Multiple sequence alignment - TraesCS3D01G524300

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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 TraesCS3D01G524300 chr3D 100.000 4933 0 0 1 4933 604363223 604368155 0.000000e+00 9110
1 TraesCS3D01G524300 chr3D 84.592 993 118 17 1014 1979 491795218 491794234 0.000000e+00 953
2 TraesCS3D01G524300 chr3D 88.664 247 18 8 4016 4257 604377017 604376776 4.830000e-75 292
3 TraesCS3D01G524300 chr3D 88.660 194 11 2 4255 4438 604376735 604376543 4.970000e-55 226
4 TraesCS3D01G524300 chrUn 90.357 4314 235 80 28 4257 42190953 42186737 0.000000e+00 5494
5 TraesCS3D01G524300 chrUn 92.217 681 40 9 4255 4932 42186679 42186009 0.000000e+00 952
6 TraesCS3D01G524300 chr3A 94.081 2923 103 30 83 2969 734004152 734007040 0.000000e+00 4375
7 TraesCS3D01G524300 chr3A 94.957 1150 46 7 2958 4101 734007201 734008344 0.000000e+00 1792
8 TraesCS3D01G524300 chr3A 94.015 685 30 6 4255 4933 734008480 734009159 0.000000e+00 1027
9 TraesCS3D01G524300 chr3A 82.042 1058 130 32 943 1979 633291915 633290897 0.000000e+00 846
10 TraesCS3D01G524300 chr3A 89.216 102 7 3 4159 4258 734008345 734008444 1.860000e-24 124
11 TraesCS3D01G524300 chr3A 96.721 61 2 0 1 61 734004097 734004157 8.740000e-18 102
12 TraesCS3D01G524300 chr5A 85.415 1529 157 25 851 2353 231069014 231067526 0.000000e+00 1528
13 TraesCS3D01G524300 chr5A 89.404 151 15 1 667 817 231091908 231091759 6.520000e-44 189
14 TraesCS3D01G524300 chr4B 87.049 1081 113 17 1290 2353 17507392 17508462 0.000000e+00 1195
15 TraesCS3D01G524300 chr7B 84.354 735 66 22 1574 2283 417055910 417056620 0.000000e+00 675
16 TraesCS3D01G524300 chr7A 79.732 671 79 27 836 1496 594570486 594571109 2.730000e-117 433
17 TraesCS3D01G524300 chr4D 77.616 411 56 20 651 1033 306379585 306379987 2.990000e-52 217
18 TraesCS3D01G524300 chr4D 89.600 125 11 1 1463 1587 447133852 447133730 1.840000e-34 158
19 TraesCS3D01G524300 chr6D 76.167 407 49 27 657 1030 472404834 472405225 2.360000e-38 171
20 TraesCS3D01G524300 chr4A 89.076 119 11 1 1469 1587 20233494 20233610 3.980000e-31 147


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 TraesCS3D01G524300 chr3D 604363223 604368155 4932 False 9110 9110 100.000 1 4933 1 chr3D.!!$F1 4932
1 TraesCS3D01G524300 chr3D 491794234 491795218 984 True 953 953 84.592 1014 1979 1 chr3D.!!$R1 965
2 TraesCS3D01G524300 chrUn 42186009 42190953 4944 True 3223 5494 91.287 28 4932 2 chrUn.!!$R1 4904
3 TraesCS3D01G524300 chr3A 734004097 734009159 5062 False 1484 4375 93.798 1 4933 5 chr3A.!!$F1 4932
4 TraesCS3D01G524300 chr3A 633290897 633291915 1018 True 846 846 82.042 943 1979 1 chr3A.!!$R1 1036
5 TraesCS3D01G524300 chr5A 231067526 231069014 1488 True 1528 1528 85.415 851 2353 1 chr5A.!!$R1 1502
6 TraesCS3D01G524300 chr4B 17507392 17508462 1070 False 1195 1195 87.049 1290 2353 1 chr4B.!!$F1 1063
7 TraesCS3D01G524300 chr7B 417055910 417056620 710 False 675 675 84.354 1574 2283 1 chr7B.!!$F1 709
8 TraesCS3D01G524300 chr7A 594570486 594571109 623 False 433 433 79.732 836 1496 1 chr7A.!!$F1 660

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
158 188 1.001406 CAGAGGAAAACAGAGGAGCGT 59.999 52.381 0.00 0.00 0.00 5.07 F
272 322 1.364171 CTCATTCTACCGGGCCTCG 59.636 63.158 6.32 4.41 38.88 4.63 F
567 640 1.462616 TTCTGGGATGGATTGCGTTG 58.537 50.000 0.00 0.00 0.00 4.10 F
1086 1208 1.900245 TGGTCTACAGCTACGACACA 58.100 50.000 10.26 4.75 0.00 3.72 F
2683 2871 0.686789 AAAGGGGGTGAATGCTTTGC 59.313 50.000 0.00 0.00 0.00 3.68 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1758 1914 0.179073 ACTGGATCAGCCGCATACAC 60.179 55.000 0.00 0.00 40.66 2.90 R
2222 2409 1.736681 GTCATCTGCAGGCAAAGAGAC 59.263 52.381 15.13 7.89 0.00 3.36 R
2450 2638 2.279784 GAGGAGAATGAGCCGCCG 60.280 66.667 0.00 0.00 0.00 6.46 R
2867 3055 2.450476 GGAAAGGTCCTGATGCACAAT 58.550 47.619 0.00 0.00 41.24 2.71 R
4034 4409 0.386476 ACTAACCTCGTTCACGCACA 59.614 50.000 0.00 0.00 39.60 4.57 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
84 85 3.756727 GTCGTGGACGGACCTCCC 61.757 72.222 0.00 0.73 40.29 4.30
87 88 3.075641 GTGGACGGACCTCCCCTC 61.076 72.222 7.32 0.00 39.86 4.30
108 136 4.154347 GGAGGGAGCAGCACCGAG 62.154 72.222 2.39 0.00 0.00 4.63
156 186 1.447945 GCAGAGGAAAACAGAGGAGC 58.552 55.000 0.00 0.00 0.00 4.70
158 188 1.001406 CAGAGGAAAACAGAGGAGCGT 59.999 52.381 0.00 0.00 0.00 5.07
159 189 1.694696 AGAGGAAAACAGAGGAGCGTT 59.305 47.619 0.00 0.00 0.00 4.84
191 232 3.267974 GCTCGTGGCCTTCCTTTG 58.732 61.111 3.32 0.00 34.27 2.77
195 236 2.680913 CGTGGCCTTCCTTTGCTCG 61.681 63.158 3.32 0.00 0.00 5.03
209 250 1.369321 GCTCGGAGGATAAGGCAGG 59.631 63.158 7.20 0.00 0.00 4.85
210 251 2.053618 CTCGGAGGATAAGGCAGGG 58.946 63.158 0.00 0.00 0.00 4.45
240 290 2.125106 AGACGAAGAATGGCCGGC 60.125 61.111 21.18 21.18 0.00 6.13
242 292 2.436646 ACGAAGAATGGCCGGCAG 60.437 61.111 30.85 10.52 0.00 4.85
245 295 2.036256 AAGAATGGCCGGCAGCTT 59.964 55.556 30.85 20.97 43.05 3.74
249 299 4.496336 ATGGCCGGCAGCTTCTCC 62.496 66.667 30.85 8.62 43.05 3.71
272 322 1.364171 CTCATTCTACCGGGCCTCG 59.636 63.158 6.32 4.41 38.88 4.63
383 439 4.154347 CCTCCTCCACGGCAGCTC 62.154 72.222 0.00 0.00 0.00 4.09
490 550 2.431683 GCAAGGTGAGCCCACTGA 59.568 61.111 0.00 0.00 42.77 3.41
491 551 1.968540 GCAAGGTGAGCCCACTGAC 60.969 63.158 0.00 0.00 42.77 3.51
495 555 2.032681 GTGAGCCCACTGACCACC 59.967 66.667 0.00 0.00 40.10 4.61
496 556 3.625897 TGAGCCCACTGACCACCG 61.626 66.667 0.00 0.00 0.00 4.94
497 557 4.394712 GAGCCCACTGACCACCGG 62.395 72.222 0.00 0.00 0.00 5.28
567 640 1.462616 TTCTGGGATGGATTGCGTTG 58.537 50.000 0.00 0.00 0.00 4.10
805 887 3.143515 GAGGACGTCCCGGTACCC 61.144 72.222 30.82 4.01 40.87 3.69
1086 1208 1.900245 TGGTCTACAGCTACGACACA 58.100 50.000 10.26 4.75 0.00 3.72
1089 1211 3.005554 GGTCTACAGCTACGACACACTA 58.994 50.000 10.26 0.00 0.00 2.74
1150 1272 3.621805 TCCGCAACCCGCTCTTCA 61.622 61.111 0.00 0.00 39.08 3.02
1202 1329 5.468072 GGAATGTCATCGATGCATTAGTCTT 59.532 40.000 30.44 18.47 35.90 3.01
1208 1335 6.478344 GTCATCGATGCATTAGTCTTTCTCTT 59.522 38.462 20.81 0.00 0.00 2.85
1461 1598 4.878397 AGTTCTACCATGTAATGCTTCTGC 59.122 41.667 0.00 0.00 44.97 4.26
1555 1692 6.484288 AGGATGACCATTTACATTGAGTGAA 58.516 36.000 0.00 0.00 38.94 3.18
1556 1693 6.375455 AGGATGACCATTTACATTGAGTGAAC 59.625 38.462 0.00 0.00 38.94 3.18
1758 1914 8.547967 AACCGCATAATATACTAGAATTGGTG 57.452 34.615 0.00 0.00 0.00 4.17
1907 2066 9.052494 AGCTATGCTGTTCTCACCATATGGTTA 62.052 40.741 25.25 16.48 41.27 2.85
2153 2335 6.849502 ACACAAAGCAGAATCAGATGTAATG 58.150 36.000 0.00 0.00 0.00 1.90
2162 2347 7.909121 GCAGAATCAGATGTAATGTTCTTTCTG 59.091 37.037 0.00 0.00 39.36 3.02
2349 2537 7.122204 AGCAAAGGGTTGGTATTTGATAGTAAC 59.878 37.037 1.32 0.00 43.57 2.50
2372 2560 6.299922 ACGATCTAGTCTAGATTGACATCCA 58.700 40.000 31.54 2.80 45.59 3.41
2450 2638 2.507407 TGAAGACCTTAATGGGTGGC 57.493 50.000 0.00 0.00 40.06 5.01
2527 2715 3.462982 AGTCACGAACACACTGCAATTA 58.537 40.909 0.00 0.00 0.00 1.40
2683 2871 0.686789 AAAGGGGGTGAATGCTTTGC 59.313 50.000 0.00 0.00 0.00 3.68
2841 3029 7.015877 GTGAGTTTATCCTTCAACGTCATTTC 58.984 38.462 0.00 0.00 0.00 2.17
2864 3052 5.714333 TCATGGGCTTAAGTATTGCTTTTGA 59.286 36.000 4.02 0.00 38.57 2.69
2867 3055 7.710676 TGGGCTTAAGTATTGCTTTTGAATA 57.289 32.000 4.02 0.00 38.57 1.75
3129 3493 1.909700 TGTCACTGGCCTTGGATTTC 58.090 50.000 3.32 0.00 0.00 2.17
3134 3498 1.353022 ACTGGCCTTGGATTTCCGTTA 59.647 47.619 3.32 0.00 39.43 3.18
3264 3628 2.698855 CCTGGACAAGGTATGAGGTG 57.301 55.000 0.00 0.00 41.74 4.00
3278 3642 4.675063 ATGAGGTGTTCCCTATTTGGTT 57.325 40.909 0.00 0.00 46.51 3.67
3291 3655 5.529060 CCCTATTTGGTTAATCTGTCTGAGC 59.471 44.000 0.00 0.00 0.00 4.26
3311 3675 2.485426 GCTTTCACTGAAGCTGCATGTA 59.515 45.455 0.00 0.00 46.55 2.29
3392 3761 1.201647 ACTCGACGATTTCATCCGTGT 59.798 47.619 0.00 0.00 39.30 4.49
3450 3819 6.405286 CCACACACCATTCTTTGTTTCTTGTA 60.405 38.462 0.00 0.00 0.00 2.41
3491 3860 9.618890 TTTAAGAAGATTTGATATCCCTCTGTG 57.381 33.333 0.00 0.00 0.00 3.66
3501 3870 2.957402 TCCCTCTGTGAACTTTGCAT 57.043 45.000 0.00 0.00 0.00 3.96
3509 3878 2.129607 GTGAACTTTGCATTGCAGGTG 58.870 47.619 11.76 8.47 40.61 4.00
3808 4182 3.376546 CCTCTAGGTTTCAAATGCAGCTC 59.623 47.826 0.00 0.00 0.00 4.09
3827 4201 9.449550 TGCAGCTCATAATTCAAAATTTATACG 57.550 29.630 0.00 0.00 0.00 3.06
3832 4206 9.669353 CTCATAATTCAAAATTTATACGCAGCT 57.331 29.630 0.00 0.00 0.00 4.24
3833 4207 9.663904 TCATAATTCAAAATTTATACGCAGCTC 57.336 29.630 0.00 0.00 0.00 4.09
3834 4208 9.449550 CATAATTCAAAATTTATACGCAGCTCA 57.550 29.630 0.00 0.00 0.00 4.26
3899 4274 2.724690 CGATAAAGTTCCGCCGTATGAG 59.275 50.000 0.00 0.00 0.00 2.90
4034 4409 6.259167 GCCCGGAAATTTTCTTTGTTTTACTT 59.741 34.615 0.73 0.00 0.00 2.24
4158 4534 4.411256 AATTTTGCCCTGCCAATCTATG 57.589 40.909 0.00 0.00 0.00 2.23
4197 4575 4.245845 TCAATGTTCAGTACGTGTGCTA 57.754 40.909 0.00 0.00 0.00 3.49
4198 4576 3.985279 TCAATGTTCAGTACGTGTGCTAC 59.015 43.478 0.00 0.00 0.00 3.58
4215 4593 2.535984 GCTACGAGTTTCATGACGATGG 59.464 50.000 10.08 0.00 0.00 3.51
4216 4594 2.743636 ACGAGTTTCATGACGATGGT 57.256 45.000 10.08 0.00 0.00 3.55
4219 4597 4.112634 ACGAGTTTCATGACGATGGTATG 58.887 43.478 10.08 0.00 0.00 2.39
4240 4618 9.640963 GGTATGTATATCAATGGTGACTCTTAC 57.359 37.037 0.00 0.00 36.31 2.34
4258 4643 8.870075 ACTCTTACTGCCTCAAATAAGAATTT 57.130 30.769 0.00 0.00 34.20 1.82
4259 4644 9.301897 ACTCTTACTGCCTCAAATAAGAATTTT 57.698 29.630 0.00 0.00 34.20 1.82
4260 4645 9.565213 CTCTTACTGCCTCAAATAAGAATTTTG 57.435 33.333 0.00 0.00 34.20 2.44
4272 4711 8.500773 CAAATAAGAATTTTGTTGCTGAGCAAT 58.499 29.630 23.86 5.71 40.76 3.56
4343 4788 5.815222 TGTATATGTTAATGCTGAGCAACGT 59.185 36.000 12.69 9.52 43.62 3.99
4370 4825 5.517054 CGCTAATCTCTGTAGAAAGGTTCAC 59.483 44.000 0.00 0.00 34.73 3.18
4422 4877 9.851043 GTCAACAAAATTCTATAACTAGCGATC 57.149 33.333 0.00 0.00 0.00 3.69
4554 5009 5.783111 ACATATTTCAGGTGCAAAAGAACC 58.217 37.500 0.00 0.00 36.66 3.62
4582 5037 4.226427 AGAAATTCAGATGCTGCCTACA 57.774 40.909 0.00 0.00 0.00 2.74
4583 5038 3.944015 AGAAATTCAGATGCTGCCTACAC 59.056 43.478 0.00 0.00 0.00 2.90
4824 5280 2.486203 TCCGACAAATTTTCCATCCACG 59.514 45.455 0.00 0.00 0.00 4.94
4850 5306 1.827399 GCCTGGGTCTTGTCCTTCGA 61.827 60.000 0.00 0.00 0.00 3.71
4851 5307 0.905357 CCTGGGTCTTGTCCTTCGAT 59.095 55.000 0.00 0.00 0.00 3.59
4853 5309 2.159085 CCTGGGTCTTGTCCTTCGATAC 60.159 54.545 0.00 0.00 0.00 2.24
4854 5310 1.829222 TGGGTCTTGTCCTTCGATACC 59.171 52.381 0.00 0.00 0.00 2.73
4863 5319 1.107538 CCTTCGATACCGGCTCTGGA 61.108 60.000 0.00 0.00 36.24 3.86
4868 5324 2.017559 GATACCGGCTCTGGAACGCT 62.018 60.000 0.00 0.00 0.00 5.07
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
2 3 4.681978 GCAGCAAGGTCGGACGGT 62.682 66.667 1.43 0.00 0.00 4.83
67 68 3.756727 GGGAGGTCCGTCCACGAC 61.757 72.222 8.18 0.00 43.02 4.34
70 71 3.075641 GAGGGGAGGTCCGTCCAC 61.076 72.222 8.18 4.35 42.88 4.02
71 72 4.753662 CGAGGGGAGGTCCGTCCA 62.754 72.222 8.18 0.00 45.14 4.02
108 136 2.832201 GCCTCCATGCTCAAGCCC 60.832 66.667 0.00 0.00 41.18 5.19
143 173 0.875059 CCCAACGCTCCTCTGTTTTC 59.125 55.000 0.00 0.00 0.00 2.29
158 188 2.282180 GCCTCCGTTGCTTCCCAA 60.282 61.111 0.00 0.00 0.00 4.12
159 189 3.249189 AGCCTCCGTTGCTTCCCA 61.249 61.111 0.00 0.00 34.87 4.37
189 230 0.465705 CTGCCTTATCCTCCGAGCAA 59.534 55.000 0.00 0.00 0.00 3.91
190 231 1.402896 CCTGCCTTATCCTCCGAGCA 61.403 60.000 0.00 0.00 0.00 4.26
191 232 1.369321 CCTGCCTTATCCTCCGAGC 59.631 63.158 0.00 0.00 0.00 5.03
195 236 3.382083 TTTTTCCCTGCCTTATCCTCC 57.618 47.619 0.00 0.00 0.00 4.30
219 260 0.457851 CGGCCATTCTTCGTCTCTCT 59.542 55.000 2.24 0.00 0.00 3.10
222 263 2.174319 GCCGGCCATTCTTCGTCTC 61.174 63.158 18.11 0.00 0.00 3.36
226 276 3.880846 GCTGCCGGCCATTCTTCG 61.881 66.667 26.77 2.88 34.27 3.79
229 279 2.439156 GAAGCTGCCGGCCATTCT 60.439 61.111 26.77 12.52 43.05 2.40
240 290 0.255318 AATGAGCCCAGGAGAAGCTG 59.745 55.000 0.00 0.00 36.87 4.24
242 292 0.545646 AGAATGAGCCCAGGAGAAGC 59.454 55.000 0.00 0.00 0.00 3.86
245 295 1.794714 GGTAGAATGAGCCCAGGAGA 58.205 55.000 0.00 0.00 0.00 3.71
249 299 1.447643 CCCGGTAGAATGAGCCCAG 59.552 63.158 0.00 0.00 0.00 4.45
339 389 1.202663 GGGAAGGAATAGTTCGGCTCC 60.203 57.143 0.00 0.00 0.00 4.70
501 561 2.301577 AATACAAGCAGACGAGAGGC 57.698 50.000 0.00 0.00 42.06 4.70
502 562 5.000012 ACTAAATACAAGCAGACGAGAGG 58.000 43.478 0.00 0.00 0.00 3.69
503 563 4.731000 CGACTAAATACAAGCAGACGAGAG 59.269 45.833 0.00 0.00 0.00 3.20
504 564 4.659088 CGACTAAATACAAGCAGACGAGA 58.341 43.478 0.00 0.00 0.00 4.04
509 569 2.500098 AGGGCGACTAAATACAAGCAGA 59.500 45.455 0.00 0.00 0.00 4.26
511 571 2.627945 CAGGGCGACTAAATACAAGCA 58.372 47.619 0.00 0.00 0.00 3.91
567 640 2.789917 CCTCGCACAGCTGCAATC 59.210 61.111 15.27 0.00 44.50 2.67
612 685 2.032528 TCGGCAGCACTCTTTGGG 59.967 61.111 0.00 0.00 0.00 4.12
960 1075 1.630244 CCTTGAACGCCAGCTTCTCG 61.630 60.000 0.00 0.00 0.00 4.04
1086 1208 3.206150 CTGCGGAATGTATGCCTTTAGT 58.794 45.455 0.00 0.00 0.00 2.24
1089 1211 1.392589 CCTGCGGAATGTATGCCTTT 58.607 50.000 0.00 0.00 0.00 3.11
1150 1272 1.654954 CGGTCGACTTCGTCCTGGAT 61.655 60.000 16.46 0.00 43.57 3.41
1177 1299 4.707105 ACTAATGCATCGATGACATTCCA 58.293 39.130 32.28 22.51 36.58 3.53
1202 1329 6.119536 ACCATAAGTTGTGTGTGAAAGAGAA 58.880 36.000 0.00 0.00 0.00 2.87
1445 1582 4.116961 CAAATGGCAGAAGCATTACATGG 58.883 43.478 0.00 0.00 44.61 3.66
1452 1589 4.312443 CAAAACTCAAATGGCAGAAGCAT 58.688 39.130 0.00 0.00 44.61 3.79
1461 1598 4.020839 AGGAGGAATGCAAAACTCAAATGG 60.021 41.667 14.31 0.00 0.00 3.16
1548 1685 4.035558 GCTTTTGAGATGTGTGTTCACTCA 59.964 41.667 9.53 9.53 44.14 3.41
1555 1692 6.207221 TCATGTAATGCTTTTGAGATGTGTGT 59.793 34.615 0.00 0.00 46.21 3.72
1556 1693 6.614160 TCATGTAATGCTTTTGAGATGTGTG 58.386 36.000 0.00 0.00 46.21 3.82
1758 1914 0.179073 ACTGGATCAGCCGCATACAC 60.179 55.000 0.00 0.00 40.66 2.90
2153 2335 7.778470 AATGGAATACTCGATCAGAAAGAAC 57.222 36.000 0.00 0.00 0.00 3.01
2162 2347 8.450964 TCAAAACTCAAAATGGAATACTCGATC 58.549 33.333 0.00 0.00 0.00 3.69
2222 2409 1.736681 GTCATCTGCAGGCAAAGAGAC 59.263 52.381 15.13 7.89 0.00 3.36
2349 2537 6.205658 TGTGGATGTCAATCTAGACTAGATCG 59.794 42.308 22.45 13.79 44.44 3.69
2450 2638 2.279784 GAGGAGAATGAGCCGCCG 60.280 66.667 0.00 0.00 0.00 6.46
2527 2715 5.894298 TGGCAACCATACTAGAGATGAAT 57.106 39.130 0.00 0.00 0.00 2.57
2651 2839 4.100808 TCACCCCCTTTGAAACAAGAAATG 59.899 41.667 0.00 0.00 0.00 2.32
2683 2871 3.139077 ACAGTGAACTTAGCCTTTTCCG 58.861 45.455 0.00 0.00 0.00 4.30
2735 2923 6.471976 AAATGATTGGACGTCATGATATCG 57.528 37.500 18.91 0.00 36.49 2.92
2736 2924 7.864686 TGAAAATGATTGGACGTCATGATATC 58.135 34.615 18.91 11.74 36.49 1.63
2743 2931 3.145286 TGCTGAAAATGATTGGACGTCA 58.855 40.909 18.91 0.00 0.00 4.35
2841 3029 5.964758 TCAAAAGCAATACTTAAGCCCATG 58.035 37.500 1.29 0.00 37.75 3.66
2864 3052 4.646492 GGAAAGGTCCTGATGCACAATATT 59.354 41.667 0.00 0.00 41.24 1.28
2867 3055 2.450476 GGAAAGGTCCTGATGCACAAT 58.550 47.619 0.00 0.00 41.24 2.71
2972 3332 9.986833 TTGTCAGAAATATCATATGTTCAAACG 57.013 29.630 1.90 0.00 0.00 3.60
3116 3478 2.241176 AGATAACGGAAATCCAAGGCCA 59.759 45.455 5.01 0.00 35.14 5.36
3262 3626 6.884836 AGACAGATTAACCAAATAGGGAACAC 59.115 38.462 0.00 0.00 43.89 3.32
3263 3627 6.884295 CAGACAGATTAACCAAATAGGGAACA 59.116 38.462 0.00 0.00 43.89 3.18
3264 3628 7.110155 TCAGACAGATTAACCAAATAGGGAAC 58.890 38.462 0.00 0.00 43.89 3.62
3278 3642 5.728637 TCAGTGAAAGCTCAGACAGATTA 57.271 39.130 0.00 0.00 27.67 1.75
3291 3655 4.959596 ATACATGCAGCTTCAGTGAAAG 57.040 40.909 7.06 2.80 0.00 2.62
3325 3690 5.577835 TCCGTTACTAAATGCATGCAAATC 58.422 37.500 26.68 8.42 0.00 2.17
3343 3712 0.249911 GTGTCAGCTCAACCTCCGTT 60.250 55.000 0.00 0.00 0.00 4.44
3392 3761 8.328758 ACATACCCTTGACTCAAGATTCATTAA 58.671 33.333 18.82 0.00 43.42 1.40
3470 3839 7.278875 AGTTCACAGAGGGATATCAAATCTTC 58.721 38.462 4.83 0.00 0.00 2.87
3472 3841 6.821616 AGTTCACAGAGGGATATCAAATCT 57.178 37.500 4.83 1.63 0.00 2.40
3485 3854 3.305964 CTGCAATGCAAAGTTCACAGAG 58.694 45.455 9.92 0.00 38.41 3.35
3491 3860 2.798976 TCACCTGCAATGCAAAGTTC 57.201 45.000 9.92 0.00 38.41 3.01
3501 3870 1.689984 TCTGCAACAATCACCTGCAA 58.310 45.000 0.00 0.00 44.94 4.08
3509 3878 5.936956 CCTCCCTATATCTTCTGCAACAATC 59.063 44.000 0.00 0.00 0.00 2.67
3808 4182 9.449550 TGAGCTGCGTATAAATTTTGAATTATG 57.550 29.630 0.00 0.00 0.00 1.90
3899 4274 1.335496 TGGAACCGCTTGCTAACAAAC 59.665 47.619 0.00 0.00 34.74 2.93
4011 4386 8.113675 CACAAGTAAAACAAAGAAAATTTCCGG 58.886 33.333 1.57 0.00 0.00 5.14
4034 4409 0.386476 ACTAACCTCGTTCACGCACA 59.614 50.000 0.00 0.00 39.60 4.57
4158 4534 0.517316 GAACATGGCAACGAGACCAC 59.483 55.000 0.00 0.00 39.19 4.16
4197 4575 2.743636 ACCATCGTCATGAAACTCGT 57.256 45.000 0.00 0.00 30.57 4.18
4198 4576 4.112634 ACATACCATCGTCATGAAACTCG 58.887 43.478 0.00 0.00 30.57 4.18
4219 4597 6.647067 GGCAGTAAGAGTCACCATTGATATAC 59.353 42.308 0.00 0.00 33.11 1.47
4240 4618 6.647895 AGCAACAAAATTCTTATTTGAGGCAG 59.352 34.615 15.81 0.00 39.56 4.85
4241 4620 6.424509 CAGCAACAAAATTCTTATTTGAGGCA 59.575 34.615 15.81 0.00 39.56 4.75
4272 4711 2.212652 CTGCAAACTACAGTGACAGCA 58.787 47.619 0.00 0.00 0.00 4.41
4343 4788 6.282199 ACCTTTCTACAGAGATTAGCGAAA 57.718 37.500 0.00 0.00 0.00 3.46
4461 4916 4.535781 TGATAACTGGATTCCATGGTTGG 58.464 43.478 12.58 3.80 45.15 3.77
4554 5009 4.329489 CAGCATCTGAATTTCTTTCGACG 58.671 43.478 0.00 0.00 37.13 5.12
4582 5037 1.160137 GTTGCGATGAGAGCCTTTGT 58.840 50.000 0.00 0.00 0.00 2.83
4583 5038 1.129998 CTGTTGCGATGAGAGCCTTTG 59.870 52.381 0.00 0.00 0.00 2.77
4713 5169 2.667536 CAGTTGTGCTCTGCGCCT 60.668 61.111 4.18 0.00 38.39 5.52
4850 5306 2.058595 AGCGTTCCAGAGCCGGTAT 61.059 57.895 1.90 0.00 0.00 2.73
4851 5307 2.678934 AGCGTTCCAGAGCCGGTA 60.679 61.111 1.90 0.00 0.00 4.02
4863 5319 2.377628 TTTCTGGAGACGGCAGCGTT 62.378 55.000 0.00 0.00 36.33 4.84
4868 5324 1.071542 TGATGTTTTCTGGAGACGGCA 59.928 47.619 0.00 0.00 36.33 5.69
4908 5364 0.249489 CGGGAGGAATCGATGACACC 60.249 60.000 0.00 3.04 0.00 4.16


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

AutoCloner maintained by Alex Coulton.