Multiple sequence alignment - TraesCS1D01G309900

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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 TraesCS1D01G309900 chr1D 100.000 3386 0 0 1 3386 405762395 405765780 0.000000e+00 6253
1 TraesCS1D01G309900 chr1A 93.409 2033 115 8 1361 3386 500988406 500990426 0.000000e+00 2994
2 TraesCS1D01G309900 chr1A 86.686 1705 179 28 1299 2983 500979723 500981399 0.000000e+00 1847
3 TraesCS1D01G309900 chr1A 80.911 461 35 21 715 1146 500985756 500986192 7.050000e-82 315
4 TraesCS1D01G309900 chr1A 84.407 295 26 9 9 287 500978362 500978652 4.310000e-69 272
5 TraesCS1D01G309900 chr1A 77.055 523 62 35 541 1039 500978887 500979375 7.260000e-62 248
6 TraesCS1D01G309900 chr1A 91.753 97 8 0 96 192 500984019 500984115 5.890000e-28 135
7 TraesCS1D01G309900 chr1A 94.253 87 5 0 9 95 500983633 500983719 2.120000e-27 134
8 TraesCS1D01G309900 chr1B 87.452 2064 169 42 398 2404 545642542 545644572 0.000000e+00 2294
9 TraesCS1D01G309900 chr1B 89.716 1760 144 17 1257 3001 545800308 545802045 0.000000e+00 2213
10 TraesCS1D01G309900 chr1B 88.103 580 48 8 2406 2983 545644622 545645182 0.000000e+00 669
11 TraesCS1D01G309900 chr1B 84.518 394 41 14 2998 3380 545802106 545802490 4.130000e-99 372
12 TraesCS1D01G309900 chr1B 95.536 224 8 2 9 232 545641594 545641815 1.160000e-94 357
13 TraesCS1D01G309900 chr1B 83.200 375 36 14 3014 3380 545645287 545645642 5.450000e-83 318
14 TraesCS1D01G309900 chr1B 79.956 459 44 24 722 1146 545799656 545800100 9.190000e-76 294
15 TraesCS1D01G309900 chr1B 84.561 285 23 10 9 287 545797762 545798031 2.590000e-66 263
16 TraesCS1D01G309900 chr1B 93.711 159 7 2 242 399 545642223 545642379 5.650000e-58 235


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 TraesCS1D01G309900 chr1D 405762395 405765780 3385 False 6253.000000 6253 100.000000 1 3386 1 chr1D.!!$F1 3385
1 TraesCS1D01G309900 chr1A 500978362 500990426 12064 False 849.285714 2994 86.924857 9 3386 7 chr1A.!!$F1 3377
2 TraesCS1D01G309900 chr1B 545797762 545802490 4728 False 785.500000 2213 84.687750 9 3380 4 chr1B.!!$F2 3371
3 TraesCS1D01G309900 chr1B 545641594 545645642 4048 False 774.600000 2294 89.600400 9 3380 5 chr1B.!!$F1 3371

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
234 5805 0.392998 CCTTTGTCCCGGTCCTCATG 60.393 60.000 0.00 0.0 0.0 3.07 F
296 6295 0.693049 ACGTCAGAGCCCTCCAAATT 59.307 50.000 0.00 0.0 0.0 1.82 F
1578 11246 1.066430 TCCACCGGTGAAGCTGTATTC 60.066 52.381 36.07 0.0 0.0 1.75 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1413 11081 0.030101 CCGCGTTTTGGCTTTCAGAA 59.970 50.0 4.92 0.0 0.00 3.02 R
1653 11321 0.598680 CGCCGATCCTTGGATGAGTC 60.599 60.0 6.92 0.0 0.00 3.36 R
3132 12961 0.244721 GGAACTGCCACAATTGCTCC 59.755 55.0 5.05 0.0 36.34 4.70 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
181 5752 1.630878 ACAGGTCAGATCTTTGTCCCC 59.369 52.381 0.00 0.00 0.00 4.81
200 5771 1.379710 TTCCCCATCACATTGCCCG 60.380 57.895 0.00 0.00 0.00 6.13
232 5803 2.221299 CCCTTTGTCCCGGTCCTCA 61.221 63.158 0.00 0.00 0.00 3.86
233 5804 1.562672 CCCTTTGTCCCGGTCCTCAT 61.563 60.000 0.00 0.00 0.00 2.90
234 5805 0.392998 CCTTTGTCCCGGTCCTCATG 60.393 60.000 0.00 0.00 0.00 3.07
235 5806 1.002624 TTTGTCCCGGTCCTCATGC 60.003 57.895 0.00 0.00 0.00 4.06
260 6229 3.473647 CGCTGATCAGAGCCCCCA 61.474 66.667 27.04 0.00 35.36 4.96
296 6295 0.693049 ACGTCAGAGCCCTCCAAATT 59.307 50.000 0.00 0.00 0.00 1.82
344 7707 5.660460 TGCAAGAGAAGCAATTCGACTATA 58.340 37.500 0.00 0.00 39.39 1.31
345 7708 6.106003 TGCAAGAGAAGCAATTCGACTATAA 58.894 36.000 0.00 0.00 39.39 0.98
364 7727 2.489938 AAAGTGAAGCAATCCGGCTA 57.510 45.000 0.00 0.00 45.07 3.93
428 7990 6.316390 CGTCTTCAGGGAGTTAATTAATTGCT 59.684 38.462 11.05 8.60 0.00 3.91
430 7992 8.831550 GTCTTCAGGGAGTTAATTAATTGCTAG 58.168 37.037 11.05 5.53 0.00 3.42
476 8038 1.129809 GACCGTCGCACGACATTTG 59.870 57.895 21.66 9.94 46.05 2.32
479 8041 1.553195 CCGTCGCACGACATTTGTCA 61.553 55.000 21.66 0.00 46.05 3.58
507 8072 6.086765 GGCAAAATGTATAATTTCGAGATGCG 59.913 38.462 0.00 0.00 42.69 4.73
511 8076 4.556233 TGTATAATTTCGAGATGCGGAGG 58.444 43.478 0.00 0.00 41.33 4.30
512 8077 4.279922 TGTATAATTTCGAGATGCGGAGGA 59.720 41.667 0.00 0.00 41.33 3.71
537 8102 2.158534 CCATCCCATTAATTCCCGTCCA 60.159 50.000 0.00 0.00 0.00 4.02
538 8103 3.561143 CATCCCATTAATTCCCGTCCAA 58.439 45.455 0.00 0.00 0.00 3.53
700 8300 9.730420 ACAAGATTTATTATGATGCGGTTTAAC 57.270 29.630 0.00 0.00 0.00 2.01
709 8309 2.201921 TGCGGTTTAACAGGGCAATA 57.798 45.000 5.50 0.00 0.00 1.90
710 8310 2.088423 TGCGGTTTAACAGGGCAATAG 58.912 47.619 5.50 0.00 0.00 1.73
745 8347 7.658525 TGTGCATAAGAATAATGTTTCCCAT 57.341 32.000 0.00 0.00 34.36 4.00
746 8348 7.715657 TGTGCATAAGAATAATGTTTCCCATC 58.284 34.615 0.00 0.00 31.75 3.51
948 8582 2.699954 CGTTGCTCTACCACTCCATTT 58.300 47.619 0.00 0.00 0.00 2.32
978 8616 2.027192 ACAAGCGAGAGAGAGAGAGAGT 60.027 50.000 0.00 0.00 0.00 3.24
982 8620 3.641436 AGCGAGAGAGAGAGAGAGTGATA 59.359 47.826 0.00 0.00 0.00 2.15
1020 8658 2.743928 GAGGGCAAGCACACCGAG 60.744 66.667 0.00 0.00 0.00 4.63
1076 8718 6.789268 TCCTCAAGATTTGAACCAGGATTTA 58.211 36.000 0.00 0.00 39.58 1.40
1078 8720 6.096001 CCTCAAGATTTGAACCAGGATTTAGG 59.904 42.308 0.00 0.00 39.58 2.69
1079 8721 6.789268 TCAAGATTTGAACCAGGATTTAGGA 58.211 36.000 0.00 0.00 36.59 2.94
1083 8725 8.071177 AGATTTGAACCAGGATTTAGGATTTG 57.929 34.615 0.00 0.00 0.00 2.32
1092 8734 8.875168 ACCAGGATTTAGGATTTGTAGATAGAG 58.125 37.037 0.00 0.00 0.00 2.43
1121 8764 1.134220 AGACAGAGTGCGAAAAACCCA 60.134 47.619 0.00 0.00 0.00 4.51
1122 8765 1.264288 GACAGAGTGCGAAAAACCCAG 59.736 52.381 0.00 0.00 0.00 4.45
1148 8792 7.665559 GGTTATTCAGCCATATATGAACTTCCA 59.334 37.037 14.54 0.00 38.19 3.53
1152 8796 7.333528 TCAGCCATATATGAACTTCCAAAAC 57.666 36.000 14.54 0.00 0.00 2.43
1153 8797 6.321181 TCAGCCATATATGAACTTCCAAAACC 59.679 38.462 14.54 0.00 0.00 3.27
1154 8798 6.322201 CAGCCATATATGAACTTCCAAAACCT 59.678 38.462 14.54 0.00 0.00 3.50
1155 8799 6.322201 AGCCATATATGAACTTCCAAAACCTG 59.678 38.462 14.54 0.00 0.00 4.00
1156 8800 6.507023 CCATATATGAACTTCCAAAACCTGC 58.493 40.000 14.54 0.00 0.00 4.85
1157 8801 6.322201 CCATATATGAACTTCCAAAACCTGCT 59.678 38.462 14.54 0.00 0.00 4.24
1158 8802 7.502226 CCATATATGAACTTCCAAAACCTGCTA 59.498 37.037 14.54 0.00 0.00 3.49
1159 8803 8.902806 CATATATGAACTTCCAAAACCTGCTAA 58.097 33.333 6.92 0.00 0.00 3.09
1161 8805 6.670695 ATGAACTTCCAAAACCTGCTAATT 57.329 33.333 0.00 0.00 0.00 1.40
1163 8807 6.512297 TGAACTTCCAAAACCTGCTAATTTC 58.488 36.000 0.00 0.00 0.00 2.17
1164 8808 6.097554 TGAACTTCCAAAACCTGCTAATTTCA 59.902 34.615 0.00 0.00 0.00 2.69
1165 8809 6.478512 ACTTCCAAAACCTGCTAATTTCAA 57.521 33.333 0.00 0.00 0.00 2.69
1166 8810 6.515832 ACTTCCAAAACCTGCTAATTTCAAG 58.484 36.000 0.00 0.00 0.00 3.02
1167 8811 5.467035 TCCAAAACCTGCTAATTTCAAGG 57.533 39.130 0.00 0.00 0.00 3.61
1168 8812 5.144100 TCCAAAACCTGCTAATTTCAAGGA 58.856 37.500 6.92 0.00 0.00 3.36
1170 8814 6.071391 TCCAAAACCTGCTAATTTCAAGGATC 60.071 38.462 6.92 0.00 0.00 3.36
1173 8817 3.950395 ACCTGCTAATTTCAAGGATCTGC 59.050 43.478 6.92 0.00 0.00 4.26
1174 8818 3.003068 CCTGCTAATTTCAAGGATCTGCG 59.997 47.826 0.00 0.00 0.00 5.18
1175 8819 3.872696 TGCTAATTTCAAGGATCTGCGA 58.127 40.909 0.00 0.00 0.00 5.10
1176 8820 3.873361 TGCTAATTTCAAGGATCTGCGAG 59.127 43.478 0.00 0.00 0.00 5.03
1177 8821 3.249559 GCTAATTTCAAGGATCTGCGAGG 59.750 47.826 0.00 0.00 0.00 4.63
1179 8823 3.634397 ATTTCAAGGATCTGCGAGGAA 57.366 42.857 0.00 0.00 0.00 3.36
1180 8824 3.634397 TTTCAAGGATCTGCGAGGAAT 57.366 42.857 0.00 0.00 0.00 3.01
1181 8825 3.634397 TTCAAGGATCTGCGAGGAATT 57.366 42.857 0.00 0.00 0.00 2.17
1187 8861 3.509575 AGGATCTGCGAGGAATTAGCTAG 59.490 47.826 0.00 0.00 0.00 3.42
1208 8882 7.036220 GCTAGAACTAGTTGATTTCTGCTGTA 58.964 38.462 14.14 0.00 35.65 2.74
1240 8914 6.932960 TCGATTGTGCAATCAGATATTCAGAT 59.067 34.615 20.56 0.00 45.60 2.90
1288 9045 4.288626 AGCCACCCAGTACTATTTCAAAGA 59.711 41.667 0.00 0.00 0.00 2.52
1290 9048 5.123979 GCCACCCAGTACTATTTCAAAGAAG 59.876 44.000 0.00 0.00 0.00 2.85
1294 9052 8.846211 CACCCAGTACTATTTCAAAGAAGAAAA 58.154 33.333 0.00 0.00 40.54 2.29
1327 9091 5.419542 TCAGTTTATCCTCACCTGAATTCG 58.580 41.667 0.04 0.00 0.00 3.34
1428 11096 5.631096 GCTCTACATTTCTGAAAGCCAAAAC 59.369 40.000 8.95 0.00 0.00 2.43
1578 11246 1.066430 TCCACCGGTGAAGCTGTATTC 60.066 52.381 36.07 0.00 0.00 1.75
1653 11321 0.036952 ATCTCGAAGTGCACTGTGGG 60.037 55.000 22.49 16.04 0.00 4.61
1770 11438 2.450476 GCCTCTGACATTGGAAATGGT 58.550 47.619 5.08 0.00 0.00 3.55
1800 11469 4.214437 GTGTGCTCTTCGACAAGATTTTG 58.786 43.478 0.00 0.00 38.02 2.44
1832 11501 9.803315 TCACTAACAAATGAGATGATACACTAC 57.197 33.333 0.00 0.00 0.00 2.73
1893 11562 1.180456 TTCCGGTGTTCCTCTACGCA 61.180 55.000 0.00 0.00 0.00 5.24
1917 11586 2.078665 ACACCCCACCAGCAAGAGT 61.079 57.895 0.00 0.00 0.00 3.24
1926 11595 1.563435 CCAGCAAGAGTGTCAGTGCG 61.563 60.000 0.00 0.00 41.90 5.34
1965 11634 1.530323 ACTACCGGCCAAATCACAAC 58.470 50.000 0.00 0.00 0.00 3.32
1969 11638 2.913765 CGGCCAAATCACAACGGCA 61.914 57.895 2.24 0.00 46.75 5.69
1978 11647 0.037447 TCACAACGGCATCCAATGGA 59.963 50.000 3.67 3.67 35.55 3.41
1983 11652 1.224315 CGGCATCCAATGGACAGGA 59.776 57.895 3.09 0.00 38.50 3.86
1986 11655 1.616725 GGCATCCAATGGACAGGACAA 60.617 52.381 3.09 0.00 36.60 3.18
2220 11889 1.291877 GCGACAACTGCACGGAGATT 61.292 55.000 0.00 0.00 0.00 2.40
2459 12179 2.358898 CTGCTGTTTAAACTGTGGCACT 59.641 45.455 19.83 0.13 0.00 4.40
2488 12209 1.340991 CCCAGACCGACCAATTCCAAT 60.341 52.381 0.00 0.00 0.00 3.16
2631 12354 0.034337 AACTTGGCAAGGCAGCATTG 59.966 50.000 29.26 15.58 35.83 2.82
2900 12626 3.373439 GTCAGCTTGCAGGAGATTTACAG 59.627 47.826 0.00 0.00 0.00 2.74
2915 12641 7.255070 GGAGATTTACAGATCCTTTTGCAGATC 60.255 40.741 5.71 5.71 39.38 2.75
3090 12916 3.012518 AGCAGCATGTACCTGTCAAATC 58.987 45.455 0.00 0.00 39.31 2.17
3096 12922 4.201783 GCATGTACCTGTCAAATCGGTAAC 60.202 45.833 0.00 0.00 35.25 2.50
3169 12998 4.065088 GTTCCACTAGCAACATCAACAGA 58.935 43.478 0.00 0.00 0.00 3.41
3217 13046 5.717119 ACCCCACTAGAAATCTAAGCATT 57.283 39.130 0.00 0.00 0.00 3.56
3380 13214 7.916977 TGATAGTTGCTAATCAATGTTCAATGC 59.083 33.333 0.00 0.00 36.99 3.56
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
35 36 3.125829 CCACGTTGATATGCTCATATGGC 59.874 47.826 7.08 6.08 34.36 4.40
39 40 5.006261 CGTTTTCCACGTTGATATGCTCATA 59.994 40.000 0.00 0.00 44.49 2.15
181 5752 1.386525 CGGGCAATGTGATGGGGAAG 61.387 60.000 0.00 0.00 0.00 3.46
260 6229 4.380531 TGACGTCTTGAGAAGAGCAATTT 58.619 39.130 17.92 0.00 38.41 1.82
296 6295 4.817318 TGCATTCTGTGTACCACTATCA 57.183 40.909 0.00 0.00 35.11 2.15
330 6329 6.371548 TGCTTCACTTTTATAGTCGAATTGCT 59.628 34.615 0.00 0.00 33.85 3.91
344 7707 1.620822 AGCCGGATTGCTTCACTTTT 58.379 45.000 5.05 0.00 38.85 2.27
345 7708 2.489938 TAGCCGGATTGCTTCACTTT 57.510 45.000 5.05 0.00 42.75 2.66
364 7727 1.476007 GCTCATGGCCGTCCTCCTAT 61.476 60.000 0.00 0.00 34.27 2.57
428 7990 3.731652 ATTTGCTGCTTTTGTGCACTA 57.268 38.095 19.41 7.83 38.12 2.74
430 7992 4.433283 CGATTATTTGCTGCTTTTGTGCAC 60.433 41.667 10.75 10.75 38.12 4.57
476 8038 8.627487 TCGAAATTATACATTTTGCCAATGAC 57.373 30.769 11.66 0.00 0.00 3.06
479 8041 9.467258 CATCTCGAAATTATACATTTTGCCAAT 57.533 29.630 0.00 0.00 0.00 3.16
507 8072 1.140312 TAATGGGATGGCAGTCCTCC 58.860 55.000 13.32 6.19 38.38 4.30
511 8076 2.893489 GGGAATTAATGGGATGGCAGTC 59.107 50.000 0.00 0.00 0.00 3.51
512 8077 2.752829 CGGGAATTAATGGGATGGCAGT 60.753 50.000 0.00 0.00 0.00 4.40
516 8081 2.158534 TGGACGGGAATTAATGGGATGG 60.159 50.000 0.00 0.00 0.00 3.51
537 8102 2.032636 GGTTTCGTCGAAAACCGTCATT 60.033 45.455 22.44 0.00 46.29 2.57
538 8103 1.528161 GGTTTCGTCGAAAACCGTCAT 59.472 47.619 22.44 0.00 46.29 3.06
700 8300 2.653726 TGGTAACATGCTATTGCCCTG 58.346 47.619 0.00 0.00 46.17 4.45
764 8366 2.478894 AGTTATCTTTGGTTGTCGCACG 59.521 45.455 0.00 0.00 0.00 5.34
768 8370 5.794687 TGCATAGTTATCTTTGGTTGTCG 57.205 39.130 0.00 0.00 0.00 4.35
948 8582 0.250234 CTCTCGCTTGTGGGGAATGA 59.750 55.000 0.00 0.00 36.45 2.57
978 8616 1.413662 CCTTCAGCTCCCCCTCTATCA 60.414 57.143 0.00 0.00 0.00 2.15
982 8620 2.690510 GCCTTCAGCTCCCCCTCT 60.691 66.667 0.00 0.00 38.99 3.69
1076 8718 7.069986 TGTTCTAGCCTCTATCTACAAATCCT 58.930 38.462 0.00 0.00 0.00 3.24
1078 8720 8.079809 GTCTGTTCTAGCCTCTATCTACAAATC 58.920 40.741 0.00 0.00 0.00 2.17
1079 8721 7.561722 TGTCTGTTCTAGCCTCTATCTACAAAT 59.438 37.037 0.00 0.00 0.00 2.32
1083 8725 6.292923 TCTGTCTGTTCTAGCCTCTATCTAC 58.707 44.000 0.00 0.00 0.00 2.59
1092 8734 1.734047 CGCACTCTGTCTGTTCTAGCC 60.734 57.143 0.00 0.00 0.00 3.93
1121 8764 7.885399 GGAAGTTCATATATGGCTGAATAACCT 59.115 37.037 12.78 0.00 34.18 3.50
1122 8765 7.665559 TGGAAGTTCATATATGGCTGAATAACC 59.334 37.037 12.78 6.17 34.18 2.85
1148 8792 6.573094 GCAGATCCTTGAAATTAGCAGGTTTT 60.573 38.462 0.00 0.00 0.00 2.43
1152 8796 3.003068 CGCAGATCCTTGAAATTAGCAGG 59.997 47.826 0.00 0.00 0.00 4.85
1153 8797 3.873361 TCGCAGATCCTTGAAATTAGCAG 59.127 43.478 0.00 0.00 0.00 4.24
1154 8798 3.872696 TCGCAGATCCTTGAAATTAGCA 58.127 40.909 0.00 0.00 0.00 3.49
1155 8799 3.249559 CCTCGCAGATCCTTGAAATTAGC 59.750 47.826 0.00 0.00 33.89 3.09
1156 8800 4.697514 TCCTCGCAGATCCTTGAAATTAG 58.302 43.478 0.00 0.00 33.89 1.73
1157 8801 4.753516 TCCTCGCAGATCCTTGAAATTA 57.246 40.909 0.00 0.00 33.89 1.40
1158 8802 3.634397 TCCTCGCAGATCCTTGAAATT 57.366 42.857 0.00 0.00 33.89 1.82
1159 8803 3.634397 TTCCTCGCAGATCCTTGAAAT 57.366 42.857 0.00 0.00 33.89 2.17
1161 8805 3.634397 AATTCCTCGCAGATCCTTGAA 57.366 42.857 0.00 0.00 33.89 2.69
1163 8807 2.805099 GCTAATTCCTCGCAGATCCTTG 59.195 50.000 0.00 0.00 33.89 3.61
1164 8808 2.703007 AGCTAATTCCTCGCAGATCCTT 59.297 45.455 0.00 0.00 33.89 3.36
1165 8809 2.324541 AGCTAATTCCTCGCAGATCCT 58.675 47.619 0.00 0.00 33.89 3.24
1166 8810 2.829741 AGCTAATTCCTCGCAGATCC 57.170 50.000 0.00 0.00 33.89 3.36
1167 8811 4.775058 TCTAGCTAATTCCTCGCAGATC 57.225 45.455 0.00 0.00 33.89 2.75
1168 8812 4.586841 AGTTCTAGCTAATTCCTCGCAGAT 59.413 41.667 0.00 0.00 33.89 2.90
1170 8814 4.314740 AGTTCTAGCTAATTCCTCGCAG 57.685 45.455 0.00 0.00 0.00 5.18
1173 8817 7.028926 TCAACTAGTTCTAGCTAATTCCTCG 57.971 40.000 4.77 0.00 0.00 4.63
1174 8818 9.825109 AAATCAACTAGTTCTAGCTAATTCCTC 57.175 33.333 4.77 0.00 0.00 3.71
1175 8819 9.825109 GAAATCAACTAGTTCTAGCTAATTCCT 57.175 33.333 4.77 0.00 0.00 3.36
1176 8820 9.825109 AGAAATCAACTAGTTCTAGCTAATTCC 57.175 33.333 4.77 0.00 40.61 3.01
1179 8823 8.482128 AGCAGAAATCAACTAGTTCTAGCTAAT 58.518 33.333 4.77 0.00 40.44 1.73
1180 8824 7.761704 CAGCAGAAATCAACTAGTTCTAGCTAA 59.238 37.037 4.77 0.00 40.44 3.09
1181 8825 7.093727 ACAGCAGAAATCAACTAGTTCTAGCTA 60.094 37.037 4.77 0.00 40.44 3.32
1187 8861 7.010923 CCAGATACAGCAGAAATCAACTAGTTC 59.989 40.741 4.77 0.00 32.27 3.01
1208 8882 2.292267 GATTGCACAATCGACCCAGAT 58.708 47.619 7.56 0.00 37.97 2.90
1253 8927 3.054361 ACTGGGTGGCTTAATTCCTAGTG 60.054 47.826 0.00 0.00 39.60 2.74
1294 9052 9.093458 AGGTGAGGATAAACTGAAATTTCAATT 57.907 29.630 20.82 15.14 36.64 2.32
1296 9054 7.723616 TCAGGTGAGGATAAACTGAAATTTCAA 59.276 33.333 20.82 7.48 36.64 2.69
1327 9091 3.334583 TGGAGCAGATGAACAAGGTAC 57.665 47.619 0.00 0.00 0.00 3.34
1385 11053 1.817357 CTTGCAGCAGATCACCTTCA 58.183 50.000 0.00 0.00 0.00 3.02
1413 11081 0.030101 CCGCGTTTTGGCTTTCAGAA 59.970 50.000 4.92 0.00 0.00 3.02
1434 11102 2.740714 GCTGATGGCGTCGACAACC 61.741 63.158 17.16 16.46 0.00 3.77
1497 11165 3.442625 CACGGTTGTAGTACTCATCCTCA 59.557 47.826 0.00 0.00 0.00 3.86
1560 11228 2.002586 CTGAATACAGCTTCACCGGTG 58.997 52.381 29.26 29.26 37.33 4.94
1578 11246 1.561542 AGTACCTTCCTGATTGGGCTG 59.438 52.381 0.00 0.00 36.20 4.85
1653 11321 0.598680 CGCCGATCCTTGGATGAGTC 60.599 60.000 6.92 0.00 0.00 3.36
1668 11336 2.277949 ATGTCATCGACGACGCCG 60.278 61.111 7.18 0.00 38.84 6.46
1783 11452 8.165428 GTGATAGAACAAAATCTTGTCGAAGAG 58.835 37.037 0.00 0.00 45.25 2.85
1832 11501 7.663493 GGAGGGAAGAGAACCAGATTATTTATG 59.337 40.741 0.00 0.00 0.00 1.90
1840 11509 1.367848 AGGGAGGGAAGAGAACCAGAT 59.632 52.381 0.00 0.00 0.00 2.90
1845 11514 2.027653 CAGAACAGGGAGGGAAGAGAAC 60.028 54.545 0.00 0.00 0.00 3.01
1893 11562 4.275508 CTGGTGGGGTGTGCTGCT 62.276 66.667 0.00 0.00 0.00 4.24
1965 11634 1.097547 GTCCTGTCCATTGGATGCCG 61.098 60.000 9.01 0.00 32.73 5.69
1969 11638 2.881403 GCACTTGTCCTGTCCATTGGAT 60.881 50.000 9.01 0.00 32.73 3.41
1978 11647 0.764369 TCAGGGAGCACTTGTCCTGT 60.764 55.000 7.91 0.00 45.07 4.00
1983 11652 2.826488 AGAGTATCAGGGAGCACTTGT 58.174 47.619 0.00 0.00 37.82 3.16
1986 11655 2.245028 TGGTAGAGTATCAGGGAGCACT 59.755 50.000 0.00 0.00 37.82 4.40
2220 11889 2.747460 GGATCCAGCAAGCACGCA 60.747 61.111 6.95 0.00 0.00 5.24
2513 12236 1.071385 CCATAGACCATCTCCAGTGCC 59.929 57.143 0.00 0.00 0.00 5.01
2520 12243 5.119694 GGTGAAGTTTCCATAGACCATCTC 58.880 45.833 0.00 0.00 0.00 2.75
2631 12354 6.389906 AGTATTTTGTCAGTTGGCATTAAGC 58.610 36.000 0.00 0.00 44.65 3.09
2900 12626 5.380043 TCTTATGGGATCTGCAAAAGGATC 58.620 41.667 5.34 5.34 38.01 3.36
2915 12641 7.749666 TCCTTATCTTCCTTCAATCTTATGGG 58.250 38.462 0.00 0.00 0.00 4.00
2959 12685 8.970859 ACCTTCATAGTCCATAATTTTCTCTG 57.029 34.615 0.00 0.00 0.00 3.35
3011 12804 4.413760 TCCTCCCGTATTTCCTACCATAG 58.586 47.826 0.00 0.00 0.00 2.23
3024 12847 1.565067 GGTTCTTTCCTCCTCCCGTA 58.435 55.000 0.00 0.00 0.00 4.02
3132 12961 0.244721 GGAACTGCCACAATTGCTCC 59.755 55.000 5.05 0.00 36.34 4.70
3169 12998 4.081406 TGTTGAATCTAGTGCTGCCATTT 58.919 39.130 0.00 0.00 0.00 2.32
3217 13046 4.985538 TTTTGACACGCCCTTCTTTTTA 57.014 36.364 0.00 0.00 0.00 1.52
3355 13189 8.133627 AGCATTGAACATTGATTAGCAACTATC 58.866 33.333 0.00 0.00 39.78 2.08


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

AutoCloner maintained by Alex Coulton.