.69
2378 5125 4.873827 GCTTGGACAAATTTCATGCATGAT 59.126 37.500 29.13 13.93 36.56 2.45
2383 5130 5.508489 GGACAAATTTCATGCATGATCGGAT 60.508 40.000 29.13 17.24 36.56 4.18
2384 5131 5.286438 ACAAATTTCATGCATGATCGGATG 58.714 37.500 29.13 23.37 36.56 3.51
2386 5133 3.974871 TTTCATGCATGATCGGATGTG 57.025 42.857 29.13 0.00 36.24 3.21
2396 5143 3.521560 TGATCGGATGTGTACAAGAAGC 58.478 45.455 0.00 0.00 0.00 3.86
2412 5159 2.636893 AGAAGCATGTCTCTGTCCAACT 59.363 45.455 0.00 0.00 0.00 3.16
2413 5160 3.834813 AGAAGCATGTCTCTGTCCAACTA 59.165 43.478 0.00 0.00 0.00 2.24
2414 5161 3.883830 AGCATGTCTCTGTCCAACTAG 57.116 47.619 0.00 0.00 0.00 2.57
2421 5168 5.194432 TGTCTCTGTCCAACTAGTATCTCC 58.806 45.833 0.00 0.00 0.00 3.71
2429 5176 4.079901 TCCAACTAGTATCTCCCGAGTCTT 60.080 45.833 0.00 0.00 0.00 3.01
2453 5238 4.074970 ACAGTGGACACAAAGATGAATCC 58.925 43.478 5.14 0.00 35.77 3.01
2484 5269 0.323633 CATGTCCTGGGCATCCAACA 60.324 55.000 11.62 0.00 43.51 3.33
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 7.765695 ATAATGAACCCACATACATCCATTC 57.234 36.000 0.00 0.00 0.00 2.67
1 2 9.300681 CTTATAATGAACCCACATACATCCATT 57.699 33.333 0.00 0.00 0.00 3.16
2 3 7.890127 CCTTATAATGAACCCACATACATCCAT 59.110 37.037 0.00 0.00 0.00 3.41
3 4 7.147213 ACCTTATAATGAACCCACATACATCCA 60.147 37.037 0.00 0.00 0.00 3.41
4 5 7.174946 CACCTTATAATGAACCCACATACATCC 59.825 40.741 0.00 0.00 0.00 3.51
5 6 7.719633 ACACCTTATAATGAACCCACATACATC 59.280 37.037 0.00 0.00 0.00 3.06
6 7 7.582719 ACACCTTATAATGAACCCACATACAT 58.417 34.615 0.00 0.00 0.00 2.29
7 8 6.964464 ACACCTTATAATGAACCCACATACA 58.036 36.000 0.00 0.00 0.00 2.29
8 9 8.208903 ACTACACCTTATAATGAACCCACATAC 58.791 37.037 0.00 0.00 0.00 2.39
9 10 8.326765 ACTACACCTTATAATGAACCCACATA 57.673 34.615 0.00 0.00 0.00 2.29
10 11 7.208064 ACTACACCTTATAATGAACCCACAT 57.792 36.000 0.00 0.00 0.00 3.21
11 12 6.630203 ACTACACCTTATAATGAACCCACA 57.370 37.500 0.00 0.00 0.00 4.17
12 13 7.789026 ACTACTACACCTTATAATGAACCCAC 58.211 38.462 0.00 0.00 0.00 4.61
13 14 7.983166 ACTACTACACCTTATAATGAACCCA 57.017 36.000 0.00 0.00 0.00 4.51
14 15 8.078596 CGTACTACTACACCTTATAATGAACCC 58.921 40.741 0.00 0.00 0.00 4.11
15 16 7.592903 GCGTACTACTACACCTTATAATGAACC 59.407 40.741 0.00 0.00 0.00 3.62
16 17 8.348507 AGCGTACTACTACACCTTATAATGAAC 58.651 37.037 0.00 0.00 0.00 3.18
17 18 8.455903 AGCGTACTACTACACCTTATAATGAA 57.544 34.615 0.00 0.00 0.00 2.57
18 19 8.455903 AAGCGTACTACTACACCTTATAATGA 57.544 34.615 0.00 0.00 0.00 2.57
21 22 8.621286 GGTAAAGCGTACTACTACACCTTATAA 58.379 37.037 0.00 0.00 0.00 0.98
22 23 7.993183 AGGTAAAGCGTACTACTACACCTTATA 59.007 37.037 10.22 0.00 30.94 0.98
23 24 6.830838 AGGTAAAGCGTACTACTACACCTTAT 59.169 38.462 10.22 0.00 30.94 1.73
24 25 6.094048 CAGGTAAAGCGTACTACTACACCTTA 59.906 42.308 12.11 0.00 32.10 2.69
25 26 5.012893 AGGTAAAGCGTACTACTACACCTT 58.987 41.667 10.22 0.00 30.94 3.50
26 27 4.397417 CAGGTAAAGCGTACTACTACACCT 59.603 45.833 10.22 10.22 33.77 4.00
27 28 4.396166 TCAGGTAAAGCGTACTACTACACC 59.604 45.833 0.00 0.26 0.00 4.16
28 29 5.551760 TCAGGTAAAGCGTACTACTACAC 57.448 43.478 0.00 0.00 0.00 2.90
29 30 5.390885 CGTTCAGGTAAAGCGTACTACTACA 60.391 44.000 0.00 0.00 0.00 2.74
30 31 5.024555 CGTTCAGGTAAAGCGTACTACTAC 58.975 45.833 0.00 0.00 0.00 2.73
31 32 4.695455 ACGTTCAGGTAAAGCGTACTACTA 59.305 41.667 0.00 0.00 33.85 1.82
32 33 3.503748 ACGTTCAGGTAAAGCGTACTACT 59.496 43.478 0.00 0.00 33.85 2.57
33 34 3.605486 CACGTTCAGGTAAAGCGTACTAC 59.395 47.826 0.00 0.00 34.27 2.73
34 35 3.501828 TCACGTTCAGGTAAAGCGTACTA 59.498 43.478 0.00 0.00 34.27 1.82
35 36 2.294233 TCACGTTCAGGTAAAGCGTACT 59.706 45.455 0.00 0.00 34.27 2.73
49 50 0.250513 AGGGCCTTGAGATCACGTTC 59.749 55.000 0.00 0.00 0.00 3.95
66 67 2.975732 TCAGCATGTCTCAGCTTAGG 57.024 50.000 0.00 0.00 39.50 2.69
68 69 2.689983 TCGATCAGCATGTCTCAGCTTA 59.310 45.455 0.00 0.00 39.50 3.09
78 79 1.270147 TGAGGCAGATCGATCAGCATG 60.270 52.381 34.46 21.99 40.59 4.06
86 87 2.110578 TCAAATCCTGAGGCAGATCGA 58.889 47.619 0.00 0.00 32.44 3.59
117 118 1.343142 TCCAGAGCGCTGACAAGTAAA 59.657 47.619 18.48 0.00 45.17 2.01
121 122 1.633852 GCTTCCAGAGCGCTGACAAG 61.634 60.000 18.48 19.10 45.17 3.16
123 124 2.047844 GCTTCCAGAGCGCTGACA 60.048 61.111 18.48 1.74 45.17 3.58
180 182 8.203485 AGCTAGTTGTAGTGGTAGTAGTAGTAG 58.797 40.741 0.00 0.00 0.00 2.57
197 199 2.633860 GCAAGGTGCAGCTAGTTGT 58.366 52.632 20.51 0.00 44.26 3.32
225 227 1.991264 CGCGCTCATGGATCTAATCTG 59.009 52.381 5.56 0.00 0.00 2.90
284 311 4.098044 TCCAGTATCTAAGAAGGAGCAACG 59.902 45.833 0.00 0.00 0.00 4.10
398 434 3.119990 GGTCAAGACTCAAGACTCGAGAG 60.120 52.174 21.68 8.34 34.47 3.20
400 436 2.413502 CGGTCAAGACTCAAGACTCGAG 60.414 54.545 11.84 11.84 36.53 4.04
402 438 1.267261 ACGGTCAAGACTCAAGACTCG 59.733 52.381 0.00 0.00 34.47 4.18
403 439 2.034812 ACACGGTCAAGACTCAAGACTC 59.965 50.000 0.00 0.00 32.98 3.36
404 440 2.032620 ACACGGTCAAGACTCAAGACT 58.967 47.619 0.00 0.00 32.98 3.24
405 441 2.510768 ACACGGTCAAGACTCAAGAC 57.489 50.000 0.00 0.00 0.00 3.01
409 445 1.478916 TGTCAACACGGTCAAGACTCA 59.521 47.619 0.00 0.00 0.00 3.41
461 512 9.740239 TGGACATGTCGATAACTTAATAACTAC 57.260 33.333 19.33 0.00 0.00 2.73
489 547 3.554934 TCATCAGGTTGGATGCCAATAC 58.445 45.455 1.79 0.00 45.80 1.89
586 659 1.403679 TGTTTACTTTGCGCACTTGCT 59.596 42.857 11.12 0.00 39.32 3.91
631 704 4.465305 TGTGTCCCTAAAGAGGTTACTAGC 59.535 45.833 0.00 0.00 41.95 3.42
679 762 6.491745 CAGCTTGGATCCTATCTCAAGTACTA 59.508 42.308 14.23 0.00 38.59 1.82
966 1391 4.559862 TCCTCTGATTTCCTGTCCTTTC 57.440 45.455 0.00 0.00 0.00 2.62
982 1410 4.971282 TCCCATGTAGTTTGATGATCCTCT 59.029 41.667 0.00 0.00 0.00 3.69
998 1426 1.987807 CTTCATCCCCGCTCCCATGT 61.988 60.000 0.00 0.00 0.00 3.21
1022 1450 3.119602 CGACAATACCTCTTCGTTCCTCA 60.120 47.826 0.00 0.00 0.00 3.86
1106 1534 1.896660 GCTTTCTTGGCCGGTGACA 60.897 57.895 1.90 0.00 0.00 3.58
1282 1710 1.617018 CGTTCTCTGATGGCCCTGGA 61.617 60.000 0.00 0.00 0.00 3.86
1395 1823 2.580815 CGCAGTGCCATCTCCTCA 59.419 61.111 10.11 0.00 0.00 3.86
1463 1897 2.923035 CCGTCACCACCTGACCCT 60.923 66.667 0.00 0.00 46.01 4.34
1535 1969 3.431486 CCTTCTTTCCAGCTAGCTACCTG 60.431 52.174 18.86 8.84 0.00 4.00
1565 3167 4.736126 AACAAAAGGAGACCAAACCTTG 57.264 40.909 0.00 0.00 44.44 3.61
1567 3169 4.610333 AGAAACAAAAGGAGACCAAACCT 58.390 39.130 0.00 0.00 38.23 3.50
1569 3171 5.961272 TCAAGAAACAAAAGGAGACCAAAC 58.039 37.500 0.00 0.00 0.00 2.93
1573 3175 4.550422 GCATCAAGAAACAAAAGGAGACC 58.450 43.478 0.00 0.00 0.00 3.85
1575 3177 3.882888 ACGCATCAAGAAACAAAAGGAGA 59.117 39.130 0.00 0.00 0.00 3.71
1576 3178 3.976942 CACGCATCAAGAAACAAAAGGAG 59.023 43.478 0.00 0.00 0.00 3.69
1577 3179 3.243367 CCACGCATCAAGAAACAAAAGGA 60.243 43.478 0.00 0.00 0.00 3.36
1578 3180 3.052036 CCACGCATCAAGAAACAAAAGG 58.948 45.455 0.00 0.00 0.00 3.11
1579 3181 3.963665 TCCACGCATCAAGAAACAAAAG 58.036 40.909 0.00 0.00 0.00 2.27
1580 3182 4.109050 GTTCCACGCATCAAGAAACAAAA 58.891 39.130 0.00 0.00 0.00 2.44
1584 3186 2.290641 AGTGTTCCACGCATCAAGAAAC 59.709 45.455 0.00 0.00 39.64 2.78
1588 3190 1.603802 ACAAGTGTTCCACGCATCAAG 59.396 47.619 0.00 0.00 39.64 3.02
1636 3271 4.008074 ACAAGATCGAACAGTGAACCAT 57.992 40.909 0.00 0.00 0.00 3.55
1637 3272 3.469008 ACAAGATCGAACAGTGAACCA 57.531 42.857 0.00 0.00 0.00 3.67
1682 3488 1.133790 CACCCCTACACTAGTGCGTAC 59.866 57.143 22.90 0.00 0.00 3.67
1690 3496 5.202765 TCGTCAATATTCACCCCTACACTA 58.797 41.667 0.00 0.00 0.00 2.74
1695 3501 5.687166 AACTTCGTCAATATTCACCCCTA 57.313 39.130 0.00 0.00 0.00 3.53
1699 3505 5.296813 AGCAAACTTCGTCAATATTCACC 57.703 39.130 0.00 0.00 0.00 4.02
1700 3506 6.961554 CCTTAGCAAACTTCGTCAATATTCAC 59.038 38.462 0.00 0.00 0.00 3.18
1711 3529 3.751175 TGAACCATCCTTAGCAAACTTCG 59.249 43.478 0.00 0.00 0.00 3.79
1715 3533 5.453567 AAACTGAACCATCCTTAGCAAAC 57.546 39.130 0.00 0.00 0.00 2.93
1755 3573 5.796350 ATGTAGAAACGAATTTTCCTCCG 57.204 39.130 0.00 0.00 44.32 4.63
1756 3574 6.806739 CCAAATGTAGAAACGAATTTTCCTCC 59.193 38.462 0.00 0.00 44.32 4.30
1774 4069 5.389859 TTTGAGATCGAATTGCCAAATGT 57.610 34.783 0.00 0.00 0.00 2.71
1779 4074 5.357596 TGATCATTTTGAGATCGAATTGCCA 59.642 36.000 0.00 0.64 43.73 4.92
1809 4113 2.572191 ATTCGTCGAACCGCAATCTA 57.428 45.000 10.39 0.00 0.00 1.98
1847 4151 2.872388 CGGCCTGGAGCATCGGTAT 61.872 63.158 0.00 0.00 46.50 2.73
1884 4188 2.282180 ATGGCCCGTGTTGTGGTC 60.282 61.111 0.00 0.00 0.00 4.02
1885 4189 1.485294 TAGATGGCCCGTGTTGTGGT 61.485 55.000 0.00 0.00 0.00 4.16
1889 4193 1.750193 AACATAGATGGCCCGTGTTG 58.250 50.000 0.00 0.00 32.30 3.33
1890 4194 2.365582 GAAACATAGATGGCCCGTGTT 58.634 47.619 0.00 1.19 34.74 3.32
1891 4195 1.408266 GGAAACATAGATGGCCCGTGT 60.408 52.381 0.00 0.00 0.00 4.49
1928 4378 1.594564 GCCTTCGATCGGGCTAACC 60.595 63.158 23.23 0.00 44.48 2.85
1967 4417 4.521639 CCATGCATCTTATAACAGGCACAT 59.478 41.667 2.12 0.00 33.67 3.21
1971 4421 3.755378 CCTCCATGCATCTTATAACAGGC 59.245 47.826 0.00 0.00 0.00 4.85
1976 4627 4.660303 ACTCCACCTCCATGCATCTTATAA 59.340 41.667 0.00 0.00 0.00 0.98
1978 4629 3.051581 ACTCCACCTCCATGCATCTTAT 58.948 45.455 0.00 0.00 0.00 1.73
1979 4630 2.481441 ACTCCACCTCCATGCATCTTA 58.519 47.619 0.00 0.00 0.00 2.10
1982 4633 3.307059 GGTATACTCCACCTCCATGCATC 60.307 52.174 0.00 0.00 32.98 3.91
1994 4645 3.490348 GGTTACGCTAGGGTATACTCCA 58.510 50.000 19.21 1.89 0.00 3.86
2019 4714 3.002656 CCGCTGCAATCTCATCGTTTAAT 59.997 43.478 0.00 0.00 0.00 1.40
2020 4715 2.351418 CCGCTGCAATCTCATCGTTTAA 59.649 45.455 0.00 0.00 0.00 1.52
2067 4762 3.699038 AGTAGAAGGTCTGTCAGCATCTC 59.301 47.826 0.00 0.00 32.82 2.75
2082 4777 5.198274 GTTTGCACGAAACTGAAGTAGAAG 58.802 41.667 0.00 0.00 40.84 2.85
2117 4855 0.032130 TAGCTAGATCGCGGCTTTGG 59.968 55.000 11.94 3.36 37.50 3.28
2137 4880 3.228759 GTATAGTGGCGGCCGGGA 61.229 66.667 29.38 1.37 0.00 5.14
2150 4893 4.142337 TGTCCAGCGTTCGATTCAAGTATA 60.142 41.667 0.00 0.00 0.00 1.47
2161 4904 1.325640 CATTCTCATGTCCAGCGTTCG 59.674 52.381 0.00 0.00 0.00 3.95
2176 4919 4.289238 GATGGGCTCATCTCATCATTCT 57.711 45.455 19.76 0.00 44.73 2.40
2199 4942 3.751246 ACGTGTGCATGCATGGGC 61.751 61.111 25.64 15.07 41.68 5.36
2200 4943 2.179767 CACGTGTGCATGCATGGG 59.820 61.111 25.64 17.38 0.00 4.00
2201 4944 1.443025 CACACGTGTGCATGCATGG 60.443 57.895 33.52 17.74 39.39 3.66
2202 4945 0.169451 ATCACACGTGTGCATGCATG 59.831 50.000 37.70 22.70 45.25 4.06
2205 4948 0.453282 GACATCACACGTGTGCATGC 60.453 55.000 35.14 28.56 45.25 4.06
2207 4950 1.465777 CATGACATCACACGTGTGCAT 59.534 47.619 37.70 30.51 45.25 3.96
2208 4951 0.867086 CATGACATCACACGTGTGCA 59.133 50.000 37.70 29.82 45.25 4.57
2209 4952 0.166597 CCATGACATCACACGTGTGC 59.833 55.000 37.70 25.77 45.25 4.57
2210 4953 0.166597 GCCATGACATCACACGTGTG 59.833 55.000 37.04 37.04 46.91 3.82
2211 4954 0.250252 TGCCATGACATCACACGTGT 60.250 50.000 17.22 17.22 0.00 4.49
2212 4955 0.166597 GTGCCATGACATCACACGTG 59.833 55.000 15.48 15.48 0.00 4.49
2213 4956 0.955428 GGTGCCATGACATCACACGT 60.955 55.000 8.92 0.00 32.69 4.49
2214 4957 0.954938 TGGTGCCATGACATCACACG 60.955 55.000 8.92 0.00 32.69 4.49
2215 4958 1.068333 GTTGGTGCCATGACATCACAC 60.068 52.381 0.00 8.61 28.08 3.82
2216 4959 1.246649 GTTGGTGCCATGACATCACA 58.753 50.000 0.00 0.00 28.08 3.58
2242 4985 0.946528 CATACATGGCCATGGTGACG 59.053 55.000 41.25 24.26 42.91 4.35
2256 4999 3.622612 CCTCGAACATGTGCATTCATACA 59.377 43.478 4.29 0.00 0.00 2.29
2257 5000 3.871006 TCCTCGAACATGTGCATTCATAC 59.129 43.478 4.29 0.00 0.00 2.39
2262 5005 3.614092 AGATTCCTCGAACATGTGCATT 58.386 40.909 4.29 0.00 0.00 3.56
2278 5021 1.204941 ACCTGGTGCACGAGTAGATTC 59.795 52.381 24.79 2.74 0.00 2.52
2287 5030 3.046087 CTGCTCACCTGGTGCACG 61.046 66.667 22.02 13.06 40.80 5.34
2292 5035 0.394565 GTTCTCACTGCTCACCTGGT 59.605 55.000 0.00 0.00 0.00 4.00
2334 5081 2.303890 CCTGCAGTCCAGCATATATCCA 59.696 50.000 13.81 0.00 44.68 3.41
2356 5103 5.231357 CGATCATGCATGAAATTTGTCCAAG 59.769 40.000 31.79 8.69 40.69 3.61
2358 5105 4.440387 CCGATCATGCATGAAATTTGTCCA 60.440 41.667 31.79 6.66 40.69 4.02
2361 5108 4.987408 TCCGATCATGCATGAAATTTGT 57.013 36.364 31.79 15.45 40.69 2.83
2370 5117 3.473923 TGTACACATCCGATCATGCAT 57.526 42.857 0.00 0.00 0.00 3.96
2378 5125 3.261580 CATGCTTCTTGTACACATCCGA 58.738 45.455 0.00 0.00 0.00 4.55
2383 5130 4.202253 ACAGAGACATGCTTCTTGTACACA 60.202 41.667 0.00 0.00 0.00 3.72
2384 5131 4.310769 ACAGAGACATGCTTCTTGTACAC 58.689 43.478 0.00 0.00 0.00 2.90
2386 5133 3.929610 GGACAGAGACATGCTTCTTGTAC 59.070 47.826 0.00 0.00 0.00 2.90
2396 5143 6.238897 GGAGATACTAGTTGGACAGAGACATG 60.239 46.154 0.00 0.00 0.00 3.21
2412 5159 4.080469 ACTGTCAAGACTCGGGAGATACTA 60.080 45.833 2.08 0.00 38.80 1.82
2413 5160 3.283751 CTGTCAAGACTCGGGAGATACT 58.716 50.000 2.08 0.00 38.80 2.12
2414 5161 3.018149 ACTGTCAAGACTCGGGAGATAC 58.982 50.000 2.08 0.00 38.80 2.24
2421 5168 0.673985 TGTCCACTGTCAAGACTCGG 59.326 55.000 1.53 0.08 0.00 4.63
2429 5176 3.836365 TCATCTTTGTGTCCACTGTCA 57.164 42.857 0.00 0.00 0.00 3.58
2453 5238 2.173669 GGACATGGACATGCCGACG 61.174 63.158 11.96 0.00 42.39 5.12


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

AutoCloner maintained by Alex Coulton.