Multiple sequence alignment - TraesCS2D01G118500

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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 TraesCS2D01G118500 chr2D 100.000 9928 0 0 1 9928 67963579 67973506 0.000000e+00 18334.0
1 TraesCS2D01G118500 chr2D 88.430 121 12 1 7975 8095 68006862 68006980 2.890000e-30 145.0
2 TraesCS2D01G118500 chr2D 85.841 113 14 2 1445 1556 67964957 67965068 1.750000e-22 119.0
3 TraesCS2D01G118500 chr2D 85.841 113 14 2 1379 1490 67965023 67965134 1.750000e-22 119.0
4 TraesCS2D01G118500 chr2D 92.857 42 3 0 8001 8042 67971532 67971573 2.990000e-05 62.1
5 TraesCS2D01G118500 chr2D 92.857 42 3 0 7954 7995 67971579 67971620 2.990000e-05 62.1
6 TraesCS2D01G118500 chr2A 97.623 8372 145 17 1379 9724 66588912 66580569 0.000000e+00 14308.0
7 TraesCS2D01G118500 chr2A 87.673 722 32 25 866 1545 66589519 66588813 0.000000e+00 787.0
8 TraesCS2D01G118500 chr2A 84.286 770 40 25 1 744 66590697 66589983 0.000000e+00 676.0
9 TraesCS2D01G118500 chr2A 91.209 182 14 2 3563 3744 375705295 375705474 7.700000e-61 246.0
10 TraesCS2D01G118500 chr2A 96.000 150 3 3 9715 9862 66580329 66580181 3.580000e-59 241.0
11 TraesCS2D01G118500 chr2A 86.139 101 14 0 1379 1479 66588846 66588746 1.050000e-19 110.0
12 TraesCS2D01G118500 chr2A 91.358 81 4 3 9846 9926 68155930 68155853 3.790000e-19 108.0
13 TraesCS2D01G118500 chr2A 92.857 42 3 0 7954 7995 66582300 66582259 2.990000e-05 62.1
14 TraesCS2D01G118500 chr2B 96.925 7902 168 23 629 8499 102427114 102419257 0.000000e+00 13176.0
15 TraesCS2D01G118500 chr2B 97.761 1429 21 3 8502 9924 102419196 102417773 0.000000e+00 2451.0
16 TraesCS2D01G118500 chr2B 87.406 397 33 9 237 632 102427889 102427509 3.290000e-119 440.0
17 TraesCS2D01G118500 chr2B 93.525 139 8 1 1 139 102428079 102427942 1.310000e-48 206.0
18 TraesCS2D01G118500 chr2B 84.821 112 16 1 1379 1490 102426272 102426162 2.930000e-20 111.0
19 TraesCS2D01G118500 chr2B 95.238 42 2 0 8001 8042 102419802 102419761 6.440000e-07 67.6
20 TraesCS2D01G118500 chr2B 92.857 42 3 0 7954 7995 102419755 102419714 2.990000e-05 62.1
21 TraesCS2D01G118500 chr6D 89.170 554 55 5 3563 4115 261701969 261701420 0.000000e+00 686.0
22 TraesCS2D01G118500 chr6D 95.714 70 3 0 9859 9928 178131389 178131320 8.150000e-21 113.0
23 TraesCS2D01G118500 chr5A 88.628 554 49 10 3563 4115 250554569 250554029 0.000000e+00 662.0
24 TraesCS2D01G118500 chr5A 90.361 83 6 2 9846 9928 68548575 68548495 3.790000e-19 108.0
25 TraesCS2D01G118500 chr5B 95.890 73 3 0 9856 9928 222371184 222371256 1.750000e-22 119.0
26 TraesCS2D01G118500 chr1A 92.308 78 6 0 9851 9928 386427681 386427604 2.930000e-20 111.0
27 TraesCS2D01G118500 chr4D 92.308 78 5 1 9851 9928 509117811 509117735 1.050000e-19 110.0
28 TraesCS2D01G118500 chr1B 93.333 75 4 1 9854 9928 56752492 56752419 1.050000e-19 110.0
29 TraesCS2D01G118500 chr1B 94.286 70 4 0 9859 9928 518802183 518802114 3.790000e-19 108.0


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 TraesCS2D01G118500 chr2D 67963579 67973506 9927 False 18334.000000 18334 100.000000 1 9928 1 chr2D.!!$F1 9927
1 TraesCS2D01G118500 chr2A 66580181 66588912 8731 True 7274.500000 14308 96.811500 1379 9862 2 chr2A.!!$R3 8483
2 TraesCS2D01G118500 chr2A 66588746 66590697 1951 True 524.333333 787 86.032667 1 1545 3 chr2A.!!$R4 1544
3 TraesCS2D01G118500 chr2B 102417773 102427114 9341 True 7813.500000 13176 97.343000 629 9924 2 chr2B.!!$R1 9295
4 TraesCS2D01G118500 chr2B 102426162 102428079 1917 True 252.333333 440 88.584000 1 1490 3 chr2B.!!$R3 1489
5 TraesCS2D01G118500 chr6D 261701420 261701969 549 True 686.000000 686 89.170000 3563 4115 1 chr6D.!!$R2 552
6 TraesCS2D01G118500 chr5A 250554029 250554569 540 True 662.000000 662 88.628000 3563 4115 1 chr5A.!!$R2 552

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
230 263 0.107508 GCAAGCCCAGATGCTAGTCA 60.108 55.000 0.00 0.00 41.80 3.41 F
319 352 0.318699 CCGAGTGAGAACGCTTCACA 60.319 55.000 14.46 5.79 36.96 3.58 F
1334 2157 0.107703 TCGATTCTCCCGCTTTGCAT 60.108 50.000 0.00 0.00 0.00 3.96 F
1344 2167 1.336148 CCGCTTTGCATGTGTGAATGT 60.336 47.619 0.00 0.00 0.00 2.71 F
2259 3188 1.946768 TGTGGCTGCAGTTAGTTTGAC 59.053 47.619 16.64 1.64 0.00 3.18 F
3443 4372 1.745087 TCGATTGAAAGAATGGGCTGC 59.255 47.619 0.00 0.00 0.00 5.25 F
3999 4929 0.478072 ATGTCAGGGACAGTTTGGCA 59.522 50.000 5.25 0.00 46.04 4.92 F
4002 4932 1.067295 TCAGGGACAGTTTGGCAGAT 58.933 50.000 0.00 0.00 0.00 2.90 F
5917 6850 0.602638 GTGATGTTCCGACCACAGCA 60.603 55.000 0.00 0.00 38.20 4.41 F
6625 7558 1.205655 GAGAAGCCCAAAGCCCAAATC 59.794 52.381 0.00 0.00 45.47 2.17 F
6628 7561 2.649129 GCCCAAAGCCCAAATCGCT 61.649 57.895 0.00 0.00 38.53 4.93 F
7195 8128 3.018423 AGTGCCTGGAAGTGTTTCTTT 57.982 42.857 0.00 0.00 36.40 2.52 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1334 2157 0.179032 AGACCGCCAACATTCACACA 60.179 50.000 0.00 0.0 0.00 3.72 R
1420 2336 0.461961 ACCGCTTCTAGGAGCACATC 59.538 55.000 22.96 0.0 42.83 3.06 R
2842 3771 0.329261 CATCAGGGCTTTCCTCCACA 59.671 55.000 0.00 0.0 46.12 4.17 R
3443 4372 2.565210 TGTCTTGCTGTTGCTGTTTG 57.435 45.000 0.00 0.0 40.48 2.93 R
3554 4483 1.071385 CTGTCACAGGTTTCAGCTCCT 59.929 52.381 0.00 0.0 33.96 3.69 R
5351 6281 0.700564 AAAGCCTTGGCCTCATCAGA 59.299 50.000 3.32 0.0 0.00 3.27 R
5917 6850 7.282332 AGCTTTTGAAGAACTTGAAGCTATT 57.718 32.000 18.66 0.0 0.00 1.73 R
6469 7402 5.358160 AGCTGCAGTTTTCTTACTTTCACTT 59.642 36.000 16.64 0.0 0.00 3.16 R
7135 8068 1.064758 GGTGACCTATGTTCCCATGCA 60.065 52.381 0.00 0.0 32.29 3.96 R
8306 9239 2.224597 TGCTCCAGTGCTCAAAATCTCA 60.225 45.455 0.00 0.0 0.00 3.27 R
8631 9630 4.046103 TCAAAAGGTATATGGTTTGGGGGT 59.954 41.667 0.00 0.0 32.91 4.95 R
9543 10546 2.504367 GCCCACTAGCTGTTTTCTCAA 58.496 47.619 0.00 0.0 0.00 3.02 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
32 33 3.618690 AGTGAAGGCCATAGACAACTC 57.381 47.619 5.01 0.00 0.00 3.01
104 115 0.608035 GTGGACCGGCATTTCTTCCA 60.608 55.000 0.00 1.58 33.85 3.53
119 130 4.762289 TCTTCCAGCCTCTTTATTCCTC 57.238 45.455 0.00 0.00 0.00 3.71
120 131 3.456277 TCTTCCAGCCTCTTTATTCCTCC 59.544 47.826 0.00 0.00 0.00 4.30
121 132 3.136641 TCCAGCCTCTTTATTCCTCCT 57.863 47.619 0.00 0.00 0.00 3.69
128 139 5.130311 AGCCTCTTTATTCCTCCTCTTTCTC 59.870 44.000 0.00 0.00 0.00 2.87
136 147 0.617820 CTCCTCTTTCTCCCCGGGAA 60.618 60.000 26.32 0.00 0.00 3.97
169 196 1.134753 TGGAACATGCCAAATCATCGC 59.865 47.619 0.00 0.00 34.31 4.58
181 214 4.873810 CATCGCCCCATCGCCCAA 62.874 66.667 0.00 0.00 0.00 4.12
197 230 1.961277 CAACCCGAAGCGCTTCAGT 60.961 57.895 40.22 33.91 39.46 3.41
202 235 1.373497 CGAAGCGCTTCAGTCCAGT 60.373 57.895 40.22 11.64 39.46 4.00
226 259 2.190313 CGGCAAGCCCAGATGCTA 59.810 61.111 5.34 0.00 41.80 3.49
227 260 1.890979 CGGCAAGCCCAGATGCTAG 60.891 63.158 5.34 0.00 41.80 3.42
228 261 1.225704 GGCAAGCCCAGATGCTAGT 59.774 57.895 0.00 0.00 41.80 2.57
229 262 0.817229 GGCAAGCCCAGATGCTAGTC 60.817 60.000 0.00 0.00 41.80 2.59
230 263 0.107508 GCAAGCCCAGATGCTAGTCA 60.108 55.000 0.00 0.00 41.80 3.41
253 286 1.134220 AGTTCACGCCTCTTTGGACAA 60.134 47.619 0.00 0.00 38.35 3.18
262 295 1.098712 TCTTTGGACAACACCGGTGC 61.099 55.000 34.26 17.63 0.00 5.01
275 308 0.875474 CCGGTGCAAAACAAGCTTGG 60.875 55.000 29.18 13.18 0.00 3.61
319 352 0.318699 CCGAGTGAGAACGCTTCACA 60.319 55.000 14.46 5.79 36.96 3.58
321 354 1.423395 GAGTGAGAACGCTTCACAGG 58.577 55.000 14.46 0.00 36.96 4.00
325 358 1.006102 AGAACGCTTCACAGGACCG 60.006 57.895 0.00 0.00 0.00 4.79
363 396 1.425428 GAATTGACGGCAAGCGAGG 59.575 57.895 10.69 0.00 37.45 4.63
366 399 2.463589 ATTGACGGCAAGCGAGGGAA 62.464 55.000 10.69 0.00 37.45 3.97
378 411 1.805495 GCGAGGGAAAGATAACGGGAC 60.805 57.143 0.00 0.00 0.00 4.46
407 440 3.131478 CCCAAACGGACGCATCCC 61.131 66.667 0.00 0.00 42.83 3.85
408 441 3.131478 CCAAACGGACGCATCCCC 61.131 66.667 0.00 0.00 42.83 4.81
409 442 2.046314 CAAACGGACGCATCCCCT 60.046 61.111 0.00 0.00 42.83 4.79
410 443 2.046314 AAACGGACGCATCCCCTG 60.046 61.111 0.00 0.00 42.83 4.45
411 444 3.622060 AAACGGACGCATCCCCTGG 62.622 63.158 0.00 0.00 42.83 4.45
441 475 1.079681 CGGGGAACATTCGAACGGA 60.080 57.895 0.00 0.00 0.00 4.69
442 476 0.461339 CGGGGAACATTCGAACGGAT 60.461 55.000 0.00 0.00 0.00 4.18
571 606 1.798087 CGTTACCATCAAACGGGGC 59.202 57.895 0.63 0.00 44.49 5.80
586 621 0.535102 GGGGCGAGAGAGAGAGAGAG 60.535 65.000 0.00 0.00 0.00 3.20
587 622 0.468226 GGGCGAGAGAGAGAGAGAGA 59.532 60.000 0.00 0.00 0.00 3.10
1175 1998 3.184683 CGCACCTCTCGCTTGCTC 61.185 66.667 0.00 0.00 33.90 4.26
1182 2005 1.681945 CTCTCGCTTGCTCGCTTCAC 61.682 60.000 0.00 0.00 0.00 3.18
1235 2058 6.040955 ACCACATGACTACCAGTAGATGTATG 59.959 42.308 11.71 11.03 32.33 2.39
1240 2063 8.630037 CATGACTACCAGTAGATGTATGTAACA 58.370 37.037 11.71 0.00 38.32 2.41
1256 2079 4.240096 TGTAACACGCCTACTTTTCTAGC 58.760 43.478 0.00 0.00 0.00 3.42
1282 2105 2.536329 CGAAATGAGCTTGATCTGCGTG 60.536 50.000 0.00 0.00 35.28 5.34
1334 2157 0.107703 TCGATTCTCCCGCTTTGCAT 60.108 50.000 0.00 0.00 0.00 3.96
1344 2167 1.336148 CCGCTTTGCATGTGTGAATGT 60.336 47.619 0.00 0.00 0.00 2.71
1347 2170 2.477375 GCTTTGCATGTGTGAATGTTGG 59.523 45.455 0.00 0.00 0.00 3.77
1366 2189 4.452733 GGTCTAGCCGTTGCCGCT 62.453 66.667 0.00 0.00 38.69 5.52
1410 2260 8.816640 ATCAATTAAAGTTTGCGAGATTTGTT 57.183 26.923 0.00 0.00 0.00 2.83
1420 2336 3.058983 TGCGAGATTTGTTGCTGTAGTTG 60.059 43.478 0.00 0.00 0.00 3.16
1424 2340 5.106948 CGAGATTTGTTGCTGTAGTTGATGT 60.107 40.000 0.00 0.00 0.00 3.06
1428 2344 2.807967 TGTTGCTGTAGTTGATGTGCTC 59.192 45.455 0.00 0.00 0.00 4.26
1491 2407 2.455674 TTGTCGCTGTAGTTCATGCT 57.544 45.000 0.00 0.00 0.00 3.79
1492 2408 2.455674 TGTCGCTGTAGTTCATGCTT 57.544 45.000 0.00 0.00 0.00 3.91
1614 2543 3.122948 CGCGTGCTGTTATATATGGAACC 59.877 47.826 0.00 0.00 0.00 3.62
1629 2558 7.814264 ATATGGAACCAAAGAAGCTAATCAG 57.186 36.000 0.00 0.00 0.00 2.90
1664 2593 6.404623 GGGTGTTGGTTTTTCGTTTACTAGTT 60.405 38.462 0.00 0.00 0.00 2.24
1686 2615 4.415596 TGTAATTTGGATTTGGCCAGTCT 58.584 39.130 5.11 0.00 39.52 3.24
1696 2625 2.836636 TGGCCAGTCTCAGTCTCTAT 57.163 50.000 0.00 0.00 0.00 1.98
1698 2627 3.027412 TGGCCAGTCTCAGTCTCTATTC 58.973 50.000 0.00 0.00 0.00 1.75
1757 2686 2.269023 TCTGTGACATGGATCAACCCT 58.731 47.619 0.00 0.00 38.00 4.34
1884 2813 7.969690 AATGGGTTCATTGTTATTACATCCA 57.030 32.000 0.00 0.00 41.62 3.41
1938 2867 4.753107 TGTTCCGAAGACAAGGTTAATGAC 59.247 41.667 0.00 0.00 0.00 3.06
2259 3188 1.946768 TGTGGCTGCAGTTAGTTTGAC 59.053 47.619 16.64 1.64 0.00 3.18
2503 3432 8.964150 CAGCATTGTCATGTACATTAATTCATG 58.036 33.333 5.37 14.07 38.10 3.07
2522 3451 6.963083 TCATGTGGCATTGATGATTTGATA 57.037 33.333 0.00 0.00 0.00 2.15
2842 3771 5.709164 CCTTGACATTTCTTCACCTTCATCT 59.291 40.000 0.00 0.00 0.00 2.90
3443 4372 1.745087 TCGATTGAAAGAATGGGCTGC 59.255 47.619 0.00 0.00 0.00 5.25
3479 4408 5.585390 CAAGACAATCAAAGCTGAAACTGT 58.415 37.500 0.00 0.00 34.49 3.55
3489 4418 4.363991 AGCTGAAACTGTCAAAGAGGAT 57.636 40.909 0.00 0.00 35.22 3.24
3554 4483 3.023119 TGGAACTTTCAGCAGCAAAGAA 58.977 40.909 11.27 2.13 35.24 2.52
3585 4514 2.092968 ACCTGTGACAGAAAAGACAGCA 60.093 45.455 15.33 0.00 35.50 4.41
3593 4522 5.008019 TGACAGAAAAGACAGCATTGACTTC 59.992 40.000 0.00 0.00 38.14 3.01
3825 4754 4.202567 ACCAAGAGTGAGGCCAAAAGAATA 60.203 41.667 5.01 0.00 0.00 1.75
3948 4878 3.173151 TCACTCCAAATCTAGCCACTCA 58.827 45.455 0.00 0.00 0.00 3.41
3997 4927 2.304180 AGAGATGTCAGGGACAGTTTGG 59.696 50.000 5.25 0.00 46.04 3.28
3999 4929 0.478072 ATGTCAGGGACAGTTTGGCA 59.522 50.000 5.25 0.00 46.04 4.92
4002 4932 1.067295 TCAGGGACAGTTTGGCAGAT 58.933 50.000 0.00 0.00 0.00 2.90
4101 5031 7.830099 ATATTGGATCAAAAGGGATTCTGAC 57.170 36.000 0.00 0.00 0.00 3.51
4829 5759 1.093159 CATGCTGCTTCTTCTGGACC 58.907 55.000 0.00 0.00 0.00 4.46
5351 6281 5.169295 GTGATTTAGCTAGTGGAGACGTTT 58.831 41.667 0.00 0.00 0.00 3.60
5479 6409 4.360889 AGTCCAAGAGAGACAAGGATGAT 58.639 43.478 0.00 0.00 36.68 2.45
5695 6625 1.318576 AGGAAACAAAGTCCAAGCCG 58.681 50.000 0.00 0.00 37.65 5.52
5721 6651 9.606631 GATAAAGTCTGAAGAACTGTATTCCAT 57.393 33.333 3.96 0.00 0.00 3.41
5917 6850 0.602638 GTGATGTTCCGACCACAGCA 60.603 55.000 0.00 0.00 38.20 4.41
6469 7402 3.127548 GCTCGAAAGGAGATTTGATTGCA 59.872 43.478 0.00 0.00 46.23 4.08
6499 7432 5.810095 AGTAAGAAAACTGCAGCTCCTATT 58.190 37.500 15.27 4.80 0.00 1.73
6625 7558 1.205655 GAGAAGCCCAAAGCCCAAATC 59.794 52.381 0.00 0.00 45.47 2.17
6628 7561 2.649129 GCCCAAAGCCCAAATCGCT 61.649 57.895 0.00 0.00 38.53 4.93
7135 8068 9.520204 CAGGTTATTTCATTTCTGCGAATAAAT 57.480 29.630 0.00 0.00 29.71 1.40
7195 8128 3.018423 AGTGCCTGGAAGTGTTTCTTT 57.982 42.857 0.00 0.00 36.40 2.52
7370 8303 5.068591 TCACTAAATGTTAGCGAGCTGGATA 59.931 40.000 7.99 0.00 0.00 2.59
7374 8307 5.984695 AATGTTAGCGAGCTGGATATAGA 57.015 39.130 7.99 0.00 0.00 1.98
7382 8315 5.246203 AGCGAGCTGGATATAGACCAAATTA 59.754 40.000 0.00 0.00 36.95 1.40
7387 8320 7.155328 AGCTGGATATAGACCAAATTACTTCG 58.845 38.462 0.00 0.00 36.95 3.79
7436 8369 5.983720 TCAAACTGTAGTCAGAAGTTACTGC 59.016 40.000 2.17 0.00 43.76 4.40
7941 8874 9.872721 AAGGTTACTAGCTTATGTAAGTTCTTC 57.127 33.333 0.00 0.00 40.17 2.87
7965 8898 7.541162 TCAAAATCCTGATTAGCAGTTCAATG 58.459 34.615 0.00 0.00 43.33 2.82
8325 9258 3.190118 GGTTGAGATTTTGAGCACTGGAG 59.810 47.826 0.00 0.00 0.00 3.86
8537 9528 3.054655 GTGGTCCAGCCTTATTCCTTGTA 60.055 47.826 0.00 0.00 38.35 2.41
8538 9529 3.785887 TGGTCCAGCCTTATTCCTTGTAT 59.214 43.478 0.00 0.00 38.35 2.29
8539 9530 4.229582 TGGTCCAGCCTTATTCCTTGTATT 59.770 41.667 0.00 0.00 38.35 1.89
8540 9531 4.822350 GGTCCAGCCTTATTCCTTGTATTC 59.178 45.833 0.00 0.00 0.00 1.75
8541 9532 5.437060 GTCCAGCCTTATTCCTTGTATTCA 58.563 41.667 0.00 0.00 0.00 2.57
9276 10279 2.353803 GGTGGTAACTCTCAGATTGCGT 60.354 50.000 0.00 0.00 37.61 5.24
9358 10361 4.385199 CCCCACTGAGCTGAATTATGGTTA 60.385 45.833 0.00 0.00 0.00 2.85
9781 11037 6.506147 TGAAACAATTTGAAGTGACTCATGG 58.494 36.000 2.79 0.00 0.00 3.66
9864 11120 7.755822 GTCGTTGAATCATAGTATCATACTCCC 59.244 40.741 0.00 0.00 40.14 4.30
9889 11145 5.935789 TCCGTCCCAAAATAAGTGTCTTAAG 59.064 40.000 0.00 0.00 0.00 1.85
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
32 33 1.395954 CATCGCATGTCCTTGTCACAG 59.604 52.381 0.00 0.00 0.00 3.66
104 115 5.036236 AGAAAGAGGAGGAATAAAGAGGCT 58.964 41.667 0.00 0.00 0.00 4.58
119 130 0.919710 AATTCCCGGGGAGAAAGAGG 59.080 55.000 23.50 0.00 31.21 3.69
120 131 3.926058 TTAATTCCCGGGGAGAAAGAG 57.074 47.619 23.50 0.00 31.21 2.85
121 132 3.308617 GGTTTAATTCCCGGGGAGAAAGA 60.309 47.826 23.50 0.60 31.21 2.52
128 139 2.153034 ACATGGTTTAATTCCCGGGG 57.847 50.000 23.50 6.77 0.00 5.73
164 191 4.873810 TTGGGCGATGGGGCGATG 62.874 66.667 0.00 0.00 43.46 3.84
192 225 2.583441 CGGGCTGGACTGGACTGAA 61.583 63.158 0.00 0.00 0.00 3.02
226 259 1.261480 AGAGGCGTGAACTGATGACT 58.739 50.000 0.00 0.00 0.00 3.41
227 260 2.086054 AAGAGGCGTGAACTGATGAC 57.914 50.000 0.00 0.00 0.00 3.06
228 261 2.416747 CAAAGAGGCGTGAACTGATGA 58.583 47.619 0.00 0.00 0.00 2.92
229 262 1.466167 CCAAAGAGGCGTGAACTGATG 59.534 52.381 0.00 0.00 0.00 3.07
230 263 1.347707 TCCAAAGAGGCGTGAACTGAT 59.652 47.619 0.00 0.00 37.29 2.90
233 266 0.468226 TGTCCAAAGAGGCGTGAACT 59.532 50.000 0.00 0.00 37.29 3.01
234 267 1.002792 GTTGTCCAAAGAGGCGTGAAC 60.003 52.381 0.00 0.00 37.29 3.18
235 268 1.305201 GTTGTCCAAAGAGGCGTGAA 58.695 50.000 0.00 0.00 37.29 3.18
239 272 1.841663 CGGTGTTGTCCAAAGAGGCG 61.842 60.000 0.00 0.00 37.29 5.52
253 286 1.140804 GCTTGTTTTGCACCGGTGT 59.859 52.632 33.92 0.00 0.00 4.16
262 295 2.803956 CTGCCATTCCAAGCTTGTTTTG 59.196 45.455 24.35 16.77 0.00 2.44
275 308 4.440525 CCACATGTGTATTTCCTGCCATTC 60.441 45.833 23.79 0.00 0.00 2.67
319 352 3.907260 TACGAGACACGCCGGTCCT 62.907 63.158 1.90 0.00 46.94 3.85
321 354 2.099831 CTACGAGACACGCCGGTC 59.900 66.667 1.90 0.00 46.94 4.79
325 358 2.280823 CTTCCCCTACGAGACACGCC 62.281 65.000 0.00 0.00 46.94 5.68
363 396 1.746171 GCTGGGTCCCGTTATCTTTCC 60.746 57.143 2.65 0.00 0.00 3.13
366 399 1.912971 GGCTGGGTCCCGTTATCTT 59.087 57.895 2.65 0.00 0.00 2.40
378 411 4.676951 TTTGGGAAGGCGGCTGGG 62.677 66.667 14.21 0.00 0.00 4.45
538 572 0.542467 TAACGACCTGGGTGCTGGTA 60.542 55.000 0.00 0.00 36.59 3.25
561 596 1.595993 CTCTCTCTCGCCCCGTTTGA 61.596 60.000 0.00 0.00 0.00 2.69
571 606 4.500545 CCTTCTCTCTCTCTCTCTCTCTCG 60.501 54.167 0.00 0.00 0.00 4.04
586 621 2.511145 CTGCTGCCGCCTTCTCTC 60.511 66.667 0.00 0.00 34.43 3.20
587 622 4.774503 GCTGCTGCCGCCTTCTCT 62.775 66.667 4.57 0.00 34.43 3.10
727 1167 0.837272 ACCCTCTCTCTCTCCTCTCG 59.163 60.000 0.00 0.00 0.00 4.04
729 1169 0.258774 GCACCCTCTCTCTCTCCTCT 59.741 60.000 0.00 0.00 0.00 3.69
730 1170 1.101049 CGCACCCTCTCTCTCTCCTC 61.101 65.000 0.00 0.00 0.00 3.71
979 1784 1.386200 ACCCACCCCACCTACACAA 60.386 57.895 0.00 0.00 0.00 3.33
1182 2005 2.707849 GGCATGGAAGCTGCAGTGG 61.708 63.158 16.64 0.00 41.47 4.00
1235 2058 3.302699 CGCTAGAAAAGTAGGCGTGTTAC 59.697 47.826 0.00 0.00 40.78 2.50
1240 2063 0.801067 CGCGCTAGAAAAGTAGGCGT 60.801 55.000 5.56 0.00 46.20 5.68
1256 2079 0.647410 ATCAAGCTCATTTCGTCGCG 59.353 50.000 0.00 0.00 0.00 5.87
1301 2124 0.656205 AATCGAACAAACGCGTGCAC 60.656 50.000 14.98 6.82 0.00 4.57
1302 2125 0.383737 GAATCGAACAAACGCGTGCA 60.384 50.000 14.98 0.00 0.00 4.57
1334 2157 0.179032 AGACCGCCAACATTCACACA 60.179 50.000 0.00 0.00 0.00 3.72
1410 2260 1.625315 AGGAGCACATCAACTACAGCA 59.375 47.619 0.00 0.00 0.00 4.41
1420 2336 0.461961 ACCGCTTCTAGGAGCACATC 59.538 55.000 22.96 0.00 42.83 3.06
1424 2340 3.064987 GCGACCGCTTCTAGGAGCA 62.065 63.158 22.96 0.00 42.83 4.26
1428 2344 1.154205 CCAATGCGACCGCTTCTAGG 61.154 60.000 15.61 8.49 42.51 3.02
1491 2407 1.456296 TGCGACCGCTTCTAGTAGAA 58.544 50.000 15.61 12.05 42.51 2.10
1492 2408 1.676746 ATGCGACCGCTTCTAGTAGA 58.323 50.000 15.61 0.00 42.51 2.59
1628 2557 0.987294 CCAACACCCCATCAGACTCT 59.013 55.000 0.00 0.00 0.00 3.24
1629 2558 0.693049 ACCAACACCCCATCAGACTC 59.307 55.000 0.00 0.00 0.00 3.36
1664 2593 4.415596 AGACTGGCCAAATCCAAATTACA 58.584 39.130 7.01 0.00 35.36 2.41
1757 2686 2.000803 TGGTAGAGGAGAGAGGGTCAA 58.999 52.381 0.00 0.00 0.00 3.18
1877 2806 7.136822 AGTAATTTATGGAGCAGTGGATGTA 57.863 36.000 0.00 0.00 0.00 2.29
2030 2959 8.926715 TGTGTATTACAATTGCTAGTGACTAG 57.073 34.615 15.12 15.12 36.06 2.57
2259 3188 7.814264 AATGTTTCTATAGAATGAAGCCAGG 57.186 36.000 15.82 0.00 33.54 4.45
2503 3432 8.408601 AGTAAACTATCAAATCATCAATGCCAC 58.591 33.333 0.00 0.00 0.00 5.01
2842 3771 0.329261 CATCAGGGCTTTCCTCCACA 59.671 55.000 0.00 0.00 46.12 4.17
3443 4372 2.565210 TGTCTTGCTGTTGCTGTTTG 57.435 45.000 0.00 0.00 40.48 2.93
3479 4408 4.597004 ACAGTCGGTAGTATCCTCTTTGA 58.403 43.478 0.00 0.00 0.00 2.69
3489 4418 4.321452 CCACTTGCTAAACAGTCGGTAGTA 60.321 45.833 0.00 0.00 0.00 1.82
3554 4483 1.071385 CTGTCACAGGTTTCAGCTCCT 59.929 52.381 0.00 0.00 33.96 3.69
3585 4514 9.160496 GTTGTATTCATCTCTTCTGAAGTCAAT 57.840 33.333 16.43 10.66 36.16 2.57
3593 4522 6.312426 GTCACTGGTTGTATTCATCTCTTCTG 59.688 42.308 0.00 0.00 0.00 3.02
3825 4754 4.202151 GCATTCTTCTTTTGTTCCCTGTGT 60.202 41.667 0.00 0.00 0.00 3.72
3967 4897 3.452264 TCCCTGACATCTCTATGTGGTTG 59.548 47.826 0.00 0.00 46.49 3.77
5185 6115 7.020827 TCTTTCCACAAGATCTCCTGTATTT 57.979 36.000 0.00 0.00 0.00 1.40
5351 6281 0.700564 AAAGCCTTGGCCTCATCAGA 59.299 50.000 3.32 0.00 0.00 3.27
5695 6625 9.606631 ATGGAATACAGTTCTTCAGACTTTATC 57.393 33.333 0.00 0.00 0.00 1.75
5721 6651 7.399634 ACCTTTTCCTAATTTAGAATCCGTCA 58.600 34.615 4.96 0.00 0.00 4.35
5917 6850 7.282332 AGCTTTTGAAGAACTTGAAGCTATT 57.718 32.000 18.66 0.00 0.00 1.73
6469 7402 5.358160 AGCTGCAGTTTTCTTACTTTCACTT 59.642 36.000 16.64 0.00 0.00 3.16
6625 7558 1.273606 TCTTTCAGAGGTGAAGGAGCG 59.726 52.381 0.00 0.00 42.27 5.03
6628 7561 3.181443 GGGTTTCTTTCAGAGGTGAAGGA 60.181 47.826 0.00 0.00 44.65 3.36
6899 7832 6.966534 TCCTTCTTTCTGCAGAGAAATTTT 57.033 33.333 17.43 0.00 45.25 1.82
7135 8068 1.064758 GGTGACCTATGTTCCCATGCA 60.065 52.381 0.00 0.00 32.29 3.96
7150 8083 6.002082 ACTTCCCAATTTACAACTAGGTGAC 58.998 40.000 16.48 0.00 0.00 3.67
7347 8280 3.521560 TCCAGCTCGCTAACATTTAGTG 58.478 45.455 0.85 0.85 0.00 2.74
7370 8303 5.730550 TGCTGTCGAAGTAATTTGGTCTAT 58.269 37.500 0.00 0.00 0.00 1.98
7374 8307 3.740115 ACTGCTGTCGAAGTAATTTGGT 58.260 40.909 0.00 0.00 0.00 3.67
7417 8350 7.011482 ACAAAAAGCAGTAACTTCTGACTACAG 59.989 37.037 0.00 0.00 44.66 2.74
7436 8369 9.683069 AGAAAACATGAATACTGCTACAAAAAG 57.317 29.630 0.00 0.00 0.00 2.27
7733 8666 8.037758 AGTAACAATGTTTGAAATTCCACAACA 58.962 29.630 3.17 5.38 0.00 3.33
7763 8696 4.040829 TGAAGATGATGGTGATTCGCCTAT 59.959 41.667 16.86 8.91 34.70 2.57
8306 9239 2.224597 TGCTCCAGTGCTCAAAATCTCA 60.225 45.455 0.00 0.00 0.00 3.27
8538 9529 9.650539 CATACAATTCCACCAATGTTTATTGAA 57.349 29.630 0.00 0.00 45.21 2.69
8539 9530 8.256605 CCATACAATTCCACCAATGTTTATTGA 58.743 33.333 0.00 0.00 45.21 2.57
8540 9531 8.040132 ACCATACAATTCCACCAATGTTTATTG 58.960 33.333 0.00 0.00 42.66 1.90
8541 9532 8.040132 CACCATACAATTCCACCAATGTTTATT 58.960 33.333 0.00 0.00 0.00 1.40
8631 9630 4.046103 TCAAAAGGTATATGGTTTGGGGGT 59.954 41.667 0.00 0.00 32.91 4.95
9276 10279 9.757227 GGTAATATTGTGCATTTGCCTATTAAA 57.243 29.630 0.00 0.00 41.18 1.52
9358 10361 5.485209 AGGAAAACCGACAGATACTCTTT 57.515 39.130 0.00 0.00 0.00 2.52
9543 10546 2.504367 GCCCACTAGCTGTTTTCTCAA 58.496 47.619 0.00 0.00 0.00 3.02
9781 11037 9.494271 TGGATTGTTCTAATATTATCTCAGTGC 57.506 33.333 0.00 0.00 0.00 4.40
9864 11120 3.939066 AGACACTTATTTTGGGACGGAG 58.061 45.455 0.00 0.00 0.00 4.63


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

AutoCloner maintained by Alex Coulton.