Multiple sequence alignment - TraesCS1D01G248600

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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 TraesCS1D01G248600 chr1D 100.000 5198 0 0 817 6014 341472740 341477937 0.000000e+00 9600.0
1 TraesCS1D01G248600 chr1D 100.000 457 0 0 1 457 341471924 341472380 0.000000e+00 845.0
2 TraesCS1D01G248600 chr1D 88.108 185 14 7 5832 6010 341494172 341494354 4.720000e-51 213.0
3 TraesCS1D01G248600 chr1B 93.319 3727 130 44 2360 6012 457318679 457322360 0.000000e+00 5393.0
4 TraesCS1D01G248600 chr1B 92.347 1555 64 19 817 2357 457317014 457318527 0.000000e+00 2161.0
5 TraesCS1D01G248600 chr1B 88.571 245 20 5 210 454 457316572 457316808 2.120000e-74 291.0
6 TraesCS1D01G248600 chr1B 87.736 212 22 2 1 212 457315881 457316088 1.670000e-60 244.0
7 TraesCS1D01G248600 chr1B 78.507 335 49 6 2391 2723 644450330 644450643 1.320000e-46 198.0
8 TraesCS1D01G248600 chr1B 84.615 195 13 11 5833 6012 457378855 457379047 1.720000e-40 178.0
9 TraesCS1D01G248600 chr1A 97.615 1677 37 3 2347 4020 441108853 441110529 0.000000e+00 2872.0
10 TraesCS1D01G248600 chr1A 96.177 1334 40 5 4011 5334 441110549 441111881 0.000000e+00 2170.0
11 TraesCS1D01G248600 chr1A 91.656 1546 75 12 817 2357 441107338 441108834 0.000000e+00 2091.0
12 TraesCS1D01G248600 chr1A 84.354 588 30 20 5443 6014 441112015 441112556 2.480000e-143 520.0
13 TraesCS1D01G248600 chr1A 83.590 195 15 9 5833 6012 441183924 441184116 3.730000e-37 167.0
14 TraesCS1D01G248600 chr1A 87.143 140 17 1 163 302 441097662 441097800 2.240000e-34 158.0
15 TraesCS1D01G248600 chr1A 91.589 107 4 4 348 454 441107024 441107125 6.280000e-30 143.0
16 TraesCS1D01G248600 chr1A 95.238 42 2 0 301 342 441106993 441107034 3.890000e-07 67.6
17 TraesCS1D01G248600 chr1A 96.970 33 1 0 5368 5400 441111879 441111911 8.420000e-04 56.5
18 TraesCS1D01G248600 chr4B 82.226 557 62 28 3127 3675 428477246 428476719 4.280000e-121 446.0
19 TraesCS1D01G248600 chrUn 91.111 315 19 2 817 1131 452954855 452955160 9.320000e-113 418.0
20 TraesCS1D01G248600 chrUn 91.589 107 4 4 348 454 452954541 452954642 6.280000e-30 143.0
21 TraesCS1D01G248600 chrUn 95.238 42 2 0 301 342 452954510 452954551 3.890000e-07 67.6
22 TraesCS1D01G248600 chr6A 81.071 560 68 28 3127 3675 602188037 602187505 4.340000e-111 412.0
23 TraesCS1D01G248600 chr6A 80.927 561 68 27 3127 3675 602183244 602182711 2.020000e-109 407.0
24 TraesCS1D01G248600 chr6A 80.454 573 73 30 3115 3675 602209468 602210013 9.390000e-108 401.0
25 TraesCS1D01G248600 chr2A 85.630 341 36 9 3127 3458 160036130 160035794 4.460000e-91 346.0
26 TraesCS1D01G248600 chr7A 83.959 293 28 12 3032 3323 28510828 28510554 4.620000e-66 263.0
27 TraesCS1D01G248600 chr7A 83.618 293 29 12 3032 3323 218924079 218924353 2.150000e-64 257.0
28 TraesCS1D01G248600 chr7A 84.615 169 19 3 3278 3445 623427268 623427430 1.730000e-35 161.0
29 TraesCS1D01G248600 chr4D 88.152 211 25 0 1 211 394111491 394111281 1.000000e-62 252.0
30 TraesCS1D01G248600 chr3A 79.292 367 51 8 2392 2755 557920758 557920414 3.620000e-57 233.0
31 TraesCS1D01G248600 chr3A 89.032 155 11 5 5863 6012 31808327 31808480 2.860000e-43 187.0
32 TraesCS1D01G248600 chr3B 78.158 380 61 10 2380 2755 808792527 808792166 7.850000e-54 222.0
33 TraesCS1D01G248600 chr2B 78.902 346 50 6 2380 2723 465799525 465799849 4.720000e-51 213.0
34 TraesCS1D01G248600 chr5D 84.884 172 19 3 3278 3448 18185863 18185698 3.730000e-37 167.0
35 TraesCS1D01G248600 chr5A 92.683 82 6 0 130 211 566175664 566175583 1.060000e-22 119.0


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 TraesCS1D01G248600 chr1D 341471924 341477937 6013 False 5222.500000 9600 100.000000 1 6014 2 chr1D.!!$F2 6013
1 TraesCS1D01G248600 chr1B 457315881 457322360 6479 False 2022.250000 5393 90.493250 1 6012 4 chr1B.!!$F3 6011
2 TraesCS1D01G248600 chr1A 441106993 441112556 5563 False 1131.442857 2872 93.371286 301 6014 7 chr1A.!!$F3 5713
3 TraesCS1D01G248600 chr4B 428476719 428477246 527 True 446.000000 446 82.226000 3127 3675 1 chr4B.!!$R1 548
4 TraesCS1D01G248600 chrUn 452954510 452955160 650 False 209.533333 418 92.646000 301 1131 3 chrUn.!!$F1 830
5 TraesCS1D01G248600 chr6A 602187505 602188037 532 True 412.000000 412 81.071000 3127 3675 1 chr6A.!!$R2 548
6 TraesCS1D01G248600 chr6A 602182711 602183244 533 True 407.000000 407 80.927000 3127 3675 1 chr6A.!!$R1 548
7 TraesCS1D01G248600 chr6A 602209468 602210013 545 False 401.000000 401 80.454000 3115 3675 1 chr6A.!!$F1 560

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
138 139 0.040958 GTGTCTTTGTTGCAGCTCCG 60.041 55.0 1.17 0.0 0.0 4.63 F
961 1453 0.464452 ATTCACCGACCCGAAGATCC 59.536 55.0 0.00 0.0 0.0 3.36 F
1663 2166 0.465705 TCGGGGATCAAGCAGATGAC 59.534 55.0 0.00 0.0 37.0 3.06 F
2954 3607 0.109226 GTCGCTCCCATAGGTATCGC 60.109 60.0 0.00 0.0 0.0 4.58 F
4386 5085 0.402121 GCCCTTCCAGACTGAGGTTT 59.598 55.0 3.32 0.0 0.0 3.27 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1156 1652 0.179004 TCTTCCTCGCCTGCCAAAAA 60.179 50.0 0.00 0.0 0.00 1.94 R
1829 2333 1.120530 CTCGCCCCTACAGGTACAAT 58.879 55.0 0.00 0.0 0.00 2.71 R
3101 3754 0.960861 GGTGACCCTAACCAAGCTGC 60.961 60.0 0.00 0.0 37.65 5.25 R
4432 5131 0.099082 TCCACAACGGTTTTGTTCGC 59.901 50.0 6.31 0.0 35.57 4.70 R
5617 6416 0.305922 GCAGATGAATCCGGCTTTCG 59.694 55.0 0.00 0.0 38.88 3.46 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
31 32 4.410099 TCCAGCAAAAATCAGAGGATTGT 58.590 39.130 0.00 0.00 42.87 2.71
88 89 0.400213 CAACTGTTCTAGCACCCCCA 59.600 55.000 0.00 0.00 0.00 4.96
89 90 1.004745 CAACTGTTCTAGCACCCCCAT 59.995 52.381 0.00 0.00 0.00 4.00
92 93 2.238898 ACTGTTCTAGCACCCCCATTAC 59.761 50.000 0.00 0.00 0.00 1.89
108 109 3.066203 CCATTACCCGGTTGTAGCAAATC 59.934 47.826 0.00 0.00 0.00 2.17
112 113 1.434555 CCGGTTGTAGCAAATCGTCA 58.565 50.000 0.00 0.00 31.65 4.35
114 115 2.412325 CCGGTTGTAGCAAATCGTCAAC 60.412 50.000 0.00 0.00 38.00 3.18
126 127 2.519377 TCGTCAACGATGGTGTCTTT 57.481 45.000 0.22 0.00 44.22 2.52
127 128 2.131972 TCGTCAACGATGGTGTCTTTG 58.868 47.619 0.22 0.00 44.22 2.77
128 129 1.864711 CGTCAACGATGGTGTCTTTGT 59.135 47.619 0.00 0.00 43.02 2.83
138 139 0.040958 GTGTCTTTGTTGCAGCTCCG 60.041 55.000 1.17 0.00 0.00 4.63
142 143 1.153066 TTTGTTGCAGCTCCGGTGA 60.153 52.632 7.92 0.00 32.22 4.02
186 187 5.797051 AGCATGGTTGTAGCAAAAATCATT 58.203 33.333 0.00 0.00 0.00 2.57
189 190 6.401367 GCATGGTTGTAGCAAAAATCATTGAC 60.401 38.462 0.00 0.00 31.84 3.18
221 708 1.239968 GGTTGCAGCTGGGAGTTCAG 61.240 60.000 17.12 0.00 37.79 3.02
232 719 1.062044 GGGAGTTCAGAGGTAGGGGAT 60.062 57.143 0.00 0.00 0.00 3.85
239 726 1.027815 AGAGGTAGGGGATTGGGAGT 58.972 55.000 0.00 0.00 0.00 3.85
241 728 2.180308 AGAGGTAGGGGATTGGGAGTAG 59.820 54.545 0.00 0.00 0.00 2.57
258 745 4.142773 GGAGTAGAGAGAAACGAGTGACAG 60.143 50.000 0.00 0.00 0.00 3.51
265 752 0.597637 AAACGAGTGACAGCGAGTGG 60.598 55.000 4.95 0.00 0.00 4.00
270 757 2.661537 TGACAGCGAGTGGTTGCG 60.662 61.111 0.00 0.00 38.25 4.85
278 765 1.634757 CGAGTGGTTGCGCTGCATTA 61.635 55.000 9.73 0.00 38.76 1.90
302 789 3.432326 GGGGATAAGACGAAGAAGTGCAT 60.432 47.826 0.00 0.00 0.00 3.96
305 792 4.870426 GGATAAGACGAAGAAGTGCATGAA 59.130 41.667 0.00 0.00 0.00 2.57
946 1438 4.460683 CCCGAACGCCCCGATTCA 62.461 66.667 0.00 0.00 0.00 2.57
961 1453 0.464452 ATTCACCGACCCGAAGATCC 59.536 55.000 0.00 0.00 0.00 3.36
966 1458 4.237207 GACCCGAAGATCCCCGCC 62.237 72.222 0.00 0.00 0.00 6.13
1025 1517 3.917760 GGATCCGGACGCCTCCTG 61.918 72.222 6.12 0.00 33.79 3.86
1122 1618 1.481871 GGGAGATACCGAGGTGTTGA 58.518 55.000 4.80 0.00 40.11 3.18
1142 1638 4.442706 TGAGTTTCTCTTGGTTGTCTCAC 58.557 43.478 0.00 0.00 0.00 3.51
1155 1651 1.005394 TCTCACGGCGAGGGTTTTC 60.005 57.895 16.62 0.00 42.55 2.29
1156 1652 1.004918 CTCACGGCGAGGGTTTTCT 60.005 57.895 16.62 0.00 38.18 2.52
1160 1656 1.066454 CACGGCGAGGGTTTTCTTTTT 59.934 47.619 16.62 0.00 0.00 1.94
1368 1864 1.231958 TTCACGGTGCGGGATTTGTC 61.232 55.000 2.51 0.00 39.67 3.18
1369 1865 2.359478 ACGGTGCGGGATTTGTCC 60.359 61.111 0.00 0.00 0.00 4.02
1477 1975 1.004560 CGCTGTTGCAGGAGGAGAA 60.005 57.895 0.00 0.00 39.64 2.87
1480 1978 0.676151 CTGTTGCAGGAGGAGAAGGC 60.676 60.000 0.00 0.00 0.00 4.35
1599 2097 6.266131 AGTTTTCTCCATTATATCTGCCCA 57.734 37.500 0.00 0.00 0.00 5.36
1628 2131 9.494271 GTGTTCTATGCCAATGATTTCTAGATA 57.506 33.333 0.00 0.00 0.00 1.98
1663 2166 0.465705 TCGGGGATCAAGCAGATGAC 59.534 55.000 0.00 0.00 37.00 3.06
1845 2349 4.224991 TGTTTATTGTACCTGTAGGGGC 57.775 45.455 2.53 0.00 40.27 5.80
1895 2399 1.478510 ACAGCCTGATGGAGAAGTACG 59.521 52.381 0.00 0.00 34.57 3.67
2038 2542 1.496060 ACATCAGGGTATTCTGCCGA 58.504 50.000 0.00 0.00 34.91 5.54
2126 2630 4.826274 CAGGAGATGGACCTTCAGTTTA 57.174 45.455 9.87 0.00 35.35 2.01
2198 2702 3.646162 ACCGGCTGATGATCAAGGTATTA 59.354 43.478 13.04 0.00 30.52 0.98
2234 2738 5.665812 TCTGCTTGACATATACCCTAACCTT 59.334 40.000 0.00 0.00 0.00 3.50
2258 2762 8.870160 TTTGTTTCAGATTCATAGTTTTGTGG 57.130 30.769 0.00 0.00 0.00 4.17
2357 2861 7.536622 GCATTGCTTCTCCGAATCTATTTTATG 59.463 37.037 0.16 0.00 0.00 1.90
2360 2895 6.017934 TGCTTCTCCGAATCTATTTTATGCAC 60.018 38.462 0.00 0.00 0.00 4.57
2368 3021 6.073548 CGAATCTATTTTATGCACAGAGGGAC 60.074 42.308 0.00 0.00 0.00 4.46
2460 3113 2.436292 GCTGAGAGCCTGCCAGTG 60.436 66.667 0.00 0.00 34.48 3.66
2601 3254 4.179926 TGAAGAACTGTTCAGGATCTCG 57.820 45.455 21.50 0.00 32.54 4.04
2625 3278 5.323382 AGGAGAGAAGCTCATCTATCTCA 57.677 43.478 12.23 0.00 45.81 3.27
2954 3607 0.109226 GTCGCTCCCATAGGTATCGC 60.109 60.000 0.00 0.00 0.00 4.58
2962 3615 4.079970 TCCCATAGGTATCGCTTCTACAG 58.920 47.826 0.00 0.00 0.00 2.74
3101 3754 7.323420 TGATATCTGGACTTCTGTTGTACTTG 58.677 38.462 3.98 0.00 0.00 3.16
3300 3956 3.066814 GCTGCCCTTGCCTCCAAG 61.067 66.667 0.00 0.00 46.38 3.61
3640 4310 2.079925 GGTGGAGATTGCAAGACACTC 58.920 52.381 18.62 16.12 0.00 3.51
3804 4474 7.769044 GCAGATGGTACTTTATTTCTGACCTTA 59.231 37.037 0.00 0.00 34.00 2.69
3995 4665 3.758715 GGTGCCAACCATAATTGCC 57.241 52.632 0.00 0.00 46.75 4.52
4009 4679 5.824624 CCATAATTGCCAACTGACAGACTAT 59.175 40.000 10.08 0.00 0.00 2.12
4133 4832 6.107901 AGTAAGAGATTCAGTTCTGCTTGT 57.892 37.500 0.00 0.00 0.00 3.16
4254 4953 2.238144 AGCTAATGAGAAGAAGGCTGCA 59.762 45.455 0.50 0.00 0.00 4.41
4386 5085 0.402121 GCCCTTCCAGACTGAGGTTT 59.598 55.000 3.32 0.00 0.00 3.27
4432 5131 3.611766 ACAAAGAGAACATCCCTACGG 57.388 47.619 0.00 0.00 0.00 4.02
4485 5184 1.024579 AAGCACGGCGGGTATCTTTG 61.025 55.000 12.27 0.00 0.00 2.77
4500 5199 0.457035 CTTTGGTTCCCATGATGCGG 59.543 55.000 0.00 0.00 31.53 5.69
4518 5217 2.817056 GCAGATCCCTCTCCAGCCC 61.817 68.421 0.00 0.00 0.00 5.19
4680 5382 0.952497 CACCACAAGCAGCAGTCGAT 60.952 55.000 0.00 0.00 0.00 3.59
4719 5424 7.445707 GTCAGAGGAAAGTTTAGAATGGAGTTT 59.554 37.037 0.00 0.00 0.00 2.66
4791 5496 3.992260 AGGAACAATATCTCGTCTCCG 57.008 47.619 0.00 0.00 0.00 4.63
4857 5562 5.212532 AGCTATGCTTCAGTATCCAGAAG 57.787 43.478 0.00 0.00 43.12 2.85
4938 5643 0.742281 TCTTTGATCCAGCTCTGCGC 60.742 55.000 0.00 0.00 39.57 6.09
4975 5680 1.431488 GAGATTCGGCAATGCGCAGA 61.431 55.000 18.32 3.80 43.55 4.26
5199 5930 7.571428 GCGATGATAAATGTCTACTTTTAGGGC 60.571 40.741 7.13 3.59 31.77 5.19
5271 6004 0.915364 AGTCTGGATGCTCTTTCCCC 59.085 55.000 0.00 0.00 31.87 4.81
5420 6171 1.211703 TCTGTTGCCTGTTGGTTCTGA 59.788 47.619 0.00 0.00 35.27 3.27
5436 6187 6.539173 TGGTTCTGATTCCTTGCTAAGTAAA 58.461 36.000 0.00 0.00 0.00 2.01
5439 6190 7.970614 GGTTCTGATTCCTTGCTAAGTAAATTG 59.029 37.037 0.00 0.00 0.00 2.32
5442 6241 9.733556 TCTGATTCCTTGCTAAGTAAATTGTAA 57.266 29.630 0.00 0.00 0.00 2.41
5443 6242 9.994432 CTGATTCCTTGCTAAGTAAATTGTAAG 57.006 33.333 0.00 0.00 0.00 2.34
5444 6243 9.515226 TGATTCCTTGCTAAGTAAATTGTAAGT 57.485 29.630 0.00 0.00 0.00 2.24
5560 6359 7.830697 TGAAAATCATCACAGATCCTGTTATGT 59.169 33.333 16.26 6.11 42.59 2.29
5562 6361 5.027293 TCATCACAGATCCTGTTATGTGG 57.973 43.478 16.26 0.00 42.59 4.17
5566 6365 2.159043 ACAGATCCTGTTATGTGGCTCG 60.159 50.000 0.00 0.00 42.59 5.03
5609 6408 6.015180 ACATGTAAAGAACACAAGCCATCAAT 60.015 34.615 0.00 0.00 42.09 2.57
5612 6411 5.649782 AAAGAACACAAGCCATCAATAGG 57.350 39.130 0.00 0.00 0.00 2.57
5617 6416 4.265073 ACACAAGCCATCAATAGGTCTTC 58.735 43.478 0.00 0.00 0.00 2.87
5625 6425 2.888594 TCAATAGGTCTTCGAAAGCCG 58.111 47.619 0.00 0.00 40.25 5.52
5673 6488 4.514401 CACCTATCAGTTAAACCAGGACC 58.486 47.826 0.00 0.00 0.00 4.46
5780 6595 8.987599 AATAATTTATGTAATCTGAACGCACG 57.012 30.769 0.00 0.00 0.00 5.34
5792 6607 2.805671 TGAACGCACGAACATTCAGATT 59.194 40.909 0.00 0.00 0.00 2.40
5862 6690 1.667724 CTCTAGCAAAACTCATGGGCG 59.332 52.381 0.00 0.00 0.00 6.13
5868 6696 1.024579 AAAACTCATGGGCGCTACCG 61.025 55.000 7.64 0.00 40.62 4.02
5924 6753 1.079543 CCTGAACCGGCAGTCTCTG 60.080 63.158 0.00 0.00 34.06 3.35
5930 6759 1.374758 CCGGCAGTCTCTGGTGAAC 60.375 63.158 0.00 0.00 31.21 3.18
5931 6760 1.734477 CGGCAGTCTCTGGTGAACG 60.734 63.158 0.00 0.00 31.21 3.95
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
4 5 3.321682 CCTCTGATTTTTGCTGGAACCAA 59.678 43.478 0.00 0.00 0.00 3.67
5 6 2.892852 CCTCTGATTTTTGCTGGAACCA 59.107 45.455 0.00 0.00 0.00 3.67
8 9 4.834496 ACAATCCTCTGATTTTTGCTGGAA 59.166 37.500 0.00 0.00 39.20 3.53
68 69 0.322546 GGGGGTGCTAGAACAGTTGG 60.323 60.000 2.51 0.00 0.00 3.77
69 70 0.400213 TGGGGGTGCTAGAACAGTTG 59.600 55.000 2.51 0.00 0.00 3.16
70 71 1.372501 ATGGGGGTGCTAGAACAGTT 58.627 50.000 2.51 0.00 0.00 3.16
73 74 1.562475 GGTAATGGGGGTGCTAGAACA 59.438 52.381 2.51 0.00 0.00 3.18
78 79 2.073716 CCGGGTAATGGGGGTGCTA 61.074 63.158 0.00 0.00 0.00 3.49
83 84 0.181824 CTACAACCGGGTAATGGGGG 59.818 60.000 6.32 0.00 0.00 5.40
88 89 2.940410 CGATTTGCTACAACCGGGTAAT 59.060 45.455 6.32 0.00 0.00 1.89
89 90 2.289569 ACGATTTGCTACAACCGGGTAA 60.290 45.455 6.32 0.00 0.00 2.85
92 93 0.725117 GACGATTTGCTACAACCGGG 59.275 55.000 6.32 0.00 0.00 5.73
108 109 1.864711 ACAAAGACACCATCGTTGACG 59.135 47.619 9.13 0.00 46.34 4.35
112 113 2.020720 TGCAACAAAGACACCATCGTT 58.979 42.857 0.00 0.00 0.00 3.85
114 115 1.664016 GCTGCAACAAAGACACCATCG 60.664 52.381 0.00 0.00 0.00 3.84
124 125 1.153066 TCACCGGAGCTGCAACAAA 60.153 52.632 9.46 0.00 0.00 2.83
125 126 1.597854 CTCACCGGAGCTGCAACAA 60.598 57.895 9.46 0.00 33.67 2.83
126 127 2.031012 CTCACCGGAGCTGCAACA 59.969 61.111 9.46 0.00 33.67 3.33
138 139 0.673644 ATGCTACAACCGTGCTCACC 60.674 55.000 0.00 0.00 0.00 4.02
142 143 1.021390 GCAGATGCTACAACCGTGCT 61.021 55.000 0.00 0.00 38.21 4.40
212 699 0.338814 TCCCCTACCTCTGAACTCCC 59.661 60.000 0.00 0.00 0.00 4.30
221 708 2.179424 TCTACTCCCAATCCCCTACCTC 59.821 54.545 0.00 0.00 0.00 3.85
232 719 3.506455 CACTCGTTTCTCTCTACTCCCAA 59.494 47.826 0.00 0.00 0.00 4.12
239 726 2.159824 CGCTGTCACTCGTTTCTCTCTA 59.840 50.000 0.00 0.00 0.00 2.43
241 728 1.069159 TCGCTGTCACTCGTTTCTCTC 60.069 52.381 0.00 0.00 0.00 3.20
265 752 2.100216 CCCGTAATGCAGCGCAAC 59.900 61.111 11.47 0.21 43.62 4.17
270 757 2.143925 GTCTTATCCCCGTAATGCAGC 58.856 52.381 0.00 0.00 0.00 5.25
275 762 4.648307 ACTTCTTCGTCTTATCCCCGTAAT 59.352 41.667 0.00 0.00 0.00 1.89
278 765 2.165845 CACTTCTTCGTCTTATCCCCGT 59.834 50.000 0.00 0.00 0.00 5.28
936 1428 4.851179 GGGTCGGTGAATCGGGGC 62.851 72.222 0.00 0.00 0.00 5.80
943 1435 1.610554 GGGATCTTCGGGTCGGTGAA 61.611 60.000 0.00 0.00 0.00 3.18
946 1438 2.762875 GGGGATCTTCGGGTCGGT 60.763 66.667 0.00 0.00 0.00 4.69
1062 1554 2.127118 CGTCGCGTACCTTGTCGT 60.127 61.111 5.77 0.00 0.00 4.34
1122 1618 3.458189 CGTGAGACAACCAAGAGAAACT 58.542 45.455 0.00 0.00 0.00 2.66
1142 1638 1.601914 CCAAAAAGAAAACCCTCGCCG 60.602 52.381 0.00 0.00 0.00 6.46
1155 1651 0.242017 CTTCCTCGCCTGCCAAAAAG 59.758 55.000 0.00 0.00 0.00 2.27
1156 1652 0.179004 TCTTCCTCGCCTGCCAAAAA 60.179 50.000 0.00 0.00 0.00 1.94
1160 1656 4.087892 GCTCTTCCTCGCCTGCCA 62.088 66.667 0.00 0.00 0.00 4.92
1368 1864 4.087892 CCTCGCCTGACACTGGGG 62.088 72.222 0.00 0.00 36.90 4.96
1369 1865 2.997315 TCCTCGCCTGACACTGGG 60.997 66.667 0.00 0.00 0.00 4.45
1576 2074 6.266131 TGGGCAGATATAATGGAGAAAACT 57.734 37.500 0.00 0.00 0.00 2.66
1580 2078 6.005823 CACAATGGGCAGATATAATGGAGAA 58.994 40.000 0.00 0.00 0.00 2.87
1596 2094 3.700539 TCATTGGCATAGAACACAATGGG 59.299 43.478 14.06 0.00 46.14 4.00
1599 2097 7.414222 AGAAATCATTGGCATAGAACACAAT 57.586 32.000 0.00 0.00 34.13 2.71
1663 2166 1.446907 GCGGAGATGGGATAATGCAG 58.553 55.000 0.00 0.00 0.00 4.41
1666 2169 1.021390 GGCGCGGAGATGGGATAATG 61.021 60.000 8.83 0.00 0.00 1.90
1829 2333 1.120530 CTCGCCCCTACAGGTACAAT 58.879 55.000 0.00 0.00 0.00 2.71
1845 2349 2.628178 TCCATCAGGCTATTGTACCTCG 59.372 50.000 0.00 0.00 32.56 4.63
2038 2542 1.527370 GGAACTTAGAGGGCGGCAT 59.473 57.895 12.47 2.18 0.00 4.40
2126 2630 2.642807 TCCTCTCTTTTTCCGTGGGAAT 59.357 45.455 0.00 0.00 41.71 3.01
2198 2702 3.388024 TGTCAAGCAGAGTAAGGACAGTT 59.612 43.478 0.00 0.00 32.13 3.16
2234 2738 8.006298 ACCACAAAACTATGAATCTGAAACAA 57.994 30.769 0.00 0.00 0.00 2.83
2258 2762 6.560253 ATGCGATTAACCTCCATTTCATAC 57.440 37.500 0.00 0.00 0.00 2.39
2336 2840 6.017934 TGTGCATAAAATAGATTCGGAGAAGC 60.018 38.462 0.00 0.00 45.90 3.86
2357 2861 3.201290 CAATCATGTAGTCCCTCTGTGC 58.799 50.000 0.00 0.00 0.00 4.57
2360 2895 7.531857 ACTATACAATCATGTAGTCCCTCTG 57.468 40.000 0.00 0.00 44.85 3.35
2368 3021 9.770097 ACATCCTTCAACTATACAATCATGTAG 57.230 33.333 0.00 0.00 44.85 2.74
2460 3113 1.134280 CCATCCATCACTGACCTCACC 60.134 57.143 0.00 0.00 0.00 4.02
2514 3167 1.607148 GTGAAGGTTTTCCCTGTTCCG 59.393 52.381 0.00 0.00 45.47 4.30
2601 3254 4.666512 AGATAGATGAGCTTCTCTCCTCC 58.333 47.826 2.54 0.00 41.18 4.30
2954 3607 5.700846 ACGAGTGTCATACAACTGTAGAAG 58.299 41.667 0.00 0.00 33.52 2.85
3000 3653 8.418597 AATCTAGGAGTAGTTGTTAACAGTCA 57.581 34.615 8.56 0.00 0.00 3.41
3047 3700 6.375736 TCCCGTTGCTGAAATAATGTCATTAA 59.624 34.615 9.31 0.00 0.00 1.40
3068 3721 6.071108 ACAGAAGTCCAGATATCATTATCCCG 60.071 42.308 5.32 0.00 35.74 5.14
3101 3754 0.960861 GGTGACCCTAACCAAGCTGC 60.961 60.000 0.00 0.00 37.65 5.25
3300 3956 2.086869 CGATATGGGATGTGGGCATTC 58.913 52.381 0.00 0.00 35.07 2.67
3640 4310 5.375417 TTGGACTTATCTGCACAAACATG 57.625 39.130 0.00 0.00 0.00 3.21
3995 4665 8.322906 TGAATTGGTTTATAGTCTGTCAGTTG 57.677 34.615 0.00 0.00 0.00 3.16
4274 4973 1.475280 GAGCTGCAAATGATGGCTTCA 59.525 47.619 5.47 5.47 39.12 3.02
4386 5085 2.551270 ACTGAAGATCCCTTACCAGCA 58.449 47.619 0.00 0.00 31.20 4.41
4432 5131 0.099082 TCCACAACGGTTTTGTTCGC 59.901 50.000 6.31 0.00 35.57 4.70
4444 5143 0.947244 CCAGCAGTCTTGTCCACAAC 59.053 55.000 0.00 0.00 0.00 3.32
4500 5199 2.817056 GGGCTGGAGAGGGATCTGC 61.817 68.421 0.00 0.00 0.00 4.26
4680 5382 1.277273 CCTCTGACATCTGGAGTTGCA 59.723 52.381 0.00 0.00 0.00 4.08
4719 5424 4.591399 AACCTGCTGCTGCTGCCA 62.591 61.111 25.44 14.14 40.48 4.92
4791 5496 1.375098 GCATCCTCAACCTCTGCTGC 61.375 60.000 0.00 0.00 0.00 5.25
4857 5562 2.829120 AGGTGAACCAAGAGCTACTCTC 59.171 50.000 1.62 0.00 40.28 3.20
4938 5643 0.394192 TCCCTGCCATTATCTGCTCG 59.606 55.000 0.00 0.00 0.00 5.03
4975 5680 0.535102 CTCTTGCCGTTGAACACCCT 60.535 55.000 0.00 0.00 0.00 4.34
5271 6004 0.833287 TAGGCAAGCAGCTTCTAGGG 59.167 55.000 4.07 0.00 44.79 3.53
5359 6093 9.797642 TCAGAATAATTGAGGCATGTAACATAT 57.202 29.630 0.00 0.00 0.00 1.78
5361 6095 7.776969 AGTCAGAATAATTGAGGCATGTAACAT 59.223 33.333 0.00 0.00 0.00 2.71
5362 6096 7.112122 AGTCAGAATAATTGAGGCATGTAACA 58.888 34.615 0.00 0.00 0.00 2.41
5363 6097 7.559590 AGTCAGAATAATTGAGGCATGTAAC 57.440 36.000 0.00 0.00 0.00 2.50
5364 6098 7.828717 TCAAGTCAGAATAATTGAGGCATGTAA 59.171 33.333 0.00 0.00 0.00 2.41
5365 6099 7.337938 TCAAGTCAGAATAATTGAGGCATGTA 58.662 34.615 0.00 0.00 0.00 2.29
5366 6100 6.182627 TCAAGTCAGAATAATTGAGGCATGT 58.817 36.000 0.00 0.00 0.00 3.21
5367 6101 6.688637 TCAAGTCAGAATAATTGAGGCATG 57.311 37.500 0.00 0.00 0.00 4.06
5368 6102 7.893124 ATTCAAGTCAGAATAATTGAGGCAT 57.107 32.000 0.00 0.00 36.51 4.40
5369 6103 7.707624 AATTCAAGTCAGAATAATTGAGGCA 57.292 32.000 0.00 0.00 37.24 4.75
5370 6104 7.009907 GCAAATTCAAGTCAGAATAATTGAGGC 59.990 37.037 0.00 0.00 37.24 4.70
5371 6105 8.248945 AGCAAATTCAAGTCAGAATAATTGAGG 58.751 33.333 0.00 0.00 37.24 3.86
5524 6323 6.433716 TCTGTGATGATTTTCACTGGCAAATA 59.566 34.615 10.32 0.00 45.07 1.40
5525 6324 5.244402 TCTGTGATGATTTTCACTGGCAAAT 59.756 36.000 10.32 0.00 45.07 2.32
5526 6325 4.583907 TCTGTGATGATTTTCACTGGCAAA 59.416 37.500 10.32 0.00 45.07 3.68
5527 6326 4.143543 TCTGTGATGATTTTCACTGGCAA 58.856 39.130 10.32 0.00 45.07 4.52
5528 6327 3.753815 TCTGTGATGATTTTCACTGGCA 58.246 40.909 10.32 0.00 45.07 4.92
5529 6328 4.201990 GGATCTGTGATGATTTTCACTGGC 60.202 45.833 10.32 4.95 45.07 4.85
5560 6359 4.620097 GCATCATCTGATTCTATCGAGCCA 60.620 45.833 0.00 0.00 31.21 4.75
5562 6361 4.326817 GTGCATCATCTGATTCTATCGAGC 59.673 45.833 0.00 0.00 31.21 5.03
5566 6365 8.543862 TTACATGTGCATCATCTGATTCTATC 57.456 34.615 9.11 0.00 34.09 2.08
5609 6408 1.481871 ATCCGGCTTTCGAAGACCTA 58.518 50.000 14.44 5.35 42.43 3.08
5612 6411 1.722011 TGAATCCGGCTTTCGAAGAC 58.278 50.000 0.00 0.00 42.43 3.01
5617 6416 0.305922 GCAGATGAATCCGGCTTTCG 59.694 55.000 0.00 0.00 38.88 3.46
5625 6425 0.465705 TCCTGTCGGCAGATGAATCC 59.534 55.000 20.91 0.00 45.28 3.01
5651 6451 4.514401 GGTCCTGGTTTAACTGATAGGTG 58.486 47.826 0.00 0.00 0.00 4.00
5654 6456 4.730949 TCGGTCCTGGTTTAACTGATAG 57.269 45.455 0.00 0.00 0.00 2.08
5658 6460 4.630069 CAGTATTCGGTCCTGGTTTAACTG 59.370 45.833 0.00 0.00 0.00 3.16
5673 6488 2.671396 CCGAGTTGGGAAACAGTATTCG 59.329 50.000 0.00 0.00 0.00 3.34
5868 6696 7.502120 TGGATGAAAAGATTTGAGCTATAGC 57.498 36.000 17.33 17.33 42.49 2.97
5924 6753 2.731587 AAACATGCAGCGCGTTCACC 62.732 55.000 8.43 0.00 0.00 4.02
5930 6759 2.099062 GGAGAAACATGCAGCGCG 59.901 61.111 0.00 0.00 0.00 6.86
5931 6760 1.136147 CTGGAGAAACATGCAGCGC 59.864 57.895 0.00 0.00 31.59 5.92


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

AutoCloner maintained by Alex Coulton.