Multiple sequence alignment - TraesCS1D01G326600

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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 TraesCS1D01G326600 chr1D 100.000 2480 0 0 1 2480 419173614 419171135 0.000000e+00 4580.0
1 TraesCS1D01G326600 chr1D 86.673 1088 92 23 566 1607 418880658 418879578 0.000000e+00 1157.0
2 TraesCS1D01G326600 chr1D 89.601 827 64 10 1661 2480 419065572 419064761 0.000000e+00 1031.0
3 TraesCS1D01G326600 chr1D 84.663 965 103 13 681 1607 418756373 418755416 0.000000e+00 920.0
4 TraesCS1D01G326600 chr1D 87.464 694 76 8 921 1607 418670465 418669776 0.000000e+00 789.0
5 TraesCS1D01G326600 chr1D 83.481 902 84 27 759 1603 419296868 419295975 0.000000e+00 780.0
6 TraesCS1D01G326600 chr1D 87.822 583 54 9 118 690 418758056 418757481 0.000000e+00 667.0
7 TraesCS1D01G326600 chr1D 91.111 450 34 4 398 841 418671055 418670606 2.730000e-169 604.0
8 TraesCS1D01G326600 chr1D 87.745 408 44 4 5 412 418996940 418996539 2.890000e-129 472.0
9 TraesCS1D01G326600 chr1D 87.255 408 45 5 5 412 418966528 418966128 2.250000e-125 459.0
10 TraesCS1D01G326600 chr1D 88.587 184 13 6 399 575 418880860 418880678 1.490000e-52 217.0
11 TraesCS1D01G326600 chr1D 96.667 60 2 0 1604 1663 418669756 418669697 1.570000e-17 100.0
12 TraesCS1D01G326600 chr1D 98.182 55 1 0 398 452 418881012 418880958 2.030000e-16 97.1
13 TraesCS1D01G326600 chr1D 95.000 60 3 0 1604 1663 418879558 418879499 7.300000e-16 95.3
14 TraesCS1D01G326600 chr1D 97.143 35 1 0 1629 1663 419295983 419295949 2.660000e-05 60.2
15 TraesCS1D01G326600 chr1B 88.257 1601 137 24 2 1561 566252191 566250601 0.000000e+00 1868.0
16 TraesCS1D01G326600 chr1B 83.601 561 75 10 907 1455 566389063 566388508 6.120000e-141 510.0
17 TraesCS1D01G326600 chr1B 90.698 344 25 2 510 851 566405483 566405145 3.760000e-123 451.0
18 TraesCS1D01G326600 chr1B 87.791 344 30 8 153 494 566406290 566405957 2.310000e-105 392.0
19 TraesCS1D01G326600 chr1B 93.902 164 9 1 1444 1607 566376013 566375851 1.900000e-61 246.0
20 TraesCS1D01G326600 chr1B 83.588 262 39 2 1674 1932 566455338 566455598 2.460000e-60 243.0
21 TraesCS1D01G326600 chr1B 79.747 237 27 16 872 1091 566184370 566184138 4.270000e-33 152.0
22 TraesCS1D01G326600 chr1B 96.667 60 2 0 1604 1663 566250452 566250393 1.570000e-17 100.0
23 TraesCS1D01G326600 chr1B 80.531 113 11 4 739 851 566184545 566184444 2.640000e-10 76.8
24 TraesCS1D01G326600 chr1A 88.235 595 51 9 1661 2248 516154719 516154137 0.000000e+00 693.0
25 TraesCS1D01G326600 chr1A 92.116 241 15 3 2240 2480 516154079 516153843 1.100000e-88 337.0
26 TraesCS1D01G326600 chr1A 97.959 49 1 0 1559 1607 516048172 516048124 4.390000e-13 86.1
27 TraesCS1D01G326600 chr1A 80.000 115 12 4 737 851 516041638 516041535 9.510000e-10 75.0


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 TraesCS1D01G326600 chr1D 419171135 419173614 2479 True 4580.000000 4580 100.000000 1 2480 1 chr1D.!!$R4 2479
1 TraesCS1D01G326600 chr1D 419064761 419065572 811 True 1031.000000 1031 89.601000 1661 2480 1 chr1D.!!$R3 819
2 TraesCS1D01G326600 chr1D 418755416 418758056 2640 True 793.500000 920 86.242500 118 1607 2 chr1D.!!$R6 1489
3 TraesCS1D01G326600 chr1D 418669697 418671055 1358 True 497.666667 789 91.747333 398 1663 3 chr1D.!!$R5 1265
4 TraesCS1D01G326600 chr1D 419295949 419296868 919 True 420.100000 780 90.312000 759 1663 2 chr1D.!!$R8 904
5 TraesCS1D01G326600 chr1D 418879499 418881012 1513 True 391.600000 1157 92.110500 398 1663 4 chr1D.!!$R7 1265
6 TraesCS1D01G326600 chr1B 566250393 566252191 1798 True 984.000000 1868 92.462000 2 1663 2 chr1B.!!$R4 1661
7 TraesCS1D01G326600 chr1B 566388508 566389063 555 True 510.000000 510 83.601000 907 1455 1 chr1B.!!$R2 548
8 TraesCS1D01G326600 chr1B 566405145 566406290 1145 True 421.500000 451 89.244500 153 851 2 chr1B.!!$R5 698
9 TraesCS1D01G326600 chr1A 516153843 516154719 876 True 515.000000 693 90.175500 1661 2480 2 chr1A.!!$R3 819

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
246 253 0.112218 TGTGGGTTGAAGTCCATGGG 59.888 55.0 13.02 0.0 35.28 4.00 F
1241 3122 1.087501 GACGCCTCCATTTCCTCAAC 58.912 55.0 0.00 0.0 0.00 3.18 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1354 3235 0.109597 GCGCATGAAGAGTTGGTTGG 60.110 55.0 0.3 0.0 0.0 3.77 R
2427 4492 0.320771 CAGAAGGAACGGAGTGGTGG 60.321 60.0 0.0 0.0 45.0 4.61 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
50 51 3.005791 GCTAATGTGCCATTGGATTACCC 59.994 47.826 6.95 0.00 34.81 3.69
204 211 5.366460 TGATTTGCATGGTTTCACAAATGT 58.634 33.333 10.29 0.00 41.48 2.71
217 224 8.287503 GGTTTCACAAATGTAAGACGAACTAAT 58.712 33.333 0.00 0.00 0.00 1.73
218 225 9.659830 GTTTCACAAATGTAAGACGAACTAATT 57.340 29.630 0.00 0.00 0.00 1.40
246 253 0.112218 TGTGGGTTGAAGTCCATGGG 59.888 55.000 13.02 0.00 35.28 4.00
271 278 7.818930 GGCTCAATGAATTTAACAATGGAAGAA 59.181 33.333 0.00 0.00 0.00 2.52
320 328 5.947663 TGTCCAACCAAGGATAAAAGAAGA 58.052 37.500 0.00 0.00 40.42 2.87
530 1152 1.133025 GAACAAATCGCATGGTCCTGG 59.867 52.381 0.00 0.00 0.00 4.45
555 1177 6.263168 GTGTTGATTTACCCTATTCCCATCAG 59.737 42.308 0.00 0.00 0.00 2.90
612 1266 6.069673 TGGGCATCTAATTAACCTTTCTCTCA 60.070 38.462 0.00 0.00 0.00 3.27
613 1267 6.828785 GGGCATCTAATTAACCTTTCTCTCAA 59.171 38.462 0.00 0.00 0.00 3.02
643 1297 9.233232 GAATGTTTCACCAGTAAAGTTTAGTTG 57.767 33.333 0.00 0.53 0.00 3.16
668 1324 9.841295 TGTTCCTACTAATCAAAGTAAAGTGTT 57.159 29.630 0.00 0.00 31.72 3.32
717 2493 1.233019 CAAGGCAGTTGTCAGGACTG 58.767 55.000 0.65 0.94 45.64 3.51
739 2515 9.141400 GACTGTCGTATAATTCAGTTTTCTCTT 57.859 33.333 0.00 0.00 40.53 2.85
791 2567 5.049405 GCCCGGTCAAGATGAATAACTAATG 60.049 44.000 0.00 0.00 0.00 1.90
841 2625 1.647629 GCATGGCGCAGATCTCAAG 59.352 57.895 10.83 0.00 41.79 3.02
848 2640 1.465354 GCGCAGATCTCAAGTTGCAAG 60.465 52.381 0.30 0.00 36.37 4.01
950 2804 2.740981 CCAGCAAGTCTTCACATCTCAC 59.259 50.000 0.00 0.00 0.00 3.51
972 2829 2.911636 CCTGCATCTCCATCTCCCTTAT 59.088 50.000 0.00 0.00 0.00 1.73
973 2830 3.330110 CCTGCATCTCCATCTCCCTTATT 59.670 47.826 0.00 0.00 0.00 1.40
974 2831 4.533707 CCTGCATCTCCATCTCCCTTATTA 59.466 45.833 0.00 0.00 0.00 0.98
1021 2879 2.357517 CTCCGCGTTCAGGTGCTT 60.358 61.111 4.92 0.00 0.00 3.91
1030 2888 2.224314 CGTTCAGGTGCTTTCTTTCTCC 59.776 50.000 0.00 0.00 0.00 3.71
1142 3020 1.843376 CCTCCACACCACCACCTCT 60.843 63.158 0.00 0.00 0.00 3.69
1215 3096 3.927142 ACTGTTATTCGCAGTGCTACTTC 59.073 43.478 14.33 0.18 44.52 3.01
1234 3115 2.436646 CCTGCGACGCCTCCATTT 60.437 61.111 18.69 0.00 0.00 2.32
1239 3120 1.218047 CGACGCCTCCATTTCCTCA 59.782 57.895 0.00 0.00 0.00 3.86
1241 3122 1.087501 GACGCCTCCATTTCCTCAAC 58.912 55.000 0.00 0.00 0.00 3.18
1270 3151 3.181534 CGTATACTGCAACGTTGAAGGTG 60.182 47.826 34.14 17.79 38.20 4.00
1293 3174 3.890527 CAACTCCTGCAGGGCTAAT 57.109 52.632 32.23 11.85 35.41 1.73
1300 3181 1.421268 CCTGCAGGGCTAATACCATCA 59.579 52.381 26.14 0.00 0.00 3.07
1312 3193 2.734755 TACCATCAAGGAATGCAGGG 57.265 50.000 0.00 0.00 41.22 4.45
1354 3235 3.764049 GCGACGAGTGCAACGACC 61.764 66.667 18.81 10.20 45.86 4.79
1357 3238 1.593209 GACGAGTGCAACGACCCAA 60.593 57.895 18.81 0.00 45.86 4.12
1364 3245 1.098712 TGCAACGACCCAACCAACTC 61.099 55.000 0.00 0.00 0.00 3.01
1371 3252 1.541588 GACCCAACCAACTCTTCATGC 59.458 52.381 0.00 0.00 0.00 4.06
1374 3255 0.877071 CAACCAACTCTTCATGCGCT 59.123 50.000 9.73 0.00 0.00 5.92
1377 3258 2.778299 ACCAACTCTTCATGCGCTTTA 58.222 42.857 9.73 0.00 0.00 1.85
1399 3280 2.793946 GCAGCACCCAATACTGCG 59.206 61.111 0.00 0.00 46.38 5.18
1402 3283 0.673333 CAGCACCCAATACTGCGACA 60.673 55.000 0.00 0.00 38.51 4.35
1418 3299 0.963962 GACAGGTGTCGTTACTGGGA 59.036 55.000 0.00 0.00 36.57 4.37
1421 3302 1.825474 CAGGTGTCGTTACTGGGAGAT 59.175 52.381 0.00 0.00 0.00 2.75
1439 3320 4.074970 GAGATCCAGAAGTGCCAGAAAAA 58.925 43.478 0.00 0.00 0.00 1.94
1444 3325 1.683385 AGAAGTGCCAGAAAAAGTGCC 59.317 47.619 0.00 0.00 0.00 5.01
1447 3328 2.049156 GCCAGAAAAAGTGCCGCC 60.049 61.111 0.00 0.00 0.00 6.13
1476 3357 3.996614 GCACCCAAATGCGTACCT 58.003 55.556 0.00 0.00 35.50 3.08
1487 3368 0.613853 TGCGTACCTTAGAGGCCTGT 60.614 55.000 12.00 9.69 39.63 4.00
1524 3411 3.410516 CGTCGCATGGTCAACGCA 61.411 61.111 0.00 0.00 0.00 5.24
1670 3663 4.137543 CCACTCTAGAATAAACCATGCCC 58.862 47.826 0.00 0.00 0.00 5.36
1671 3664 4.141390 CCACTCTAGAATAAACCATGCCCT 60.141 45.833 0.00 0.00 0.00 5.19
1676 3669 3.026694 AGAATAAACCATGCCCTCAAGC 58.973 45.455 0.00 0.00 0.00 4.01
1677 3670 2.834638 ATAAACCATGCCCTCAAGCT 57.165 45.000 0.00 0.00 0.00 3.74
1681 3674 1.302285 CCATGCCCTCAAGCTGACT 59.698 57.895 0.00 0.00 0.00 3.41
1707 3700 3.320256 TCAGATGAGGATGGAGATTGACG 59.680 47.826 0.00 0.00 0.00 4.35
1711 3704 1.043116 AGGATGGAGATTGACGGCGA 61.043 55.000 16.62 0.00 0.00 5.54
1716 3709 3.254470 TGGAGATTGACGGCGAATAAA 57.746 42.857 16.62 2.01 0.00 1.40
1720 3713 3.458189 AGATTGACGGCGAATAAAGAGG 58.542 45.455 16.62 0.00 0.00 3.69
1725 3718 2.997986 GACGGCGAATAAAGAGGTCAAA 59.002 45.455 16.62 0.00 0.00 2.69
1726 3719 2.740447 ACGGCGAATAAAGAGGTCAAAC 59.260 45.455 16.62 0.00 0.00 2.93
1769 3762 4.500499 AATGAGGAGAGGACAAAGGATG 57.500 45.455 0.00 0.00 0.00 3.51
1772 3765 1.558756 AGGAGAGGACAAAGGATGCAG 59.441 52.381 0.00 0.00 0.00 4.41
1783 3776 2.359169 GGATGCAGACCCGGACAGA 61.359 63.158 0.73 0.00 0.00 3.41
1786 3779 0.620556 ATGCAGACCCGGACAGATTT 59.379 50.000 0.73 0.00 0.00 2.17
1810 3803 3.016474 GCGAAGACGACCTTGCTGC 62.016 63.158 0.00 0.00 42.66 5.25
1821 3814 3.147132 TTGCTGCCGAGGAAGACA 58.853 55.556 0.16 0.00 0.00 3.41
1833 3826 3.471680 GAGGAAGACAAAGACAAGCTGT 58.528 45.455 0.00 0.00 0.00 4.40
1871 3864 0.248843 AGAGAAGCTCGCCAAAGGAG 59.751 55.000 0.00 0.00 35.36 3.69
1878 3871 0.674581 CTCGCCAAAGGAGCACATGA 60.675 55.000 0.00 0.00 0.00 3.07
1879 3872 0.250684 TCGCCAAAGGAGCACATGAA 60.251 50.000 0.00 0.00 0.00 2.57
1882 3875 1.340889 GCCAAAGGAGCACATGAACAA 59.659 47.619 0.00 0.00 0.00 2.83
1884 3877 3.383761 CCAAAGGAGCACATGAACAAAC 58.616 45.455 0.00 0.00 0.00 2.93
1901 3894 2.150397 AACGAGACAAGAAGGAACGG 57.850 50.000 0.00 0.00 0.00 4.44
1927 3920 8.463607 GGCTACCACTACATCTAGATAAAGATC 58.536 40.741 16.57 0.00 33.87 2.75
1928 3921 8.178964 GCTACCACTACATCTAGATAAAGATCG 58.821 40.741 16.57 2.35 37.15 3.69
1929 3922 9.438228 CTACCACTACATCTAGATAAAGATCGA 57.562 37.037 16.57 0.00 37.15 3.59
1935 3928 7.674471 ACATCTAGATAAAGATCGACGATGA 57.326 36.000 16.49 3.11 37.78 2.92
1941 3934 0.248661 AAGATCGACGATGACGCCAG 60.249 55.000 16.49 0.00 43.96 4.85
1980 3973 1.607178 CCCTGGACCAATGCAGCAA 60.607 57.895 0.00 0.00 42.73 3.91
1988 3981 1.154413 CAATGCAGCAACGACGGAC 60.154 57.895 0.00 0.00 0.00 4.79
1992 3985 2.244651 GCAGCAACGACGGACAGTT 61.245 57.895 0.00 0.00 0.00 3.16
2018 4011 3.382111 AGGAGAGAACCTGGCACG 58.618 61.111 0.00 0.00 39.01 5.34
2046 4039 9.303537 GGATACTATCTCGTAATATTTTGCCTC 57.696 37.037 0.00 0.00 0.00 4.70
2047 4040 9.856488 GATACTATCTCGTAATATTTTGCCTCA 57.144 33.333 0.00 0.00 0.00 3.86
2091 4091 6.406093 TTCAAAAGTCAACTTAACGTCGAA 57.594 33.333 0.00 0.00 34.61 3.71
2098 4098 7.757223 AAGTCAACTTAACGTCGAAAGGATCG 61.757 42.308 0.00 0.00 42.86 3.69
2189 4189 9.612066 AAAAAGAAGTCAAAAATGCTTGGATAA 57.388 25.926 0.00 0.00 0.00 1.75
2190 4190 9.783081 AAAAGAAGTCAAAAATGCTTGGATAAT 57.217 25.926 0.00 0.00 0.00 1.28
2202 4202 6.558771 TGCTTGGATAATATGTCGATTTGG 57.441 37.500 0.00 0.00 0.00 3.28
2205 4205 6.621596 GCTTGGATAATATGTCGATTTGGAGC 60.622 42.308 0.00 0.00 0.00 4.70
2206 4206 5.863965 TGGATAATATGTCGATTTGGAGCA 58.136 37.500 0.00 0.00 0.00 4.26
2207 4207 5.934043 TGGATAATATGTCGATTTGGAGCAG 59.066 40.000 0.00 0.00 0.00 4.24
2208 4208 5.163814 GGATAATATGTCGATTTGGAGCAGC 60.164 44.000 0.00 0.00 0.00 5.25
2224 4224 2.812591 AGCAGCATATCTACAGCATTGC 59.187 45.455 0.00 0.00 31.85 3.56
2246 4311 2.584492 GCACTTGGCACATAATTCCC 57.416 50.000 0.00 0.00 43.97 3.97
2248 4313 2.497273 GCACTTGGCACATAATTCCCTT 59.503 45.455 0.00 0.00 43.97 3.95
2249 4314 3.699038 GCACTTGGCACATAATTCCCTTA 59.301 43.478 0.00 0.00 43.97 2.69
2250 4315 4.202050 GCACTTGGCACATAATTCCCTTAG 60.202 45.833 0.00 0.00 43.97 2.18
2251 4316 4.949856 CACTTGGCACATAATTCCCTTAGT 59.050 41.667 0.00 0.00 39.30 2.24
2276 4341 7.917505 GTGAGCCAGAATTTATTTAGTTCATGG 59.082 37.037 0.00 0.00 0.00 3.66
2277 4342 6.809869 AGCCAGAATTTATTTAGTTCATGGC 58.190 36.000 14.36 14.36 41.34 4.40
2278 4343 6.608808 AGCCAGAATTTATTTAGTTCATGGCT 59.391 34.615 16.96 16.96 43.48 4.75
2279 4344 6.698766 GCCAGAATTTATTTAGTTCATGGCTG 59.301 38.462 14.67 0.00 39.84 4.85
2300 4365 6.039616 GCTGCCTATATACTGTAGATTCTGC 58.960 44.000 0.00 0.00 0.00 4.26
2306 4371 8.090831 CCTATATACTGTAGATTCTGCTTGCAA 58.909 37.037 0.00 0.00 0.00 4.08
2335 4400 6.698008 TGATCACTGTGACTTCAAACATTT 57.302 33.333 13.50 0.00 0.00 2.32
2367 4432 5.643379 ATTACGCCATTGAACTTTGATGT 57.357 34.783 0.00 0.00 0.00 3.06
2422 4487 7.709613 TGGTAGAAGTGTCAAAGAACTTTACTC 59.290 37.037 0.00 1.94 36.77 2.59
2423 4488 7.927092 GGTAGAAGTGTCAAAGAACTTTACTCT 59.073 37.037 0.00 3.72 36.77 3.24
2427 4492 9.917872 GAAGTGTCAAAGAACTTTACTCTTTAC 57.082 33.333 15.71 0.00 40.37 2.01
2436 4501 5.224821 ACTTTACTCTTTACCACCACTCC 57.775 43.478 0.00 0.00 0.00 3.85
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 7.994334 TGATCACAGTCATTGGATCATTGATAA 59.006 33.333 0.00 0.00 37.97 1.75
50 51 0.677731 ATCTGCAACATGGACCACCG 60.678 55.000 0.00 0.00 39.42 4.94
204 211 9.635632 CACAAAACGTTTAATTAGTTCGTCTTA 57.364 29.630 15.03 0.00 33.67 2.10
217 224 5.388408 ACTTCAACCCACAAAACGTTTAA 57.612 34.783 15.03 0.43 0.00 1.52
218 225 4.142425 GGACTTCAACCCACAAAACGTTTA 60.142 41.667 15.03 0.00 0.00 2.01
219 226 3.367600 GGACTTCAACCCACAAAACGTTT 60.368 43.478 7.96 7.96 0.00 3.60
220 227 2.164827 GGACTTCAACCCACAAAACGTT 59.835 45.455 0.00 0.00 0.00 3.99
221 228 1.746787 GGACTTCAACCCACAAAACGT 59.253 47.619 0.00 0.00 0.00 3.99
222 229 1.746220 TGGACTTCAACCCACAAAACG 59.254 47.619 0.00 0.00 0.00 3.60
246 253 8.761575 TTCTTCCATTGTTAAATTCATTGAGC 57.238 30.769 0.00 0.00 0.00 4.26
271 278 8.477419 TGAAGTTTTCTCCATCCATTTAAACT 57.523 30.769 0.00 0.00 36.29 2.66
506 1127 2.083774 GACCATGCGATTTGTTCCTCA 58.916 47.619 0.00 0.00 0.00 3.86
530 1152 6.126409 TGATGGGAATAGGGTAAATCAACAC 58.874 40.000 0.00 0.00 0.00 3.32
555 1177 2.038837 GTGGCCGCCAAGGTTACTC 61.039 63.158 15.39 0.00 43.70 2.59
612 1266 5.768164 ACTTTACTGGTGAAACATTCCGATT 59.232 36.000 0.00 0.00 39.98 3.34
613 1267 5.313712 ACTTTACTGGTGAAACATTCCGAT 58.686 37.500 0.00 0.00 39.98 4.18
717 2493 8.809478 GGAGAAGAGAAAACTGAATTATACGAC 58.191 37.037 0.00 0.00 0.00 4.34
739 2515 4.773674 TGGGTTCGATAGTTTAAGTGGAGA 59.226 41.667 0.00 0.00 37.40 3.71
903 2752 4.694982 CACATACGATGCCATTTATAGCCA 59.305 41.667 0.00 0.00 0.00 4.75
950 2804 0.767446 AGGGAGATGGAGATGCAGGG 60.767 60.000 0.00 0.00 0.00 4.45
972 2829 3.537580 GTGGACACACAACCAAGACTAA 58.462 45.455 0.00 0.00 46.90 2.24
973 2830 3.188159 GTGGACACACAACCAAGACTA 57.812 47.619 0.00 0.00 46.90 2.59
974 2831 2.038387 GTGGACACACAACCAAGACT 57.962 50.000 0.00 0.00 46.90 3.24
1021 2879 1.671054 CGGCCGCTTGGAGAAAGAA 60.671 57.895 14.67 0.00 38.24 2.52
1215 3096 2.859273 AAATGGAGGCGTCGCAGGAG 62.859 60.000 20.50 0.00 0.00 3.69
1286 3167 3.507622 GCATTCCTTGATGGTATTAGCCC 59.492 47.826 0.00 0.00 37.07 5.19
1288 3169 4.217118 CCTGCATTCCTTGATGGTATTAGC 59.783 45.833 0.00 0.00 37.07 3.09
1290 3171 4.728772 CCCTGCATTCCTTGATGGTATTA 58.271 43.478 0.00 0.00 37.07 0.98
1292 3173 2.754186 GCCCTGCATTCCTTGATGGTAT 60.754 50.000 0.00 0.00 37.07 2.73
1293 3174 1.410083 GCCCTGCATTCCTTGATGGTA 60.410 52.381 0.00 0.00 37.07 3.25
1300 3181 2.363406 GCTGGCCCTGCATTCCTT 60.363 61.111 7.85 0.00 0.00 3.36
1354 3235 0.109597 GCGCATGAAGAGTTGGTTGG 60.110 55.000 0.30 0.00 0.00 3.77
1357 3238 1.609208 AAAGCGCATGAAGAGTTGGT 58.391 45.000 11.47 0.00 0.00 3.67
1374 3255 0.893270 ATTGGGTGCTGCACGCTAAA 60.893 50.000 37.86 28.81 45.53 1.85
1377 3258 2.040544 GTATTGGGTGCTGCACGCT 61.041 57.895 37.86 26.54 45.53 5.07
1385 3266 1.369091 CCTGTCGCAGTATTGGGTGC 61.369 60.000 2.22 0.00 38.34 5.01
1399 3280 0.963962 TCCCAGTAACGACACCTGTC 59.036 55.000 0.00 0.00 41.47 3.51
1402 3283 2.100989 GATCTCCCAGTAACGACACCT 58.899 52.381 0.00 0.00 0.00 4.00
1414 3295 0.547471 TGGCACTTCTGGATCTCCCA 60.547 55.000 0.00 0.00 44.25 4.37
1418 3299 3.795688 TTTTCTGGCACTTCTGGATCT 57.204 42.857 0.00 0.00 0.00 2.75
1421 3302 2.951642 CACTTTTTCTGGCACTTCTGGA 59.048 45.455 0.00 0.00 0.00 3.86
1427 3308 2.032981 CGGCACTTTTTCTGGCACT 58.967 52.632 0.00 0.00 33.84 4.40
1476 3357 6.208994 GCTATAGCTAGTTTACAGGCCTCTAA 59.791 42.308 17.75 0.00 38.21 2.10
1487 3368 5.196341 ACGCACATGCTATAGCTAGTTTA 57.804 39.130 24.61 4.45 42.66 2.01
1524 3411 5.238868 GCACATAGATGCATCACAAGAAGAT 59.761 40.000 27.81 6.98 45.39 2.40
1552 3439 6.421801 CGATGTCATAGCATCTCATACACAAA 59.578 38.462 4.82 0.00 42.14 2.83
1677 3670 5.074239 TCTCCATCCTCATCTGATCTAGTCA 59.926 44.000 0.00 0.00 35.05 3.41
1681 3674 6.436847 GTCAATCTCCATCCTCATCTGATCTA 59.563 42.308 0.00 0.00 0.00 1.98
1690 3683 0.465705 GCCGTCAATCTCCATCCTCA 59.534 55.000 0.00 0.00 0.00 3.86
1707 3700 2.422479 GGGTTTGACCTCTTTATTCGCC 59.578 50.000 0.00 0.00 38.64 5.54
1711 3704 4.721132 TGTTCGGGTTTGACCTCTTTATT 58.279 39.130 0.00 0.00 38.64 1.40
1716 3709 2.721425 TTTGTTCGGGTTTGACCTCT 57.279 45.000 0.00 0.00 38.64 3.69
1720 3713 4.084589 GCATTGATTTTGTTCGGGTTTGAC 60.085 41.667 0.00 0.00 0.00 3.18
1725 3718 1.967066 TGGCATTGATTTTGTTCGGGT 59.033 42.857 0.00 0.00 0.00 5.28
1726 3719 2.230992 TCTGGCATTGATTTTGTTCGGG 59.769 45.455 0.00 0.00 0.00 5.14
1769 3762 1.026718 CCAAATCTGTCCGGGTCTGC 61.027 60.000 0.00 0.00 0.00 4.26
1772 3765 1.749258 GGCCAAATCTGTCCGGGTC 60.749 63.158 0.00 0.00 0.00 4.46
1783 3776 1.003839 TCGTCTTCGCAGGCCAAAT 60.004 52.632 5.01 0.00 36.96 2.32
1786 3779 4.373116 GGTCGTCTTCGCAGGCCA 62.373 66.667 5.01 0.00 36.96 5.36
1791 3784 1.664649 CAGCAAGGTCGTCTTCGCA 60.665 57.895 13.08 0.00 34.34 5.10
1810 3803 1.801178 GCTTGTCTTTGTCTTCCTCGG 59.199 52.381 0.00 0.00 0.00 4.63
1821 3814 2.930950 TGGTAGCAACAGCTTGTCTTT 58.069 42.857 0.00 0.00 39.77 2.52
1833 3826 1.691976 CTCGTATCCCCATGGTAGCAA 59.308 52.381 11.73 0.00 0.00 3.91
1871 3864 3.002246 TCTTGTCTCGTTTGTTCATGTGC 59.998 43.478 0.00 0.00 0.00 4.57
1878 3871 3.308866 CGTTCCTTCTTGTCTCGTTTGTT 59.691 43.478 0.00 0.00 0.00 2.83
1879 3872 2.864343 CGTTCCTTCTTGTCTCGTTTGT 59.136 45.455 0.00 0.00 0.00 2.83
1882 3875 1.270147 CCCGTTCCTTCTTGTCTCGTT 60.270 52.381 0.00 0.00 0.00 3.85
1884 3877 1.014564 GCCCGTTCCTTCTTGTCTCG 61.015 60.000 0.00 0.00 0.00 4.04
1901 3894 7.762588 TCTTTATCTAGATGTAGTGGTAGCC 57.237 40.000 15.79 0.00 0.00 3.93
1927 3920 3.250323 CTGCTGGCGTCATCGTCG 61.250 66.667 0.00 0.00 45.30 5.12
1928 3921 2.887568 CCTGCTGGCGTCATCGTC 60.888 66.667 0.00 0.00 42.45 4.20
1929 3922 3.362399 CTCCTGCTGGCGTCATCGT 62.362 63.158 4.42 0.00 39.49 3.73
1935 3928 3.699894 CTCCACTCCTGCTGGCGT 61.700 66.667 4.42 1.38 0.00 5.68
1941 3934 3.077617 GAGCAATCTCCACTCCTGC 57.922 57.895 0.00 0.00 33.19 4.85
1994 3987 4.821589 GGTTCTCTCCTGGCGCCG 62.822 72.222 23.90 16.52 0.00 6.46
2018 4011 9.303537 GGCAAAATATTACGAGATAGTATCCTC 57.696 37.037 6.53 3.59 0.00 3.71
2038 4031 8.891720 GGAATATGCAAAATATTTGAGGCAAAA 58.108 29.630 19.78 14.00 36.90 2.44
2039 4032 8.266473 AGGAATATGCAAAATATTTGAGGCAAA 58.734 29.630 19.78 0.00 37.75 3.68
2040 4033 7.794041 AGGAATATGCAAAATATTTGAGGCAA 58.206 30.769 19.78 12.75 34.64 4.52
2041 4034 7.364149 AGGAATATGCAAAATATTTGAGGCA 57.636 32.000 18.78 18.78 35.54 4.75
2042 4035 8.667076 AAAGGAATATGCAAAATATTTGAGGC 57.333 30.769 0.39 7.07 0.00 4.70
2091 4091 1.115467 AAGTGGCGATCTCGATCCTT 58.885 50.000 3.33 0.00 43.02 3.36
2098 4098 5.294306 TGTTGATTATGAAAGTGGCGATCTC 59.706 40.000 0.00 0.00 0.00 2.75
2168 4168 9.807649 ACATATTATCCAAGCATTTTTGACTTC 57.192 29.630 0.00 0.00 0.00 3.01
2169 4169 9.807649 GACATATTATCCAAGCATTTTTGACTT 57.192 29.630 0.00 0.00 0.00 3.01
2170 4170 8.131100 CGACATATTATCCAAGCATTTTTGACT 58.869 33.333 0.00 0.00 0.00 3.41
2180 4180 6.621596 GCTCCAAATCGACATATTATCCAAGC 60.622 42.308 0.00 0.00 0.00 4.01
2189 4189 3.198409 TGCTGCTCCAAATCGACATAT 57.802 42.857 0.00 0.00 0.00 1.78
2190 4190 2.689553 TGCTGCTCCAAATCGACATA 57.310 45.000 0.00 0.00 0.00 2.29
2202 4202 3.120269 GCAATGCTGTAGATATGCTGCTC 60.120 47.826 8.58 0.00 0.00 4.26
2205 4205 4.093115 GCTAGCAATGCTGTAGATATGCTG 59.907 45.833 19.25 0.71 43.39 4.41
2206 4206 4.252073 GCTAGCAATGCTGTAGATATGCT 58.748 43.478 19.25 3.42 45.31 3.79
2207 4207 3.999001 TGCTAGCAATGCTGTAGATATGC 59.001 43.478 19.25 9.15 40.10 3.14
2208 4208 5.236282 AGTGCTAGCAATGCTGTAGATATG 58.764 41.667 21.29 0.00 40.10 1.78
2224 4224 3.316308 GGGAATTATGTGCCAAGTGCTAG 59.684 47.826 0.00 0.00 42.00 3.42
2248 4313 9.905713 ATGAACTAAATAAATTCTGGCTCACTA 57.094 29.630 0.00 0.00 0.00 2.74
2249 4314 8.680903 CATGAACTAAATAAATTCTGGCTCACT 58.319 33.333 0.00 0.00 0.00 3.41
2250 4315 7.917505 CCATGAACTAAATAAATTCTGGCTCAC 59.082 37.037 0.00 0.00 0.00 3.51
2251 4316 7.416664 GCCATGAACTAAATAAATTCTGGCTCA 60.417 37.037 14.22 0.00 40.13 4.26
2276 4341 6.039616 GCAGAATCTACAGTATATAGGCAGC 58.960 44.000 0.00 0.00 0.00 5.25
2277 4342 7.403312 AGCAGAATCTACAGTATATAGGCAG 57.597 40.000 0.00 0.00 0.00 4.85
2278 4343 7.606349 CAAGCAGAATCTACAGTATATAGGCA 58.394 38.462 0.00 0.00 0.00 4.75
2279 4344 6.533367 GCAAGCAGAATCTACAGTATATAGGC 59.467 42.308 0.00 0.00 0.00 3.93
2300 4365 5.628193 GTCACAGTGATCAAATCTTTGCAAG 59.372 40.000 6.51 0.00 38.05 4.01
2306 4371 7.067372 TGTTTGAAGTCACAGTGATCAAATCTT 59.933 33.333 25.06 15.31 37.56 2.40
2318 4383 6.692681 CACCAGTAAAATGTTTGAAGTCACAG 59.307 38.462 0.00 0.00 0.00 3.66
2335 4400 4.580868 TCAATGGCGTAATTCACCAGTAA 58.419 39.130 1.17 0.00 36.78 2.24
2367 4432 7.816995 AGTTGCTTGTATTTGTTTCTTGTGAAA 59.183 29.630 0.00 0.00 39.59 2.69
2381 4446 7.068226 ACACTTCTACCAAAAGTTGCTTGTATT 59.932 33.333 0.00 0.00 34.79 1.89
2386 4451 4.947388 TGACACTTCTACCAAAAGTTGCTT 59.053 37.500 0.00 0.00 34.79 3.91
2422 4487 1.346722 AGGAACGGAGTGGTGGTAAAG 59.653 52.381 0.00 0.00 45.00 1.85
2423 4488 1.426751 AGGAACGGAGTGGTGGTAAA 58.573 50.000 0.00 0.00 45.00 2.01
2427 4492 0.320771 CAGAAGGAACGGAGTGGTGG 60.321 60.000 0.00 0.00 45.00 4.61
2436 4501 0.802607 GAGGTAGCGCAGAAGGAACG 60.803 60.000 11.47 0.00 0.00 3.95


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

AutoCloner maintained by Alex Coulton.