Multiple sequence alignment - TraesCS6A01G307300

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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 TraesCS6A01G307300 chr6A 100.000 4944 0 0 1 4944 541403864 541398921 0.000000e+00 9130
1 TraesCS6A01G307300 chr6D 92.197 4998 189 74 27 4944 394923971 394919095 0.000000e+00 6883
2 TraesCS6A01G307300 chr6D 77.841 352 65 12 4474 4819 450085540 450085884 6.490000e-49 206
3 TraesCS6A01G307300 chr6B 92.722 2487 101 37 413 2859 591236012 591233566 0.000000e+00 3517
4 TraesCS6A01G307300 chr6B 92.177 1649 84 23 2846 4474 591233545 591231922 0.000000e+00 2289
5 TraesCS6A01G307300 chr6B 96.774 341 11 0 2 342 591236810 591236470 2.000000e-158 569
6 TraesCS6A01G307300 chr6B 86.425 442 43 6 4479 4919 591231706 591231281 7.490000e-128 468
7 TraesCS6A01G307300 chr7A 87.552 241 29 1 1255 1495 143144982 143145221 1.360000e-70 278
8 TraesCS6A01G307300 chr7A 81.897 232 37 3 1258 1488 676403724 676403497 1.820000e-44 191
9 TraesCS6A01G307300 chr7B 87.190 242 28 3 1256 1496 106340131 106340370 6.310000e-69 272
10 TraesCS6A01G307300 chr7B 85.124 242 27 2 3684 3916 106342700 106342941 6.400000e-59 239
11 TraesCS6A01G307300 chr7B 85.294 204 28 2 2915 3117 106341818 106342020 5.010000e-50 209
12 TraesCS6A01G307300 chr7D 86.722 241 31 1 1255 1495 141188385 141188146 2.930000e-67 267
13 TraesCS6A01G307300 chr7D 84.109 258 32 3 3684 3935 141185831 141185577 1.780000e-59 241
14 TraesCS6A01G307300 chr7D 76.471 391 69 20 2915 3285 141186714 141186327 1.820000e-44 191
15 TraesCS6A01G307300 chr5D 77.230 426 93 4 4474 4896 438468572 438468996 3.820000e-61 246
16 TraesCS6A01G307300 chrUn 77.841 352 65 12 4474 4819 126795929 126795585 6.490000e-49 206
17 TraesCS6A01G307300 chr4D 77.841 352 65 12 4474 4819 379345343 379344999 6.490000e-49 206
18 TraesCS6A01G307300 chr1D 77.841 352 65 12 4474 4819 397635618 397635274 6.490000e-49 206
19 TraesCS6A01G307300 chr1D 77.841 352 65 12 4474 4819 432549682 432549338 6.490000e-49 206
20 TraesCS6A01G307300 chr1D 77.841 352 65 12 4474 4819 453827730 453828074 6.490000e-49 206
21 TraesCS6A01G307300 chr4A 82.128 235 37 3 1255 1488 599536014 599535784 3.900000e-46 196
22 TraesCS6A01G307300 chr3A 81.356 236 37 5 1255 1488 700004673 700004443 8.450000e-43 185
23 TraesCS6A01G307300 chr5B 80.498 241 41 4 1255 1494 551170217 551170452 3.930000e-41 180


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 TraesCS6A01G307300 chr6A 541398921 541403864 4943 True 9130.00 9130 100.000000 1 4944 1 chr6A.!!$R1 4943
1 TraesCS6A01G307300 chr6D 394919095 394923971 4876 True 6883.00 6883 92.197000 27 4944 1 chr6D.!!$R1 4917
2 TraesCS6A01G307300 chr6B 591231281 591236810 5529 True 1710.75 3517 92.024500 2 4919 4 chr6B.!!$R1 4917
3 TraesCS6A01G307300 chr7B 106340131 106342941 2810 False 240.00 272 85.869333 1256 3916 3 chr7B.!!$F1 2660
4 TraesCS6A01G307300 chr7D 141185577 141188385 2808 True 233.00 267 82.434000 1255 3935 3 chr7D.!!$R1 2680

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
453 848 0.674895 CTTTCTCCGGAGCAACCCTG 60.675 60.0 27.39 6.51 34.64 4.45 F
1169 1581 0.103208 GTGAGCCAGACCGATCGATT 59.897 55.0 18.66 2.17 0.00 3.34 F
1222 1634 0.247460 CGACCACTGGATTCAGAGCA 59.753 55.0 8.39 0.00 43.49 4.26 F
1939 2387 0.250124 GGGTGTTGTCATGGACGTGA 60.250 55.0 0.00 0.00 34.95 4.35 F
2608 3915 0.442310 CTTTACATGTGTCGTGGCCG 59.558 55.0 9.11 0.00 0.00 6.13 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1696 2108 0.943835 TGTGCGACTTGTGTCATCCG 60.944 55.000 0.00 0.0 43.06 4.18 R
2726 4049 0.967380 CCCCAAATCTCACAGCACCC 60.967 60.000 0.00 0.0 0.00 4.61 R
3142 4516 2.086869 AGGTCGACAAATGGCAATCAG 58.913 47.619 18.91 0.0 0.00 2.90 R
3457 4843 0.534203 TCAACGACTCCTGTTTGGCC 60.534 55.000 0.00 0.0 35.26 5.36 R
4006 5697 0.041751 CGCACGCACACACATAACAA 60.042 50.000 0.00 0.0 0.00 2.83 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
134 135 4.157656 TGAATTTGATAGCTTGGGTTTCGG 59.842 41.667 0.00 0.00 0.00 4.30
173 175 7.488792 TGCATTTGAAAAATATCCAGTTGATCG 59.511 33.333 0.00 0.00 34.76 3.69
344 349 1.871039 TCAACCTAAACACAAGCTCGC 59.129 47.619 0.00 0.00 0.00 5.03
346 351 1.961793 ACCTAAACACAAGCTCGCAA 58.038 45.000 0.00 0.00 0.00 4.85
361 366 3.114616 CAAGCGTGAGGCCGTGAG 61.115 66.667 0.00 0.00 45.17 3.51
414 809 6.411675 TCCCATGAAATATCCATCCATCAT 57.588 37.500 0.00 0.00 0.00 2.45
417 812 6.096423 CCCATGAAATATCCATCCATCATCAC 59.904 42.308 0.00 0.00 0.00 3.06
419 814 6.458630 TGAAATATCCATCCATCATCACCT 57.541 37.500 0.00 0.00 0.00 4.00
420 815 7.572546 TGAAATATCCATCCATCATCACCTA 57.427 36.000 0.00 0.00 0.00 3.08
421 816 7.397221 TGAAATATCCATCCATCATCACCTAC 58.603 38.462 0.00 0.00 0.00 3.18
422 817 6.957853 AATATCCATCCATCATCACCTACA 57.042 37.500 0.00 0.00 0.00 2.74
423 818 6.957853 ATATCCATCCATCATCACCTACAA 57.042 37.500 0.00 0.00 0.00 2.41
453 848 0.674895 CTTTCTCCGGAGCAACCCTG 60.675 60.000 27.39 6.51 34.64 4.45
475 870 3.181513 GGCTTAAAAGAATCGGTTCGTCC 60.182 47.826 2.06 0.00 39.38 4.79
562 957 6.308766 GCGAATTTACAACTGCAATCATTTCT 59.691 34.615 0.00 0.00 0.00 2.52
563 958 7.148755 GCGAATTTACAACTGCAATCATTTCTT 60.149 33.333 0.00 0.00 0.00 2.52
585 980 4.421058 TCTATCGGCCGATTGAAATATCG 58.579 43.478 42.74 19.78 45.27 2.92
658 1053 1.902938 AAGCAGAAGAGAACAAGCCC 58.097 50.000 0.00 0.00 0.00 5.19
684 1079 5.290885 GGATTTGGTTTATTTCGTCCAATGC 59.709 40.000 0.00 0.00 39.27 3.56
969 1381 0.831288 AGCTCAGTCTCAGGTGCTGT 60.831 55.000 0.00 0.00 32.61 4.40
1134 1546 2.783288 CGCCGACTACTTCCCTCCC 61.783 68.421 0.00 0.00 0.00 4.30
1160 1572 1.338579 CCTCAAGAAGGTGAGCCAGAC 60.339 57.143 0.00 0.00 43.18 3.51
1164 1576 0.616111 AGAAGGTGAGCCAGACCGAT 60.616 55.000 0.00 0.00 38.64 4.18
1169 1581 0.103208 GTGAGCCAGACCGATCGATT 59.897 55.000 18.66 2.17 0.00 3.34
1213 1625 3.986006 GCGTGACCGACCACTGGA 61.986 66.667 0.71 0.00 35.02 3.86
1214 1626 2.970639 CGTGACCGACCACTGGAT 59.029 61.111 0.71 0.00 35.02 3.41
1218 1630 0.608130 TGACCGACCACTGGATTCAG 59.392 55.000 0.71 0.00 46.10 3.02
1219 1631 0.895530 GACCGACCACTGGATTCAGA 59.104 55.000 8.39 0.00 43.49 3.27
1220 1632 0.898320 ACCGACCACTGGATTCAGAG 59.102 55.000 8.39 0.00 43.49 3.35
1221 1633 0.460987 CCGACCACTGGATTCAGAGC 60.461 60.000 8.39 0.00 43.49 4.09
1222 1634 0.247460 CGACCACTGGATTCAGAGCA 59.753 55.000 8.39 0.00 43.49 4.26
1225 1637 1.911357 ACCACTGGATTCAGAGCATGA 59.089 47.619 8.39 0.00 43.49 3.07
1245 1657 2.880822 ATGAATGACGCGAACTGTTG 57.119 45.000 15.93 0.00 0.00 3.33
1279 1691 2.342648 GTGTCGGAGGTGGTGTCC 59.657 66.667 0.00 0.00 0.00 4.02
1507 1919 3.504863 ACTACATACGTTACGCAACAGG 58.495 45.455 4.09 0.00 34.05 4.00
1630 2042 6.748198 ACGTTAATCTTCTCGCTTTCTCTTAG 59.252 38.462 0.00 0.00 0.00 2.18
1648 2060 7.663827 TCTCTTAGTCTGTTATTTCCAACGAA 58.336 34.615 0.00 0.00 0.00 3.85
1649 2061 7.813148 TCTCTTAGTCTGTTATTTCCAACGAAG 59.187 37.037 0.00 0.00 0.00 3.79
1678 2090 1.156736 CAAACACCCCACTCATCGAC 58.843 55.000 0.00 0.00 0.00 4.20
1828 2276 5.916883 CCACAGTTGCTTCAGTATTTGAAAG 59.083 40.000 0.00 0.00 44.84 2.62
1845 2293 1.809684 AAGACCGTTTTCAGGCTAGC 58.190 50.000 6.04 6.04 0.00 3.42
1846 2294 0.977395 AGACCGTTTTCAGGCTAGCT 59.023 50.000 15.72 0.00 0.00 3.32
1847 2295 2.176889 AGACCGTTTTCAGGCTAGCTA 58.823 47.619 15.72 0.00 0.00 3.32
1848 2296 2.166664 AGACCGTTTTCAGGCTAGCTAG 59.833 50.000 16.84 16.84 0.00 3.42
1939 2387 0.250124 GGGTGTTGTCATGGACGTGA 60.250 55.000 0.00 0.00 34.95 4.35
1940 2388 1.610624 GGGTGTTGTCATGGACGTGAT 60.611 52.381 0.00 0.00 34.95 3.06
1941 2389 2.354303 GGGTGTTGTCATGGACGTGATA 60.354 50.000 0.00 0.00 34.95 2.15
1942 2390 3.531538 GGTGTTGTCATGGACGTGATAT 58.468 45.455 0.00 0.00 34.95 1.63
2248 2851 8.215050 TCTAGTTGGAGTTTGTTGGAAGAAATA 58.785 33.333 0.00 0.00 0.00 1.40
2309 2912 2.959507 TATGTGTGAGGTGTGATCGG 57.040 50.000 0.00 0.00 0.00 4.18
2355 3627 5.863935 CGGTCGCATCAGATATATGAAAAGA 59.136 40.000 3.78 1.51 31.76 2.52
2378 3663 7.373778 GAAAGCCTTTTCTAGTCGGAAAATA 57.626 36.000 0.00 0.00 42.07 1.40
2379 3664 7.939784 AAAGCCTTTTCTAGTCGGAAAATAT 57.060 32.000 0.00 0.00 42.07 1.28
2380 3665 6.927294 AGCCTTTTCTAGTCGGAAAATATG 57.073 37.500 0.00 0.00 42.07 1.78
2381 3666 6.650120 AGCCTTTTCTAGTCGGAAAATATGA 58.350 36.000 0.00 0.00 42.07 2.15
2526 3817 2.088950 CCGACCGGTTTAACACTGAT 57.911 50.000 9.42 0.00 32.74 2.90
2539 3830 6.956299 TTAACACTGATACCGCTTTTAGTC 57.044 37.500 0.00 0.00 0.00 2.59
2587 3894 1.088340 CGGCTCGACCTAGAAGACGA 61.088 60.000 4.29 0.00 35.61 4.20
2608 3915 0.442310 CTTTACATGTGTCGTGGCCG 59.558 55.000 9.11 0.00 0.00 6.13
2643 3950 3.818787 CCTGCGTACGTACCGGCT 61.819 66.667 19.67 0.00 0.00 5.52
2647 3954 3.818787 CGTACGTACCGGCTGCCT 61.819 66.667 19.67 0.70 0.00 4.75
2689 3996 1.990424 CCATGTCTGTGTGGGGCTA 59.010 57.895 0.00 0.00 0.00 3.93
2692 3999 0.911525 ATGTCTGTGTGGGGCTAGCT 60.912 55.000 15.72 0.00 0.00 3.32
2693 4000 1.219393 GTCTGTGTGGGGCTAGCTC 59.781 63.158 15.72 11.22 0.00 4.09
2695 4002 4.082523 TGTGTGGGGCTAGCTCGC 62.083 66.667 15.72 13.95 0.00 5.03
2696 4003 4.082523 GTGTGGGGCTAGCTCGCA 62.083 66.667 15.72 16.29 0.00 5.10
2697 4004 3.774528 TGTGGGGCTAGCTCGCAG 61.775 66.667 15.72 0.00 0.00 5.18
2698 4005 4.537433 GTGGGGCTAGCTCGCAGG 62.537 72.222 15.72 0.00 0.00 4.85
2700 4007 3.787001 GGGGCTAGCTCGCAGGTT 61.787 66.667 15.72 0.00 0.00 3.50
2701 4008 2.202946 GGGCTAGCTCGCAGGTTC 60.203 66.667 15.72 0.00 0.00 3.62
2702 4009 2.583593 GGCTAGCTCGCAGGTTCG 60.584 66.667 15.72 0.00 0.00 3.95
2703 4010 2.182030 GCTAGCTCGCAGGTTCGT 59.818 61.111 7.70 0.00 0.00 3.85
2704 4011 1.874466 GCTAGCTCGCAGGTTCGTC 60.874 63.158 7.70 0.00 0.00 4.20
2705 4012 1.583967 CTAGCTCGCAGGTTCGTCG 60.584 63.158 0.00 0.00 0.00 5.12
2706 4013 1.978712 CTAGCTCGCAGGTTCGTCGA 61.979 60.000 0.00 0.00 0.00 4.20
2708 4015 2.202492 CTCGCAGGTTCGTCGAGG 60.202 66.667 0.00 0.00 44.06 4.63
2709 4016 3.685214 CTCGCAGGTTCGTCGAGGG 62.685 68.421 5.12 0.00 44.06 4.30
2711 4018 4.373116 GCAGGTTCGTCGAGGGCA 62.373 66.667 5.12 0.00 0.00 5.36
2712 4019 2.432628 CAGGTTCGTCGAGGGCAC 60.433 66.667 5.12 2.80 0.00 5.01
2713 4020 4.052229 AGGTTCGTCGAGGGCACG 62.052 66.667 5.12 0.00 38.67 5.34
2822 4145 1.668151 GATCGGCACCCTATTCCGC 60.668 63.158 0.00 0.00 42.65 5.54
2823 4146 3.178540 ATCGGCACCCTATTCCGCC 62.179 63.158 0.00 0.00 42.65 6.13
2981 4336 2.035442 GTCCTTCGTGCTCAAGGCC 61.035 63.158 0.00 0.00 40.43 5.19
3285 4664 7.147724 CCTCCATCTTCGCAGGGTAAATATATA 60.148 40.741 0.00 0.00 0.00 0.86
3286 4665 7.553334 TCCATCTTCGCAGGGTAAATATATAC 58.447 38.462 0.00 0.00 0.00 1.47
3292 4671 7.764141 TCGCAGGGTAAATATATACACTACA 57.236 36.000 0.00 0.00 37.43 2.74
3406 4792 2.031508 TCACGCCCAAAACGAGAAATTC 60.032 45.455 0.00 0.00 0.00 2.17
3457 4843 2.525592 TTGGCACCCAAGGGAAGG 59.474 61.111 13.15 2.06 38.75 3.46
3522 4911 1.372683 CCGTATCCTCCATGGCCTG 59.627 63.158 6.96 0.00 35.26 4.85
3535 4924 1.071128 GGCCTGAGCTAGCATGGAG 59.929 63.158 18.83 6.42 39.73 3.86
3547 4936 4.552365 ATGGAGCGATGGGGCACG 62.552 66.667 0.00 0.00 34.64 5.34
3602 5285 2.789339 CGCGTCAGACGATGAATATGTT 59.211 45.455 27.29 0.00 46.05 2.71
3603 5286 3.972502 CGCGTCAGACGATGAATATGTTA 59.027 43.478 27.29 0.00 46.05 2.41
3604 5287 4.087225 CGCGTCAGACGATGAATATGTTAG 59.913 45.833 27.29 0.00 46.05 2.34
3605 5288 4.976731 GCGTCAGACGATGAATATGTTAGT 59.023 41.667 27.29 0.00 46.05 2.24
3606 5289 5.115773 GCGTCAGACGATGAATATGTTAGTC 59.884 44.000 27.29 0.00 46.05 2.59
3643 5328 9.823647 ATGCTCTGATATAATAAACGGGATTAG 57.176 33.333 0.00 0.00 0.00 1.73
4004 5695 2.158813 CCAGTGTGTGTCCTTGGTAGTT 60.159 50.000 0.00 0.00 0.00 2.24
4005 5696 2.872245 CAGTGTGTGTCCTTGGTAGTTG 59.128 50.000 0.00 0.00 0.00 3.16
4006 5697 2.504175 AGTGTGTGTCCTTGGTAGTTGT 59.496 45.455 0.00 0.00 0.00 3.32
4022 5713 2.680841 AGTTGTTGTTATGTGTGTGCGT 59.319 40.909 0.00 0.00 0.00 5.24
4099 5794 1.523501 CGCGCATGTGTATGTTTGTC 58.476 50.000 8.75 0.00 36.65 3.18
4173 5868 4.437587 CTGAGCTTGGGGGCCTGG 62.438 72.222 0.84 0.00 0.00 4.45
4204 5900 2.849120 ATCAGTCCGCACTCTGCAGC 62.849 60.000 9.47 0.00 45.36 5.25
4205 5901 3.619767 AGTCCGCACTCTGCAGCA 61.620 61.111 9.47 0.00 45.36 4.41
4206 5902 3.117171 GTCCGCACTCTGCAGCAG 61.117 66.667 17.10 17.10 45.36 4.24
4387 6085 8.886719 TGAAGTATGATTGTGATTCATCTTCAC 58.113 33.333 16.04 0.00 39.48 3.18
4514 6430 2.919228 AGACAGCGTGAAAGGTTCTTT 58.081 42.857 0.00 0.00 0.00 2.52
4577 6493 0.175760 ATCGTCGGATCCAACCACTG 59.824 55.000 13.41 0.00 0.00 3.66
4630 6546 1.270907 AGGACTGAGCAAATCCGAGT 58.729 50.000 0.00 0.00 37.60 4.18
4690 6607 6.239572 GCCATTGCCAGGTATAACCAATTAAT 60.240 38.462 0.00 0.00 41.95 1.40
4695 6612 8.472007 TGCCAGGTATAACCAATTAATTTAGG 57.528 34.615 0.00 0.39 41.95 2.69
4752 6669 5.675684 ACTCAAGAAACACCACCAAAATT 57.324 34.783 0.00 0.00 0.00 1.82
4753 6670 6.048732 ACTCAAGAAACACCACCAAAATTT 57.951 33.333 0.00 0.00 0.00 1.82
4805 6722 2.545742 CGCGATCCCATCAACTACATGA 60.546 50.000 0.00 0.00 0.00 3.07
4852 6769 0.610232 AGCAAGTGAAGACCATGCCC 60.610 55.000 0.00 0.00 36.52 5.36
4863 6780 2.333938 CATGCCCGCATAAGCAGC 59.666 61.111 1.04 0.00 43.38 5.25
4873 6790 1.747709 CATAAGCAGCCAGTCAAGCT 58.252 50.000 0.00 0.00 42.70 3.74
4886 6803 1.069906 GTCAAGCTACAACAAGTGCCG 60.070 52.381 0.00 0.00 0.00 5.69
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
44 45 4.101274 GGGGTTATCTTAACCACTCTCTCC 59.899 50.000 16.13 4.86 40.53 3.71
123 124 1.243342 TGCTCATGCCGAAACCCAAG 61.243 55.000 0.00 0.00 38.71 3.61
125 126 1.228398 TTGCTCATGCCGAAACCCA 60.228 52.632 0.00 0.00 38.71 4.51
173 175 0.533755 CCAGATCAACGATGGAGCCC 60.534 60.000 0.00 0.00 36.09 5.19
344 349 3.114616 CTCACGGCCTCACGCTTG 61.115 66.667 0.00 0.00 37.74 4.01
355 360 4.838152 CGTCCCCATGGCTCACGG 62.838 72.222 6.09 1.26 0.00 4.94
356 361 4.838152 CCGTCCCCATGGCTCACG 62.838 72.222 17.14 17.14 0.00 4.35
357 362 3.399181 TCCGTCCCCATGGCTCAC 61.399 66.667 6.09 0.78 0.00 3.51
358 363 3.399181 GTCCGTCCCCATGGCTCA 61.399 66.667 6.09 0.00 0.00 4.26
359 364 4.530857 CGTCCGTCCCCATGGCTC 62.531 72.222 6.09 0.00 0.00 4.70
361 366 3.441011 CTACGTCCGTCCCCATGGC 62.441 68.421 6.09 0.00 0.00 4.40
362 367 2.792947 CCTACGTCCGTCCCCATGG 61.793 68.421 4.14 4.14 0.00 3.66
363 368 1.735376 CTCCTACGTCCGTCCCCATG 61.735 65.000 0.00 0.00 0.00 3.66
364 369 1.455217 CTCCTACGTCCGTCCCCAT 60.455 63.158 0.00 0.00 0.00 4.00
366 371 2.117779 GTCTCCTACGTCCGTCCCC 61.118 68.421 0.00 0.00 0.00 4.81
370 400 2.044551 GGGGTCTCCTACGTCCGT 60.045 66.667 0.00 0.00 0.00 4.69
395 428 7.040913 AGGTGATGATGGATGGATATTTCAT 57.959 36.000 0.00 0.00 0.00 2.57
453 848 3.181513 GGACGAACCGATTCTTTTAAGCC 60.182 47.826 0.00 0.00 32.12 4.35
562 957 4.862574 CGATATTTCAATCGGCCGATAGAA 59.137 41.667 39.08 30.22 43.92 2.10
563 958 4.421058 CGATATTTCAATCGGCCGATAGA 58.579 43.478 39.08 24.55 43.92 1.98
609 1004 3.687212 TGCATAAACGTGTTAGGACCATG 59.313 43.478 0.00 0.00 0.00 3.66
614 1009 2.680841 GGCATGCATAAACGTGTTAGGA 59.319 45.455 21.36 0.00 0.00 2.94
658 1053 3.440872 TGGACGAAATAAACCAAATCCCG 59.559 43.478 0.00 0.00 0.00 5.14
684 1079 1.206578 GAACACGTTGTCGCATGGG 59.793 57.895 2.76 2.76 41.18 4.00
729 1124 1.852067 CGCCCTCCGTGTTTTTCCAG 61.852 60.000 0.00 0.00 0.00 3.86
855 1253 2.027469 CGGGGTATTTATAGGGCTGGAC 60.027 54.545 0.00 0.00 0.00 4.02
969 1381 2.359214 CGACCAACTAGCAGAGCTATCA 59.641 50.000 0.00 0.00 40.54 2.15
986 1398 0.526211 GGCCATTTCCAAAGTCGACC 59.474 55.000 13.01 0.00 0.00 4.79
1169 1581 2.665794 GCGCAGTTCTATGATCGATCGA 60.666 50.000 21.86 21.86 0.00 3.59
1172 1584 1.667177 CGGCGCAGTTCTATGATCGAT 60.667 52.381 10.83 0.00 0.00 3.59
1202 1614 0.460987 GCTCTGAATCCAGTGGTCGG 60.461 60.000 9.54 5.64 41.16 4.79
1206 1618 2.704464 TCATGCTCTGAATCCAGTGG 57.296 50.000 1.40 1.40 41.16 4.00
1218 1630 1.594397 TCGCGTCATTCATTCATGCTC 59.406 47.619 5.77 0.00 0.00 4.26
1219 1631 1.655484 TCGCGTCATTCATTCATGCT 58.345 45.000 5.77 0.00 0.00 3.79
1220 1632 2.104144 GTTCGCGTCATTCATTCATGC 58.896 47.619 5.77 0.00 0.00 4.06
1221 1633 3.181517 ACAGTTCGCGTCATTCATTCATG 60.182 43.478 5.77 0.00 0.00 3.07
1222 1634 3.002791 ACAGTTCGCGTCATTCATTCAT 58.997 40.909 5.77 0.00 0.00 2.57
1225 1637 2.548057 ACAACAGTTCGCGTCATTCATT 59.452 40.909 5.77 0.00 0.00 2.57
1245 1657 1.016130 CACCACCTGCAGATCGACAC 61.016 60.000 17.39 0.00 0.00 3.67
1279 1691 1.831389 CGAACACCAGCAGGAACGTG 61.831 60.000 0.35 0.00 38.69 4.49
1507 1919 0.946221 CGACTGCCCAGAGTTGTGTC 60.946 60.000 1.69 0.00 0.00 3.67
1630 2042 6.814146 AGATCTCTTCGTTGGAAATAACAGAC 59.186 38.462 0.00 0.00 0.00 3.51
1648 2060 1.272147 GGGGTGTTTGCCAAGATCTCT 60.272 52.381 0.00 0.00 0.00 3.10
1649 2061 1.177401 GGGGTGTTTGCCAAGATCTC 58.823 55.000 0.00 0.00 0.00 2.75
1696 2108 0.943835 TGTGCGACTTGTGTCATCCG 60.944 55.000 0.00 0.00 43.06 4.18
1828 2276 2.165845 TCTAGCTAGCCTGAAAACGGTC 59.834 50.000 16.35 0.00 0.00 4.79
1845 2293 5.768662 AGCATGTGATCATCCCATTTTCTAG 59.231 40.000 0.00 0.00 31.15 2.43
1846 2294 5.533528 CAGCATGTGATCATCCCATTTTCTA 59.466 40.000 0.00 0.00 31.15 2.10
1847 2295 4.341235 CAGCATGTGATCATCCCATTTTCT 59.659 41.667 0.00 0.00 31.15 2.52
1848 2296 4.340097 TCAGCATGTGATCATCCCATTTTC 59.660 41.667 0.00 0.00 37.40 2.29
1939 2387 7.928307 AGCGATTGAATTTGGCAGTATATAT 57.072 32.000 0.00 0.00 0.00 0.86
1940 2388 7.661437 AGAAGCGATTGAATTTGGCAGTATATA 59.339 33.333 0.00 0.00 0.00 0.86
1941 2389 6.488006 AGAAGCGATTGAATTTGGCAGTATAT 59.512 34.615 0.00 0.00 0.00 0.86
1942 2390 5.822519 AGAAGCGATTGAATTTGGCAGTATA 59.177 36.000 0.00 0.00 0.00 1.47
2192 2795 3.119096 GAAAGGGACGTGCGAGGC 61.119 66.667 0.00 0.00 0.00 4.70
2273 2876 5.871524 CACACATATAGCCTGCCTAATAGTG 59.128 44.000 0.00 0.00 0.00 2.74
2309 2912 1.439679 CTTTAGGTTGGTGCCTCGAC 58.560 55.000 0.00 0.00 39.94 4.20
2355 3627 7.610305 TCATATTTTCCGACTAGAAAAGGCTTT 59.390 33.333 6.68 6.68 46.00 3.51
2579 3870 4.557205 GACACATGTAAAGGTCGTCTTCT 58.443 43.478 0.00 0.00 33.94 2.85
2587 3894 1.519408 GCCACGACACATGTAAAGGT 58.481 50.000 0.00 0.00 0.00 3.50
2689 3996 3.329688 CTCGACGAACCTGCGAGCT 62.330 63.158 0.00 0.00 43.88 4.09
2692 3999 3.744719 CCCTCGACGAACCTGCGA 61.745 66.667 0.00 0.00 34.83 5.10
2695 4002 2.432628 GTGCCCTCGACGAACCTG 60.433 66.667 0.00 0.00 0.00 4.00
2696 4003 4.052229 CGTGCCCTCGACGAACCT 62.052 66.667 0.00 0.00 39.21 3.50
2726 4049 0.967380 CCCCAAATCTCACAGCACCC 60.967 60.000 0.00 0.00 0.00 4.61
2878 4233 3.918294 TCATCCATCAGAACAGATGCA 57.082 42.857 0.00 0.00 43.15 3.96
2981 4336 2.436646 GTGATGGGGTGGAGCACG 60.437 66.667 0.00 0.00 34.83 5.34
3142 4516 2.086869 AGGTCGACAAATGGCAATCAG 58.913 47.619 18.91 0.00 0.00 2.90
3457 4843 0.534203 TCAACGACTCCTGTTTGGCC 60.534 55.000 0.00 0.00 35.26 5.36
3522 4911 0.669932 CCATCGCTCCATGCTAGCTC 60.670 60.000 17.23 0.00 40.11 4.09
3547 4936 3.616821 TCATGTCATTGTACTTAGCGTGC 59.383 43.478 0.00 0.00 0.00 5.34
3548 4937 5.973651 ATCATGTCATTGTACTTAGCGTG 57.026 39.130 0.00 0.00 0.00 5.34
3549 4938 6.106003 TCAATCATGTCATTGTACTTAGCGT 58.894 36.000 6.93 0.00 35.56 5.07
3643 5328 4.492570 CGCGTCTCAGTTTTATTCCATCAC 60.493 45.833 0.00 0.00 0.00 3.06
3979 5670 0.886490 CAAGGACACACACTGGGAGC 60.886 60.000 0.00 0.00 0.00 4.70
4004 5695 1.268285 GCACGCACACACATAACAACA 60.268 47.619 0.00 0.00 0.00 3.33
4005 5696 1.394697 GCACGCACACACATAACAAC 58.605 50.000 0.00 0.00 0.00 3.32
4006 5697 0.041751 CGCACGCACACACATAACAA 60.042 50.000 0.00 0.00 0.00 2.83
4022 5713 2.198406 GAGTTACAAGTGACACACGCA 58.802 47.619 8.59 0.00 39.64 5.24
4173 5868 2.676471 ACTGATGCGCCCCCAAAC 60.676 61.111 4.18 0.00 0.00 2.93
4406 6104 8.339344 TCCCTAACGAAAGGTTATTTTTAAGG 57.661 34.615 6.98 0.00 40.22 2.69
4407 6105 8.456471 CCTCCCTAACGAAAGGTTATTTTTAAG 58.544 37.037 6.98 0.00 40.22 1.85
4415 6119 1.205417 CGCCTCCCTAACGAAAGGTTA 59.795 52.381 6.98 0.00 40.09 2.85
4418 6122 1.153429 CCGCCTCCCTAACGAAAGG 60.153 63.158 0.00 0.00 36.30 3.11
4421 6125 0.612732 TTCTCCGCCTCCCTAACGAA 60.613 55.000 0.00 0.00 0.00 3.85
4514 6430 3.967326 TCTTGCTAGAGGCCTTGCTATTA 59.033 43.478 21.35 4.88 40.88 0.98
4577 6493 1.919240 AAACCCGGGATTTGACCTTC 58.081 50.000 32.02 0.00 0.00 3.46
4630 6546 5.566032 CGTCGGTATCTTATGGAAGGCATTA 60.566 44.000 0.00 0.00 33.09 1.90
4690 6607 2.321719 GGTGAAAACCCAAGGCCTAAA 58.678 47.619 5.16 0.00 0.00 1.85
4726 6643 2.775384 TGGTGGTGTTTCTTGAGTACCT 59.225 45.455 0.00 0.00 32.68 3.08
4752 6669 3.435327 GGCGACAACACATGATGACTTAA 59.565 43.478 0.00 0.00 0.00 1.85
4753 6670 3.000041 GGCGACAACACATGATGACTTA 59.000 45.455 0.00 0.00 0.00 2.24
4805 6722 3.009723 CTCACATCAAAACCGTGCCTAT 58.990 45.455 0.00 0.00 0.00 2.57
4852 6769 0.376152 CTTGACTGGCTGCTTATGCG 59.624 55.000 0.00 0.00 43.34 4.73
4863 6780 2.031682 GCACTTGTTGTAGCTTGACTGG 60.032 50.000 0.00 0.00 0.00 4.00
4873 6790 2.026522 GCAACCGGCACTTGTTGTA 58.973 52.632 0.00 0.00 42.91 2.41


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

AutoCloner maintained by Alex Coulton.