Multiple sequence alignment - TraesCS3A01G095200

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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 TraesCS3A01G095200 chr3A 100.000 4950 0 0 1 4950 60634100 60629151 0.000000e+00 9142.0
1 TraesCS3A01G095200 chr3D 93.133 4893 185 57 1 4827 48427713 48422906 0.000000e+00 7035.0
2 TraesCS3A01G095200 chr3D 90.123 81 8 0 4812 4892 48422879 48422799 6.780000e-19 106.0
3 TraesCS3A01G095200 chr3B 93.646 4407 178 39 580 4950 76485687 76481347 0.000000e+00 6493.0
4 TraesCS3A01G095200 chr3B 84.134 479 47 11 1 467 76489428 76488967 2.120000e-118 436.0
5 TraesCS3A01G095200 chr3B 83.929 336 32 13 1 322 76486194 76485867 8.050000e-78 302.0
6 TraesCS3A01G095200 chr4B 80.220 182 36 0 3085 3266 379418503 379418684 2.400000e-28 137.0
7 TraesCS3A01G095200 chr4B 88.235 68 8 0 2441 2508 379417862 379417929 1.140000e-11 82.4
8 TraesCS3A01G095200 chr4D 90.769 65 5 1 2445 2508 304264974 304265038 8.830000e-13 86.1
9 TraesCS3A01G095200 chr4A 89.706 68 6 1 2445 2511 175001440 175001373 8.830000e-13 86.1
10 TraesCS3A01G095200 chr6A 97.059 34 0 1 3866 3899 520431344 520431376 6.920000e-04 56.5
11 TraesCS3A01G095200 chr2A 92.105 38 2 1 1245 1282 263594943 263594979 9.000000e-03 52.8


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 TraesCS3A01G095200 chr3A 60629151 60634100 4949 True 9142.000000 9142 100.000000 1 4950 1 chr3A.!!$R1 4949
1 TraesCS3A01G095200 chr3D 48422799 48427713 4914 True 3570.500000 7035 91.628000 1 4892 2 chr3D.!!$R1 4891
2 TraesCS3A01G095200 chr3B 76481347 76489428 8081 True 2410.333333 6493 87.236333 1 4950 3 chr3B.!!$R1 4949

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
164 170 0.598680 GACGATCTCCAGCATTCCGG 60.599 60.0 0.0 0.0 0.00 5.14 F
1288 4500 0.117140 TCCTCTTCCTCTTGCTCCCA 59.883 55.0 0.0 0.0 0.00 4.37 F
1292 4504 0.179062 CTTCCTCTTGCTCCCATCCG 60.179 60.0 0.0 0.0 0.00 4.18 F
1295 4507 0.179062 CCTCTTGCTCCCATCCGAAG 60.179 60.0 0.0 0.0 0.00 3.79 F
1489 4702 0.179134 CGTCGTGGGATCTTCAGGTC 60.179 60.0 0.0 0.0 0.00 3.85 F
1943 5174 0.463620 TCCTTTTGTTGGCACTTGGC 59.536 50.0 0.0 0.0 43.74 4.52 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1950 5181 0.107654 GACCCTAATCAGCGCCAGTT 60.108 55.000 2.29 0.0 0.00 3.16 R
3129 6367 0.474660 AGTCCCTGAAGCCTCTTGGT 60.475 55.000 0.00 0.0 35.27 3.67 R
3463 6701 5.045872 GGGATGAAAACATTGCTTGCTATC 58.954 41.667 0.00 0.0 0.00 2.08 R
3512 6750 1.284982 CTGCGGTGACCTTCGACAAG 61.285 60.000 0.00 0.0 0.00 3.16 R
3631 6869 4.773323 AGTTCTGTTGCCATTAGAAAGC 57.227 40.909 0.00 0.0 32.76 3.51 R
4014 7252 3.138304 GCTGTACAAAGTCATGGTGTCA 58.862 45.455 0.00 0.0 0.00 3.58 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
161 167 4.595116 CAATTTGACGATCTCCAGCATTC 58.405 43.478 0.00 0.00 0.00 2.67
164 170 0.598680 GACGATCTCCAGCATTCCGG 60.599 60.000 0.00 0.00 0.00 5.14
172 178 1.675310 CAGCATTCCGGAGCAACCA 60.675 57.895 17.13 0.00 38.90 3.67
188 194 6.165700 AGCAACCAAAGAAAGATTGACAAT 57.834 33.333 0.00 0.00 0.00 2.71
204 210 9.467258 AGATTGACAATAATTAATTGATTGCCG 57.533 29.630 11.05 0.00 46.81 5.69
205 211 7.462109 TTGACAATAATTAATTGATTGCCGC 57.538 32.000 11.05 9.63 46.81 6.53
219 225 7.658179 TTGATTGCCGCATTTAATAAACAAA 57.342 28.000 0.00 0.00 0.00 2.83
220 226 7.288317 TGATTGCCGCATTTAATAAACAAAG 57.712 32.000 0.00 0.00 0.00 2.77
305 311 9.730705 ATGATCAAGGAATACCAATATGTAGTG 57.269 33.333 0.00 0.00 38.94 2.74
436 449 3.010420 AGGCGAATTTACCTTGAGAAGC 58.990 45.455 0.00 0.00 29.74 3.86
448 461 3.372206 CCTTGAGAAGCACTTATCCAACG 59.628 47.826 2.79 0.00 30.29 4.10
471 484 5.660460 GCTTGGTTTTATTAGTTCCCATGG 58.340 41.667 4.14 4.14 0.00 3.66
639 3831 1.295423 CTAGTCCACCACCAACCGG 59.705 63.158 0.00 0.00 38.77 5.28
703 3912 1.452108 GCCTCCCTGTCCCATTTCG 60.452 63.158 0.00 0.00 0.00 3.46
704 3913 1.452108 CCTCCCTGTCCCATTTCGC 60.452 63.158 0.00 0.00 0.00 4.70
705 3914 1.452108 CTCCCTGTCCCATTTCGCC 60.452 63.158 0.00 0.00 0.00 5.54
709 3918 1.452108 CTGTCCCATTTCGCCCTCC 60.452 63.158 0.00 0.00 0.00 4.30
755 3967 6.628352 GCTCGAAGCTTTTTGCAATTGCAG 62.628 45.833 30.25 20.68 44.74 4.41
779 3991 3.206150 ACTATTAATGGCTGCCGTTCTG 58.794 45.455 28.23 18.01 34.27 3.02
792 4004 2.268298 CCGTTCTGAACTAATCACGGG 58.732 52.381 17.60 5.83 39.99 5.28
809 4021 1.761822 GGGGCCATTACTAGCTCCC 59.238 63.158 4.39 0.00 44.46 4.30
811 4023 1.371558 GGCCATTACTAGCTCCCGG 59.628 63.158 0.00 0.00 0.00 5.73
845 4057 3.569690 CCCATAAACGCCGTCGCC 61.570 66.667 0.00 0.00 39.84 5.54
894 4106 4.778143 GTGCCCCTGGTGGTAGCG 62.778 72.222 0.00 0.00 34.53 4.26
903 4115 2.742372 GTGGTAGCGGCAGTGGTG 60.742 66.667 1.45 0.00 0.00 4.17
1011 4223 4.176752 GGGGAGATGGTCGTGGCC 62.177 72.222 0.00 0.00 0.00 5.36
1012 4224 3.399181 GGGAGATGGTCGTGGCCA 61.399 66.667 0.00 0.00 43.48 5.36
1265 4477 3.767131 AGGAGTAAGTGCTCTCTTCTTCC 59.233 47.826 0.00 1.34 35.89 3.46
1267 4479 4.142249 GGAGTAAGTGCTCTCTTCTTCCTC 60.142 50.000 0.00 0.00 35.89 3.71
1288 4500 0.117140 TCCTCTTCCTCTTGCTCCCA 59.883 55.000 0.00 0.00 0.00 4.37
1289 4501 1.211456 CCTCTTCCTCTTGCTCCCAT 58.789 55.000 0.00 0.00 0.00 4.00
1290 4502 1.140652 CCTCTTCCTCTTGCTCCCATC 59.859 57.143 0.00 0.00 0.00 3.51
1291 4503 1.140652 CTCTTCCTCTTGCTCCCATCC 59.859 57.143 0.00 0.00 0.00 3.51
1292 4504 0.179062 CTTCCTCTTGCTCCCATCCG 60.179 60.000 0.00 0.00 0.00 4.18
1293 4505 0.617535 TTCCTCTTGCTCCCATCCGA 60.618 55.000 0.00 0.00 0.00 4.55
1294 4506 0.617535 TCCTCTTGCTCCCATCCGAA 60.618 55.000 0.00 0.00 0.00 4.30
1295 4507 0.179062 CCTCTTGCTCCCATCCGAAG 60.179 60.000 0.00 0.00 0.00 3.79
1296 4508 0.813210 CTCTTGCTCCCATCCGAAGC 60.813 60.000 0.00 0.00 36.56 3.86
1297 4509 1.222936 CTTGCTCCCATCCGAAGCT 59.777 57.895 0.00 0.00 36.96 3.74
1298 4510 0.393537 CTTGCTCCCATCCGAAGCTT 60.394 55.000 0.00 0.00 36.96 3.74
1299 4511 0.392998 TTGCTCCCATCCGAAGCTTC 60.393 55.000 16.84 16.84 36.96 3.86
1300 4512 1.524849 GCTCCCATCCGAAGCTTCC 60.525 63.158 20.62 3.48 33.23 3.46
1305 4517 1.153086 CATCCGAAGCTTCCCCCTG 60.153 63.158 20.62 9.31 0.00 4.45
1353 4566 4.021925 GGCGAGCTGGTGGTTCCT 62.022 66.667 0.00 0.00 37.07 3.36
1389 4602 1.204312 GAGTCAAACGCGGCAGTTC 59.796 57.895 12.47 0.00 32.43 3.01
1416 4629 2.868196 CGACGCCGTCTCTTCTGA 59.132 61.111 16.07 0.00 0.00 3.27
1483 4696 2.107041 TTGTGCCGTCGTGGGATCTT 62.107 55.000 0.00 0.00 41.76 2.40
1489 4702 0.179134 CGTCGTGGGATCTTCAGGTC 60.179 60.000 0.00 0.00 0.00 3.85
1505 4718 3.063704 TCGCATTGGGGCTGCAAG 61.064 61.111 0.50 0.00 39.64 4.01
1519 4738 3.004024 CTGCAAGCGTTCTGAATTTGT 57.996 42.857 0.00 0.00 0.00 2.83
1523 4742 3.705604 CAAGCGTTCTGAATTTGTGGTT 58.294 40.909 0.00 0.00 0.00 3.67
1526 4745 2.043411 CGTTCTGAATTTGTGGTTGCG 58.957 47.619 0.00 0.00 0.00 4.85
1528 4747 3.443976 GTTCTGAATTTGTGGTTGCGTT 58.556 40.909 0.00 0.00 0.00 4.84
1531 4750 4.499183 TCTGAATTTGTGGTTGCGTTTTT 58.501 34.783 0.00 0.00 0.00 1.94
1537 4756 3.684103 TGTGGTTGCGTTTTTGTAGAG 57.316 42.857 0.00 0.00 0.00 2.43
1563 4783 2.338809 TCTGAACCTGGACCTGAATGT 58.661 47.619 0.00 0.00 0.00 2.71
1655 4877 2.385013 TGACATCACTGGAACATCCG 57.615 50.000 0.00 0.00 40.17 4.18
1659 4881 2.768527 ACATCACTGGAACATCCGATCT 59.231 45.455 0.00 0.00 40.17 2.75
1731 4953 2.991190 CCTTTGCTGCTTTATGTTGCTG 59.009 45.455 0.00 0.00 0.00 4.41
1736 4962 4.691175 TGCTGCTTTATGTTGCTGAAAAA 58.309 34.783 0.00 0.00 0.00 1.94
1905 5136 5.850557 AGTCACCAAACAATGACATTTGA 57.149 34.783 0.00 0.00 46.34 2.69
1909 5140 7.014134 AGTCACCAAACAATGACATTTGACATA 59.986 33.333 21.70 0.00 46.34 2.29
1940 5171 2.689983 CTCAGTCCTTTTGTTGGCACTT 59.310 45.455 0.00 0.00 0.00 3.16
1941 5172 2.426738 TCAGTCCTTTTGTTGGCACTTG 59.573 45.455 0.00 0.00 0.00 3.16
1942 5173 1.756538 AGTCCTTTTGTTGGCACTTGG 59.243 47.619 0.00 0.00 0.00 3.61
1943 5174 0.463620 TCCTTTTGTTGGCACTTGGC 59.536 50.000 0.00 0.00 43.74 4.52
1950 5181 4.560743 TGGCACTTGGCACTGCGA 62.561 61.111 0.49 4.00 46.12 5.10
2073 5305 4.679905 CGGGGTTTGTACCTTAGCTAGAAG 60.680 50.000 0.00 0.00 44.38 2.85
2205 5438 3.340814 ACATTAGTGCTCCCTGAACTG 57.659 47.619 0.00 0.00 34.82 3.16
2239 5472 3.344535 TCTGGGCTGATCCAAGGTATA 57.655 47.619 0.00 0.00 36.47 1.47
2240 5473 3.664320 TCTGGGCTGATCCAAGGTATAA 58.336 45.455 0.00 0.00 36.47 0.98
2244 5481 5.385198 TGGGCTGATCCAAGGTATAATTTC 58.615 41.667 0.00 0.00 36.21 2.17
2249 5486 7.175104 GCTGATCCAAGGTATAATTTCCCATA 58.825 38.462 0.00 0.00 0.00 2.74
2250 5487 7.836183 GCTGATCCAAGGTATAATTTCCCATAT 59.164 37.037 0.00 0.00 0.00 1.78
2255 5492 9.802039 TCCAAGGTATAATTTCCCATATAACAC 57.198 33.333 0.00 0.00 0.00 3.32
2604 5842 3.610040 ATCAGCTGGTCAAACGATACA 57.390 42.857 15.13 0.00 0.00 2.29
2664 5902 4.084849 GCACGCTGCATTTAGTAGTGATAG 60.085 45.833 0.00 0.00 44.26 2.08
2866 6104 0.622665 CTCCACAGATTGAGGCCCTT 59.377 55.000 0.00 0.00 0.00 3.95
2893 6131 6.003950 CAGAAAACTTATCTCCACCCTTCAA 58.996 40.000 0.00 0.00 0.00 2.69
3071 6309 5.551233 CTTCAGTAGGAACCAACTGATCAA 58.449 41.667 6.04 0.00 46.47 2.57
3072 6310 4.894784 TCAGTAGGAACCAACTGATCAAC 58.105 43.478 0.00 0.00 43.78 3.18
3073 6311 4.593206 TCAGTAGGAACCAACTGATCAACT 59.407 41.667 0.00 0.00 43.78 3.16
3129 6367 8.082242 GGAAAGAAAAGGAAATCGATTCTGAAA 58.918 33.333 11.83 0.00 38.18 2.69
3152 6390 1.439543 AGAGGCTTCAGGGACTTTGT 58.560 50.000 0.00 0.00 34.60 2.83
3347 6585 6.524734 ACAATGTTCTCTGAGACATGTGTTA 58.475 36.000 1.15 0.00 0.00 2.41
3463 6701 1.732259 GCACTGGACTACATGGTTTCG 59.268 52.381 0.00 0.00 0.00 3.46
3512 6750 7.365741 CAGTTATGATGGAAATATGGCAAGAC 58.634 38.462 0.00 0.00 0.00 3.01
3551 6789 2.509964 AGGTTGGCTTCTCCGGAATATT 59.490 45.455 5.23 0.00 37.80 1.28
3557 6795 4.157656 TGGCTTCTCCGGAATATTTTGTTG 59.842 41.667 5.23 0.00 37.80 3.33
3608 6846 5.393962 AGTTTGCGTGCTCTTTTGATTATC 58.606 37.500 0.00 0.00 0.00 1.75
3689 6927 3.565307 TGATGAACCTTTTGGCTGTTCT 58.435 40.909 0.00 0.00 45.59 3.01
3799 7037 1.139654 TCCTGGGATGAATTCTCTGCG 59.860 52.381 7.05 0.00 0.00 5.18
4014 7252 1.113788 TAGCATAGCGTTAACCCGGT 58.886 50.000 0.00 0.00 41.95 5.28
4089 7327 8.723942 ATTATTCACTTTAGGTACAAGCAGAG 57.276 34.615 0.00 0.00 0.00 3.35
4217 7455 1.005340 CTCTGCTCGATTGCCACTTC 58.995 55.000 0.00 0.00 0.00 3.01
4292 7531 1.488393 CACTCTCCATTCCCCCTTCTC 59.512 57.143 0.00 0.00 0.00 2.87
4400 7641 7.771826 TGTTCTTTTGTACTAGTTACCAAAGCT 59.228 33.333 0.00 0.00 40.72 3.74
4486 7728 7.368833 GCTCCAAGATAAGATGATCCATTTTG 58.631 38.462 0.00 0.00 0.00 2.44
4549 7791 6.449635 TTGTTGAACTGTATGCAAACTTCT 57.550 33.333 0.00 0.00 0.00 2.85
4588 7831 0.881118 TGCTTCTGCGAATTTGACCC 59.119 50.000 0.00 0.00 43.34 4.46
4635 7878 0.032540 CAACTGCAAAGGAACCAGCC 59.967 55.000 0.00 0.00 0.00 4.85
4658 7903 6.702723 GCCTGATCTCATGCATATATCTCTTC 59.297 42.308 0.00 0.00 37.43 2.87
4690 7961 6.463614 CCTCTGAAATCCCTAGATAAGTGGTG 60.464 46.154 0.00 0.00 30.42 4.17
4691 7962 5.036117 TGAAATCCCTAGATAAGTGGTGC 57.964 43.478 0.00 0.00 30.42 5.01
4692 7963 4.473196 TGAAATCCCTAGATAAGTGGTGCA 59.527 41.667 0.00 0.00 30.42 4.57
4693 7964 5.132648 TGAAATCCCTAGATAAGTGGTGCAT 59.867 40.000 0.00 0.00 30.42 3.96
4694 7965 4.899352 ATCCCTAGATAAGTGGTGCATC 57.101 45.455 0.00 0.00 0.00 3.91
4695 7966 2.972713 TCCCTAGATAAGTGGTGCATCC 59.027 50.000 0.00 0.00 0.00 3.51
4696 7967 2.705658 CCCTAGATAAGTGGTGCATCCA 59.294 50.000 0.00 0.00 45.01 3.41
4697 7968 7.838045 AATCCCTAGATAAGTGGTGCATCCAA 61.838 42.308 9.23 0.00 39.01 3.53
4710 7981 2.995466 CATCCAATGCAGTGTTTCGT 57.005 45.000 13.82 0.00 0.00 3.85
4711 7982 2.855180 CATCCAATGCAGTGTTTCGTC 58.145 47.619 13.82 0.00 0.00 4.20
4712 7983 1.234821 TCCAATGCAGTGTTTCGTCC 58.765 50.000 13.82 0.00 0.00 4.79
4713 7984 0.110238 CCAATGCAGTGTTTCGTCCG 60.110 55.000 13.82 0.00 0.00 4.79
4714 7985 0.586319 CAATGCAGTGTTTCGTCCGT 59.414 50.000 5.87 0.00 0.00 4.69
4736 8007 3.186909 GCAAGTTTTGGACTTTGGTGAC 58.813 45.455 0.00 0.00 46.34 3.67
4755 8044 3.056821 TGACGTGTCCTAGAGATTTGGTG 60.057 47.826 0.00 0.00 0.00 4.17
4780 8069 4.825085 AGTGTAATCGGTTGTCCAAACATT 59.175 37.500 0.00 0.00 34.73 2.71
4840 8171 5.551760 AAATGCTCTAGAATCGTTTGGTG 57.448 39.130 9.72 0.00 0.00 4.17
4856 8187 5.465935 GTTTGGTGTTTTCTGTGAACAAGA 58.534 37.500 0.00 0.00 38.60 3.02
4858 8189 3.126171 TGGTGTTTTCTGTGAACAAGACG 59.874 43.478 0.00 0.00 38.60 4.18
4873 8204 3.621794 CAAGACGGAACTTGCTTTTCTG 58.378 45.455 0.00 0.00 40.24 3.02
4924 8255 7.438564 ACTACTTTTACGGCCAAATTTTCAAT 58.561 30.769 2.24 0.00 0.00 2.57
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
141 147 3.209410 GGAATGCTGGAGATCGTCAAAT 58.791 45.455 0.00 0.00 0.00 2.32
147 153 1.742146 TCCGGAATGCTGGAGATCG 59.258 57.895 0.00 0.00 44.72 3.69
161 167 1.604604 TCTTTCTTTGGTTGCTCCGG 58.395 50.000 0.00 0.00 39.52 5.14
164 170 5.186996 TGTCAATCTTTCTTTGGTTGCTC 57.813 39.130 0.00 0.00 0.00 4.26
198 204 7.897575 TTCTTTGTTTATTAAATGCGGCAAT 57.102 28.000 6.82 0.00 0.00 3.56
394 406 7.760794 TCGCCTATTTTAATTTAGAAGTGTCGA 59.239 33.333 0.00 0.00 0.00 4.20
395 407 7.902032 TCGCCTATTTTAATTTAGAAGTGTCG 58.098 34.615 0.00 0.00 0.00 4.35
426 439 3.372206 CGTTGGATAAGTGCTTCTCAAGG 59.628 47.826 0.91 0.00 0.00 3.61
448 461 5.420739 TCCATGGGAACTAATAAAACCAAGC 59.579 40.000 13.02 0.00 0.00 4.01
509 3587 9.226606 CTGAAATCTCCGAGATACTAGATAAGT 57.773 37.037 11.39 0.00 42.62 2.24
510 3588 8.181573 GCTGAAATCTCCGAGATACTAGATAAG 58.818 40.741 11.39 3.29 32.89 1.73
511 3589 7.665974 TGCTGAAATCTCCGAGATACTAGATAA 59.334 37.037 11.39 0.00 32.89 1.75
512 3590 7.168905 TGCTGAAATCTCCGAGATACTAGATA 58.831 38.462 11.39 1.75 32.89 1.98
514 3592 5.377478 TGCTGAAATCTCCGAGATACTAGA 58.623 41.667 11.39 0.00 32.89 2.43
515 3593 5.697473 TGCTGAAATCTCCGAGATACTAG 57.303 43.478 11.39 10.32 32.89 2.57
516 3594 6.656632 AATGCTGAAATCTCCGAGATACTA 57.343 37.500 11.39 0.65 32.89 1.82
517 3595 5.543507 AATGCTGAAATCTCCGAGATACT 57.456 39.130 11.39 2.23 32.89 2.12
518 3596 5.107683 CGAAATGCTGAAATCTCCGAGATAC 60.108 44.000 11.39 9.34 32.89 2.24
523 3601 3.190079 CTCGAAATGCTGAAATCTCCGA 58.810 45.455 0.00 0.00 0.00 4.55
524 3602 2.286294 CCTCGAAATGCTGAAATCTCCG 59.714 50.000 0.00 0.00 0.00 4.63
578 3770 9.769093 AACGCGGCAATTATTAATATTCTAATC 57.231 29.630 12.47 0.00 0.00 1.75
703 3912 1.416030 GGAAGAGAAGAGATGGAGGGC 59.584 57.143 0.00 0.00 0.00 5.19
704 3913 3.044873 AGGAAGAGAAGAGATGGAGGG 57.955 52.381 0.00 0.00 0.00 4.30
705 3914 3.568007 CGTAGGAAGAGAAGAGATGGAGG 59.432 52.174 0.00 0.00 0.00 4.30
709 3918 5.518487 GCTTTTCGTAGGAAGAGAAGAGATG 59.482 44.000 17.22 0.00 36.70 2.90
755 3967 0.512952 CGGCAGCCATTAATAGTCGC 59.487 55.000 13.30 0.00 0.00 5.19
779 3991 0.182775 ATGGCCCCCGTGATTAGTTC 59.817 55.000 0.00 0.00 0.00 3.01
792 4004 1.371558 CGGGAGCTAGTAATGGCCC 59.628 63.158 0.00 0.00 0.00 5.80
809 4021 1.952635 GGGATTAACTACGCCGCCG 60.953 63.158 0.00 0.00 41.14 6.46
811 4023 1.596203 GGGGGATTAACTACGCCGC 60.596 63.158 0.00 0.00 39.50 6.53
845 4057 0.319125 GCGAAGGATTAGAGCGGGAG 60.319 60.000 0.00 0.00 0.00 4.30
882 4094 3.706373 ACTGCCGCTACCACCAGG 61.706 66.667 0.00 0.00 42.21 4.45
894 4106 0.249398 CTAGTACCACCACCACTGCC 59.751 60.000 0.00 0.00 0.00 4.85
903 4115 1.547472 AACCGCCACCTAGTACCACC 61.547 60.000 0.00 0.00 0.00 4.61
990 4202 2.121832 ACGACCATCTCCCCACCA 59.878 61.111 0.00 0.00 0.00 4.17
1265 4477 1.756538 GAGCAAGAGGAAGAGGAGGAG 59.243 57.143 0.00 0.00 0.00 3.69
1267 4479 0.829990 GGAGCAAGAGGAAGAGGAGG 59.170 60.000 0.00 0.00 0.00 4.30
1288 4500 3.049080 GCAGGGGGAAGCTTCGGAT 62.049 63.158 19.91 3.48 0.00 4.18
1289 4501 3.717294 GCAGGGGGAAGCTTCGGA 61.717 66.667 19.91 0.00 0.00 4.55
1290 4502 4.803908 GGCAGGGGGAAGCTTCGG 62.804 72.222 19.91 8.11 0.00 4.30
1291 4503 4.803908 GGGCAGGGGGAAGCTTCG 62.804 72.222 19.91 7.13 0.00 3.79
1292 4504 2.845638 GAAGGGCAGGGGGAAGCTTC 62.846 65.000 18.54 18.54 0.00 3.86
1293 4505 2.866015 AAGGGCAGGGGGAAGCTT 60.866 61.111 0.00 0.00 0.00 3.74
1294 4506 3.342477 GAAGGGCAGGGGGAAGCT 61.342 66.667 0.00 0.00 0.00 3.74
1295 4507 4.448976 GGAAGGGCAGGGGGAAGC 62.449 72.222 0.00 0.00 0.00 3.86
1296 4508 4.115199 CGGAAGGGCAGGGGGAAG 62.115 72.222 0.00 0.00 0.00 3.46
1297 4509 4.995058 ACGGAAGGGCAGGGGGAA 62.995 66.667 0.00 0.00 0.00 3.97
1305 4517 1.209747 AGACTAATTCCACGGAAGGGC 59.790 52.381 4.58 0.00 37.56 5.19
1353 4566 2.272146 GAGCTCCGCCCAAATCCA 59.728 61.111 0.87 0.00 0.00 3.41
1389 4602 3.403057 CGGCGTCGTTGACCACAG 61.403 66.667 0.00 0.00 0.00 3.66
1412 4625 0.308068 GATCGAGCCGAATCGTCAGA 59.692 55.000 0.82 0.00 43.20 3.27
1414 4627 1.010013 CGATCGAGCCGAATCGTCA 60.010 57.895 10.26 0.00 43.20 4.35
1416 4629 2.353607 GCGATCGAGCCGAATCGT 60.354 61.111 21.57 0.00 43.20 3.73
1483 4696 3.329889 AGCCCCAATGCGACCTGA 61.330 61.111 0.00 0.00 36.02 3.86
1489 4702 4.807039 GCTTGCAGCCCCAATGCG 62.807 66.667 0.00 0.00 46.87 4.73
1505 4718 1.786579 GCAACCACAAATTCAGAACGC 59.213 47.619 0.00 0.00 0.00 4.84
1519 4738 1.335496 GCCTCTACAAAAACGCAACCA 59.665 47.619 0.00 0.00 0.00 3.67
1523 4742 1.961793 ACAGCCTCTACAAAAACGCA 58.038 45.000 0.00 0.00 0.00 5.24
1526 4745 5.505819 GGTTCAGAACAGCCTCTACAAAAAC 60.506 44.000 15.36 0.00 0.00 2.43
1528 4747 4.134563 GGTTCAGAACAGCCTCTACAAAA 58.865 43.478 15.36 0.00 0.00 2.44
1531 4750 2.300152 CAGGTTCAGAACAGCCTCTACA 59.700 50.000 15.36 0.00 0.00 2.74
1537 4756 0.606673 GGTCCAGGTTCAGAACAGCC 60.607 60.000 15.36 5.55 0.00 4.85
1563 4783 7.121168 GGAAATGAAGATTGAGGTATGAACACA 59.879 37.037 0.00 0.00 0.00 3.72
1655 4877 0.664767 ATCGAGCGCGCCTTAAGATC 60.665 55.000 30.33 16.04 37.46 2.75
1659 4881 2.164663 CACATCGAGCGCGCCTTAA 61.165 57.895 30.33 11.85 37.46 1.85
1736 4962 9.325198 TGCGAAATACTCTGTATCATTTGTTAT 57.675 29.630 0.00 0.00 0.00 1.89
1905 5136 6.365970 AAGGACTGAGACAACAAGATATGT 57.634 37.500 0.00 0.00 46.82 2.29
1909 5140 5.440610 ACAAAAGGACTGAGACAACAAGAT 58.559 37.500 0.00 0.00 0.00 2.40
1950 5181 0.107654 GACCCTAATCAGCGCCAGTT 60.108 55.000 2.29 0.00 0.00 3.16
2017 5249 0.109723 TAAGGCCTCCGTTGCAAGTT 59.890 50.000 5.23 0.00 0.00 2.66
2205 5438 3.696548 CAGCCCAGAAAGACCTTTTATCC 59.303 47.826 0.00 0.00 32.11 2.59
2255 5492 6.955963 GCTCGTGTTTGATGTTATAGAAACAG 59.044 38.462 0.00 0.00 38.60 3.16
2328 5565 7.537715 TGAATGACATTTACAATAGCACAAGG 58.462 34.615 1.39 0.00 0.00 3.61
2390 5627 9.761504 ACAAACAATCATGAACATATTTCACAA 57.238 25.926 0.00 0.00 0.00 3.33
2604 5842 8.654094 ACATTATTTACCCGCTTTAGGTAGTAT 58.346 33.333 0.00 0.00 40.87 2.12
2683 5921 3.771216 AGCTTTCAGGTCCACATGATTT 58.229 40.909 0.00 0.00 36.49 2.17
2866 6104 3.561313 GGGTGGAGATAAGTTTTCTGCCA 60.561 47.826 11.30 10.04 31.17 4.92
2893 6131 2.360801 CACAACAAATTCCCCACTTCGT 59.639 45.455 0.00 0.00 0.00 3.85
3113 6351 5.163713 CCTCTTGGTTTCAGAATCGATTTCC 60.164 44.000 12.81 8.78 34.67 3.13
3129 6367 0.474660 AGTCCCTGAAGCCTCTTGGT 60.475 55.000 0.00 0.00 35.27 3.67
3463 6701 5.045872 GGGATGAAAACATTGCTTGCTATC 58.954 41.667 0.00 0.00 0.00 2.08
3512 6750 1.284982 CTGCGGTGACCTTCGACAAG 61.285 60.000 0.00 0.00 0.00 3.16
3591 6829 6.602179 TGTTTCTGATAATCAAAAGAGCACG 58.398 36.000 0.00 0.00 0.00 5.34
3631 6869 4.773323 AGTTCTGTTGCCATTAGAAAGC 57.227 40.909 0.00 0.00 32.76 3.51
3799 7037 4.704833 TGCGCCTCCTTCACAGCC 62.705 66.667 4.18 0.00 0.00 4.85
4014 7252 3.138304 GCTGTACAAAGTCATGGTGTCA 58.862 45.455 0.00 0.00 0.00 3.58
4292 7531 4.278975 AGAGTCAGAGCCCTAAACAAAG 57.721 45.455 0.00 0.00 0.00 2.77
4369 7608 5.857822 AACTAGTACAAAAGAACATCGGC 57.142 39.130 0.00 0.00 0.00 5.54
4549 7791 1.003839 GGACAACAGCCACATCGGA 60.004 57.895 0.00 0.00 36.56 4.55
4635 7878 9.878667 AAAGAAGAGATATATGCATGAGATCAG 57.121 33.333 10.16 0.00 0.00 2.90
4658 7903 6.054860 TCTAGGGATTTCAGAGGAACAAAG 57.945 41.667 0.00 0.00 31.35 2.77
4691 7962 2.414559 GGACGAAACACTGCATTGGATG 60.415 50.000 9.06 0.00 0.00 3.51
4692 7963 1.812571 GGACGAAACACTGCATTGGAT 59.187 47.619 9.06 0.00 0.00 3.41
4693 7964 1.234821 GGACGAAACACTGCATTGGA 58.765 50.000 9.06 0.00 0.00 3.53
4694 7965 0.110238 CGGACGAAACACTGCATTGG 60.110 55.000 9.06 0.00 0.00 3.16
4695 7966 0.586319 ACGGACGAAACACTGCATTG 59.414 50.000 1.95 1.95 0.00 2.82
4696 7967 0.586319 CACGGACGAAACACTGCATT 59.414 50.000 0.00 0.00 0.00 3.56
4697 7968 1.841663 GCACGGACGAAACACTGCAT 61.842 55.000 0.00 0.00 0.00 3.96
4698 7969 2.530497 GCACGGACGAAACACTGCA 61.530 57.895 0.00 0.00 0.00 4.41
4699 7970 2.042520 TTGCACGGACGAAACACTGC 62.043 55.000 0.00 0.00 0.00 4.40
4700 7971 0.042188 CTTGCACGGACGAAACACTG 60.042 55.000 0.00 0.00 0.00 3.66
4701 7972 0.461339 ACTTGCACGGACGAAACACT 60.461 50.000 0.00 0.00 0.00 3.55
4702 7973 0.375803 AACTTGCACGGACGAAACAC 59.624 50.000 0.00 0.00 0.00 3.32
4703 7974 1.088306 AAACTTGCACGGACGAAACA 58.912 45.000 0.00 0.00 0.00 2.83
4704 7975 1.843753 CAAAACTTGCACGGACGAAAC 59.156 47.619 0.00 0.00 0.00 2.78
4705 7976 1.202200 CCAAAACTTGCACGGACGAAA 60.202 47.619 0.00 0.00 0.00 3.46
4706 7977 0.378962 CCAAAACTTGCACGGACGAA 59.621 50.000 0.00 0.00 0.00 3.85
4707 7978 0.462225 TCCAAAACTTGCACGGACGA 60.462 50.000 0.00 0.00 0.00 4.20
4708 7979 0.316689 GTCCAAAACTTGCACGGACG 60.317 55.000 0.00 0.00 37.04 4.79
4709 7980 1.021968 AGTCCAAAACTTGCACGGAC 58.978 50.000 0.00 0.00 45.34 4.79
4710 7981 1.757682 AAGTCCAAAACTTGCACGGA 58.242 45.000 0.00 0.00 46.61 4.69
4736 8007 3.594603 ACACCAAATCTCTAGGACACG 57.405 47.619 0.00 0.00 0.00 4.49
4755 8044 4.751098 TGTTTGGACAACCGATTACACTAC 59.249 41.667 0.00 0.00 39.42 2.73
4780 8069 3.697542 CACAAGATGATCTCCATGCCAAA 59.302 43.478 0.00 0.00 35.17 3.28
4840 8171 4.094442 AGTTCCGTCTTGTTCACAGAAAAC 59.906 41.667 0.00 0.00 0.00 2.43
4856 8187 4.450082 AAAACAGAAAAGCAAGTTCCGT 57.550 36.364 0.00 0.00 0.00 4.69
4858 8189 6.811665 ACACTAAAAACAGAAAAGCAAGTTCC 59.188 34.615 0.00 0.00 0.00 3.62
4898 8229 7.507733 TGAAAATTTGGCCGTAAAAGTAGTA 57.492 32.000 0.00 0.00 0.00 1.82


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

AutoCloner maintained by Alex Coulton.