Multiple sequence alignment - TraesCS3B01G253900

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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 TraesCS3B01G253900 chr3B 100.000 3663 0 0 782 4444 409044494 409040832 0.000000e+00 6765
1 TraesCS3B01G253900 chr3B 100.000 604 0 0 1 604 409045275 409044672 0.000000e+00 1116
2 TraesCS3B01G253900 chr3B 81.290 465 57 21 2315 2759 446138462 446138008 2.540000e-92 350
3 TraesCS3B01G253900 chr3B 79.828 466 66 15 2315 2759 446145873 446145415 9.280000e-82 315
4 TraesCS3B01G253900 chr3D 92.706 3688 181 34 782 4444 312160176 312163800 0.000000e+00 5240
5 TraesCS3B01G253900 chr3D 86.682 443 32 24 167 589 312159738 312160173 2.420000e-127 466
6 TraesCS3B01G253900 chr3D 91.124 169 13 2 4184 4350 312163702 312163870 1.240000e-55 228
7 TraesCS3B01G253900 chr3D 85.119 168 10 8 10 167 312159522 312159684 1.650000e-34 158
8 TraesCS3B01G253900 chr3D 86.869 99 13 0 4346 4444 312163539 312163637 1.310000e-20 111
9 TraesCS3B01G253900 chr3A 94.479 2590 106 21 782 3360 420171585 420169022 0.000000e+00 3956
10 TraesCS3B01G253900 chr3A 88.180 1066 92 20 3391 4444 420169027 420167984 0.000000e+00 1240
11 TraesCS3B01G253900 chr3A 92.727 275 11 5 167 434 420172347 420172075 5.390000e-104 388
12 TraesCS3B01G253900 chr3A 91.558 154 9 3 429 580 420171751 420171600 4.500000e-50 209
13 TraesCS3B01G253900 chr3A 81.868 182 10 16 2 164 420172556 420172379 1.000000e-26 132
14 TraesCS3B01G253900 chr3A 87.000 100 11 2 4346 4444 420168246 420168148 1.310000e-20 111
15 TraesCS3B01G253900 chr1D 81.789 615 76 26 2255 2836 483143334 483143945 2.400000e-132 483
16 TraesCS3B01G253900 chr1A 81.068 618 74 30 2255 2837 579862808 579863417 1.880000e-123 453
17 TraesCS3B01G253900 chr1B 80.484 620 81 27 2255 2836 673174554 673175171 5.280000e-119 438


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 TraesCS3B01G253900 chr3B 409040832 409045275 4443 True 3940.5 6765 100.000 1 4444 2 chr3B.!!$R3 4443
1 TraesCS3B01G253900 chr3D 312159522 312163870 4348 False 1240.6 5240 88.500 10 4444 5 chr3D.!!$F1 4434
2 TraesCS3B01G253900 chr3A 420167984 420172556 4572 True 1006.0 3956 89.302 2 4444 6 chr3A.!!$R1 4442
3 TraesCS3B01G253900 chr1D 483143334 483143945 611 False 483.0 483 81.789 2255 2836 1 chr1D.!!$F1 581
4 TraesCS3B01G253900 chr1A 579862808 579863417 609 False 453.0 453 81.068 2255 2837 1 chr1A.!!$F1 582
5 TraesCS3B01G253900 chr1B 673174554 673175171 617 False 438.0 438 80.484 2255 2836 1 chr1B.!!$F1 581

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
817 1234 0.106918 AACAGAGACGGGGCAACAAA 60.107 50.0 0.0 0.0 39.74 2.83 F
1542 1966 0.249398 GGTACGACAGGGACATGCTT 59.751 55.0 0.0 0.0 0.00 3.91 F
3246 3735 0.033699 GCTTCAGGGGAGCTGGAAAT 60.034 55.0 0.0 0.0 0.00 2.17 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1971 2395 0.179026 CCATGAGCTGGTCCATGAGG 60.179 60.0 13.26 0.00 41.88 3.86 R
3292 3781 0.320683 TCTCGGTGATGCCACACAAG 60.321 55.0 11.40 8.43 44.93 3.16 R
4415 4923 0.176680 CCGGTGAGGAGGTGATGAAG 59.823 60.0 0.00 0.00 45.00 3.02 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
71 77 3.961408 AGCAATTCGACCAGGATAGTAGT 59.039 43.478 0.00 0.00 0.00 2.73
73 79 5.241949 AGCAATTCGACCAGGATAGTAGTAG 59.758 44.000 0.00 0.00 0.00 2.57
74 80 5.462405 CAATTCGACCAGGATAGTAGTAGC 58.538 45.833 0.00 0.00 0.00 3.58
77 83 3.118149 TCGACCAGGATAGTAGTAGCACA 60.118 47.826 0.00 0.00 0.00 4.57
78 84 3.630769 CGACCAGGATAGTAGTAGCACAA 59.369 47.826 0.00 0.00 0.00 3.33
79 85 4.497674 CGACCAGGATAGTAGTAGCACAAC 60.498 50.000 0.00 0.00 0.00 3.32
80 86 3.380637 ACCAGGATAGTAGTAGCACAACG 59.619 47.826 0.00 0.00 0.00 4.10
81 87 3.630769 CCAGGATAGTAGTAGCACAACGA 59.369 47.826 0.00 0.00 0.00 3.85
109 121 3.428282 CGGCCTTGCGGTTACACC 61.428 66.667 0.00 0.00 34.05 4.16
111 123 1.677633 GGCCTTGCGGTTACACCAT 60.678 57.895 0.00 0.00 38.47 3.55
114 126 1.663695 CCTTGCGGTTACACCATAGG 58.336 55.000 0.00 0.00 38.47 2.57
115 127 1.014352 CTTGCGGTTACACCATAGGC 58.986 55.000 0.00 0.00 38.47 3.93
116 128 0.616371 TTGCGGTTACACCATAGGCT 59.384 50.000 0.00 0.00 38.47 4.58
117 129 0.107897 TGCGGTTACACCATAGGCTG 60.108 55.000 0.00 0.00 38.47 4.85
164 186 0.390603 CGTTCGTGCCCCATAACTCA 60.391 55.000 0.00 0.00 0.00 3.41
165 187 1.084289 GTTCGTGCCCCATAACTCAC 58.916 55.000 0.00 0.00 0.00 3.51
167 189 0.907704 TCGTGCCCCATAACTCACCT 60.908 55.000 0.00 0.00 0.00 4.00
168 190 0.462047 CGTGCCCCATAACTCACCTC 60.462 60.000 0.00 0.00 0.00 3.85
169 191 0.618458 GTGCCCCATAACTCACCTCA 59.382 55.000 0.00 0.00 0.00 3.86
271 349 3.181495 GGATCTCTACGTCAGTCAACTGG 60.181 52.174 10.13 0.00 43.91 4.00
281 359 2.028658 TCAGTCAACTGGTGCATCTCTC 60.029 50.000 10.13 0.00 43.91 3.20
364 443 3.814005 GCCAAAGCAATCCATCTTCAT 57.186 42.857 0.00 0.00 39.53 2.57
365 444 3.714391 GCCAAAGCAATCCATCTTCATC 58.286 45.455 0.00 0.00 39.53 2.92
366 445 3.383825 GCCAAAGCAATCCATCTTCATCT 59.616 43.478 0.00 0.00 39.53 2.90
414 496 4.078516 GAACCCCGTGAGTCCCCG 62.079 72.222 0.00 0.00 0.00 5.73
425 507 1.456705 AGTCCCCGCATCTCTCTCC 60.457 63.158 0.00 0.00 0.00 3.71
434 516 2.233271 GCATCTCTCTCCCTCTCTCTG 58.767 57.143 0.00 0.00 0.00 3.35
435 517 2.233271 CATCTCTCTCCCTCTCTCTGC 58.767 57.143 0.00 0.00 0.00 4.26
469 881 2.996621 GGCAGCGTTCCATATCAGATAC 59.003 50.000 0.00 0.00 0.00 2.24
475 887 4.674623 GCGTTCCATATCAGATACTACCGG 60.675 50.000 0.00 0.00 0.00 5.28
503 915 5.209977 GTTTTTAATCACGCGTTCCTTTCT 58.790 37.500 10.22 0.00 0.00 2.52
504 916 4.398549 TTTAATCACGCGTTCCTTTCTG 57.601 40.909 10.22 0.00 0.00 3.02
519 931 7.041644 CGTTCCTTTCTGTATTAGTTGTTCCAA 60.042 37.037 0.00 0.00 0.00 3.53
547 959 0.234884 GTGAAGCAGGTTCCGTTTCG 59.765 55.000 9.88 0.00 33.75 3.46
561 973 1.059264 CGTTTCGTGATCGCTTCTTCC 59.941 52.381 4.48 0.00 36.96 3.46
591 1007 9.528489 ACTAATTTGGTAGTAATTTGATGGTGT 57.472 29.630 0.00 0.00 32.42 4.16
592 1008 9.787532 CTAATTTGGTAGTAATTTGATGGTGTG 57.212 33.333 0.00 0.00 0.00 3.82
593 1009 7.775053 ATTTGGTAGTAATTTGATGGTGTGT 57.225 32.000 0.00 0.00 0.00 3.72
594 1010 6.567687 TTGGTAGTAATTTGATGGTGTGTG 57.432 37.500 0.00 0.00 0.00 3.82
595 1011 5.626142 TGGTAGTAATTTGATGGTGTGTGT 58.374 37.500 0.00 0.00 0.00 3.72
596 1012 5.471797 TGGTAGTAATTTGATGGTGTGTGTG 59.528 40.000 0.00 0.00 0.00 3.82
597 1013 5.472137 GGTAGTAATTTGATGGTGTGTGTGT 59.528 40.000 0.00 0.00 0.00 3.72
598 1014 5.437289 AGTAATTTGATGGTGTGTGTGTG 57.563 39.130 0.00 0.00 0.00 3.82
599 1015 4.887071 AGTAATTTGATGGTGTGTGTGTGT 59.113 37.500 0.00 0.00 0.00 3.72
600 1016 3.713858 ATTTGATGGTGTGTGTGTGTG 57.286 42.857 0.00 0.00 0.00 3.82
601 1017 1.387539 TTGATGGTGTGTGTGTGTGG 58.612 50.000 0.00 0.00 0.00 4.17
602 1018 0.254462 TGATGGTGTGTGTGTGTGGT 59.746 50.000 0.00 0.00 0.00 4.16
603 1019 0.662619 GATGGTGTGTGTGTGTGGTG 59.337 55.000 0.00 0.00 0.00 4.17
811 1227 1.157585 GAAAGAAACAGAGACGGGGC 58.842 55.000 0.00 0.00 0.00 5.80
817 1234 0.106918 AACAGAGACGGGGCAACAAA 60.107 50.000 0.00 0.00 39.74 2.83
849 1266 5.179929 GTGCAATCTTCAAAAATTCCCCAAG 59.820 40.000 0.00 0.00 0.00 3.61
850 1267 4.696877 GCAATCTTCAAAAATTCCCCAAGG 59.303 41.667 0.00 0.00 0.00 3.61
851 1268 5.247862 CAATCTTCAAAAATTCCCCAAGGG 58.752 41.667 0.00 0.00 46.11 3.95
939 1359 7.734924 TCTCAGTTGATACATGCCAATATTC 57.265 36.000 0.00 0.00 0.00 1.75
946 1366 7.734924 TGATACATGCCAATATTCTCAAGAC 57.265 36.000 0.00 0.00 0.00 3.01
1010 1430 1.084289 GGCCGTACCATCTCAACAAC 58.916 55.000 0.00 0.00 38.86 3.32
1017 1437 4.084537 CGTACCATCTCAACAACACAAGAC 60.085 45.833 0.00 0.00 0.00 3.01
1523 1947 2.684843 GGCTTCTGCTCGCCAACAG 61.685 63.158 0.00 0.00 45.59 3.16
1542 1966 0.249398 GGTACGACAGGGACATGCTT 59.751 55.000 0.00 0.00 0.00 3.91
1833 2257 1.001503 GGTGCAATGGATGGGGGAA 59.998 57.895 0.00 0.00 0.00 3.97
1971 2395 4.090819 AGGAGAGGAAGGAGTACTTTGTC 58.909 47.826 0.00 0.00 40.21 3.18
1972 2396 3.196039 GGAGAGGAAGGAGTACTTTGTCC 59.804 52.174 0.00 4.22 40.21 4.02
2116 2540 1.292223 GAGTACCTGCACGCCAAGA 59.708 57.895 0.00 0.00 0.00 3.02
2228 2652 4.166011 GCAGTCCGGCATCGCAAC 62.166 66.667 0.00 0.00 34.56 4.17
2277 2701 3.723235 CTGCATCTGGTACGCGCCT 62.723 63.158 5.73 0.00 0.00 5.52
3062 3545 6.261158 TGTTGATTCGTACCATTTCTGAACAA 59.739 34.615 0.00 0.00 0.00 2.83
3067 3550 5.996219 TCGTACCATTTCTGAACAATTGTG 58.004 37.500 12.82 0.00 0.00 3.33
3068 3551 4.616802 CGTACCATTTCTGAACAATTGTGC 59.383 41.667 12.82 11.28 0.00 4.57
3069 3552 4.669206 ACCATTTCTGAACAATTGTGCA 57.331 36.364 18.43 18.43 31.56 4.57
3070 3553 4.370917 ACCATTTCTGAACAATTGTGCAC 58.629 39.130 15.66 10.75 28.83 4.57
3071 3554 4.099881 ACCATTTCTGAACAATTGTGCACT 59.900 37.500 15.66 0.00 28.83 4.40
3072 3555 5.301551 ACCATTTCTGAACAATTGTGCACTA 59.698 36.000 15.66 11.52 28.83 2.74
3073 3556 5.630680 CCATTTCTGAACAATTGTGCACTAC 59.369 40.000 15.66 0.00 28.83 2.73
3074 3557 4.829064 TTCTGAACAATTGTGCACTACC 57.171 40.909 15.66 1.10 28.83 3.18
3075 3558 4.085357 TCTGAACAATTGTGCACTACCT 57.915 40.909 15.66 0.00 28.83 3.08
3076 3559 3.814842 TCTGAACAATTGTGCACTACCTG 59.185 43.478 15.66 13.62 28.83 4.00
3077 3560 3.550820 TGAACAATTGTGCACTACCTGT 58.449 40.909 15.66 14.25 0.00 4.00
3088 3571 2.743938 CACTACCTGTGTGTCTGTCAC 58.256 52.381 0.00 0.00 46.31 3.67
3119 3602 0.960364 GGCATCCGCAGAAGGTGAAA 60.960 55.000 0.00 0.00 41.24 2.69
3186 3669 4.047059 TGAAGACCGACGGCGTCC 62.047 66.667 31.86 19.19 35.23 4.79
3210 3693 3.650907 TTCCTGCCGCGCGACATTA 62.651 57.895 34.63 14.30 0.00 1.90
3224 3713 2.186076 GACATTAGAAGCGGACTCGTG 58.814 52.381 0.00 0.00 38.89 4.35
3239 3728 2.360475 GTGGTGCTTCAGGGGAGC 60.360 66.667 0.00 0.00 0.00 4.70
3245 3734 1.380302 GCTTCAGGGGAGCTGGAAA 59.620 57.895 0.00 0.00 0.00 3.13
3246 3735 0.033699 GCTTCAGGGGAGCTGGAAAT 60.034 55.000 0.00 0.00 0.00 2.17
3263 3752 3.636929 ATTGGAATGCCGGTGCCGA 62.637 57.895 12.71 0.00 42.83 5.54
3288 3777 4.718961 AGTGTGCCTTTGATCAACTAGTT 58.281 39.130 7.89 1.12 0.00 2.24
3292 3781 5.008613 TGTGCCTTTGATCAACTAGTTGTTC 59.991 40.000 29.83 29.04 41.16 3.18
3293 3782 5.239525 GTGCCTTTGATCAACTAGTTGTTCT 59.760 40.000 31.88 20.90 41.16 3.01
3295 3784 6.145535 GCCTTTGATCAACTAGTTGTTCTTG 58.854 40.000 31.88 24.04 41.16 3.02
3368 3859 6.844279 CGCATAGTTATTCGTTTGATTGGTAC 59.156 38.462 0.00 0.00 0.00 3.34
3369 3860 7.254319 CGCATAGTTATTCGTTTGATTGGTACT 60.254 37.037 0.00 0.00 0.00 2.73
3377 3868 8.842358 ATTCGTTTGATTGGTACTAGAAAAGA 57.158 30.769 0.00 0.00 0.00 2.52
3378 3869 7.884816 TCGTTTGATTGGTACTAGAAAAGAG 57.115 36.000 0.00 0.00 0.00 2.85
3476 3969 8.034804 AGAGAAGAAGCTATTTTCAAGAGAGAC 58.965 37.037 0.00 0.00 0.00 3.36
3507 4001 3.800506 GGGAAATGACGTGGTATTACTCG 59.199 47.826 0.00 9.19 0.00 4.18
3513 4007 1.331756 ACGTGGTATTACTCGGCTACG 59.668 52.381 13.18 0.00 42.74 3.51
3526 4020 0.828343 GGCTACGAGGGGAGTGCTAT 60.828 60.000 0.00 0.00 0.00 2.97
3528 4022 1.693627 CTACGAGGGGAGTGCTATGT 58.306 55.000 0.00 0.00 0.00 2.29
3531 4025 0.103208 CGAGGGGAGTGCTATGTGTC 59.897 60.000 0.00 0.00 0.00 3.67
3536 4031 0.462759 GGAGTGCTATGTGTCTGCCC 60.463 60.000 0.00 0.00 0.00 5.36
3622 4117 6.777101 TGCAACATATATTGTGTTACGGAAC 58.223 36.000 2.68 2.68 38.99 3.62
3662 4157 7.281774 AGGTCATGTTGCAGAAGATATTTGTAG 59.718 37.037 0.00 0.00 0.00 2.74
3704 4203 6.952773 TTTTAACAGAGGTTATGTTGCAGT 57.047 33.333 1.74 0.00 40.92 4.40
3705 4204 6.952773 TTTAACAGAGGTTATGTTGCAGTT 57.047 33.333 1.74 0.00 40.92 3.16
3706 4205 6.952773 TTAACAGAGGTTATGTTGCAGTTT 57.047 33.333 1.74 0.00 40.92 2.66
3707 4206 5.852282 AACAGAGGTTATGTTGCAGTTTT 57.148 34.783 0.00 0.00 39.36 2.43
3708 4207 5.852282 ACAGAGGTTATGTTGCAGTTTTT 57.148 34.783 0.00 0.00 0.00 1.94
3773 4277 0.242825 CTGCACCATTGAGTTGCCAG 59.757 55.000 0.00 0.00 0.00 4.85
3811 4316 4.443913 TTCAGAATCATCGACGGTGTTA 57.556 40.909 8.18 0.00 0.00 2.41
3828 4333 6.987992 ACGGTGTTACAAAATCTTGAGACTTA 59.012 34.615 0.00 0.00 36.33 2.24
3862 4367 2.592287 TCCGAAACGTGGTTGGCC 60.592 61.111 0.00 0.00 0.00 5.36
3932 4437 5.640147 TCATTTCCCCAGTTACAATCAACT 58.360 37.500 0.00 0.00 39.34 3.16
3937 4442 6.195600 TCCCCAGTTACAATCAACTTTAGT 57.804 37.500 0.00 0.00 36.61 2.24
3986 4491 5.182487 CCAAACATGGCACTGTACTATACA 58.818 41.667 0.00 0.00 37.13 2.29
4011 4516 1.964373 GACGTGCCCGGTCATGTTT 60.964 57.895 12.32 0.00 36.42 2.83
4015 4520 3.053291 GCCCGGTCATGTTTGCGA 61.053 61.111 0.00 0.00 0.00 5.10
4017 4522 1.953017 CCCGGTCATGTTTGCGAAA 59.047 52.632 0.00 0.00 0.00 3.46
4024 4529 3.243068 GGTCATGTTTGCGAAAAGTGACT 60.243 43.478 23.49 0.00 37.28 3.41
4041 4546 4.104102 AGTGACTGGTTAACCCTCAAATCA 59.896 41.667 21.97 12.51 34.29 2.57
4089 4594 9.132923 TCATATCTCGTATCCTAAATCCATACC 57.867 37.037 0.00 0.00 0.00 2.73
4090 4595 8.914011 CATATCTCGTATCCTAAATCCATACCA 58.086 37.037 0.00 0.00 0.00 3.25
4097 4602 3.135712 TCCTAAATCCATACCACGCATGT 59.864 43.478 0.00 0.00 0.00 3.21
4100 4605 5.529430 CCTAAATCCATACCACGCATGTAAA 59.471 40.000 0.00 0.00 0.00 2.01
4101 4606 6.206634 CCTAAATCCATACCACGCATGTAAAT 59.793 38.462 0.00 0.00 0.00 1.40
4247 4752 5.130477 ACGAAAATAAAGATAGAGAGGGCCA 59.870 40.000 6.18 0.00 0.00 5.36
4305 4811 2.223611 CGATCACCGAAGCGACTATAGT 59.776 50.000 4.68 4.68 41.76 2.12
4364 4870 4.420143 CCGACGGGCATAGTTCTG 57.580 61.111 5.81 0.00 0.00 3.02
4407 4915 6.642733 AATGGAAATAAAGACAGAGAGGGA 57.357 37.500 0.00 0.00 0.00 4.20
4409 4917 4.844085 TGGAAATAAAGACAGAGAGGGACA 59.156 41.667 0.00 0.00 0.00 4.02
4410 4918 5.179533 GGAAATAAAGACAGAGAGGGACAC 58.820 45.833 0.00 0.00 0.00 3.67
4411 4919 5.280011 GGAAATAAAGACAGAGAGGGACACA 60.280 44.000 0.00 0.00 0.00 3.72
4415 4923 2.243810 AGACAGAGAGGGACACACTTC 58.756 52.381 0.00 0.00 0.00 3.01
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
17 18 1.971695 CGTTTGGCAAGAGGGGGTC 60.972 63.158 0.00 0.00 0.00 4.46
19 20 2.676471 CCGTTTGGCAAGAGGGGG 60.676 66.667 13.27 3.23 0.00 5.40
71 77 0.607217 TCGGGAGACTCGTTGTGCTA 60.607 55.000 0.00 0.00 0.00 3.49
73 79 0.802607 GATCGGGAGACTCGTTGTGC 60.803 60.000 0.00 0.00 44.82 4.57
74 80 0.523546 CGATCGGGAGACTCGTTGTG 60.524 60.000 7.38 0.00 44.82 3.33
77 83 2.772691 GCCGATCGGGAGACTCGTT 61.773 63.158 33.98 0.00 44.82 3.85
78 84 3.210528 GCCGATCGGGAGACTCGT 61.211 66.667 33.98 0.00 44.82 4.18
79 85 3.967335 GGCCGATCGGGAGACTCG 61.967 72.222 33.98 7.82 44.82 4.18
80 86 2.128507 AAGGCCGATCGGGAGACTC 61.129 63.158 33.98 16.71 44.82 3.36
81 87 2.042843 AAGGCCGATCGGGAGACT 60.043 61.111 33.98 14.40 44.82 3.24
109 121 1.884579 GATCAACCATGCCAGCCTATG 59.115 52.381 0.00 0.00 0.00 2.23
111 123 0.179048 CGATCAACCATGCCAGCCTA 60.179 55.000 0.00 0.00 0.00 3.93
114 126 2.484062 CCCGATCAACCATGCCAGC 61.484 63.158 0.00 0.00 0.00 4.85
115 127 0.394216 TTCCCGATCAACCATGCCAG 60.394 55.000 0.00 0.00 0.00 4.85
116 128 0.038890 TTTCCCGATCAACCATGCCA 59.961 50.000 0.00 0.00 0.00 4.92
117 129 0.455815 GTTTCCCGATCAACCATGCC 59.544 55.000 0.00 0.00 0.00 4.40
119 131 1.732941 TCGTTTCCCGATCAACCATG 58.267 50.000 0.00 0.00 41.60 3.66
120 132 2.356135 CTTCGTTTCCCGATCAACCAT 58.644 47.619 0.00 0.00 46.75 3.55
164 186 0.609681 GAGACGAGGTGAGGTGAGGT 60.610 60.000 0.00 0.00 0.00 3.85
165 187 1.649390 CGAGACGAGGTGAGGTGAGG 61.649 65.000 0.00 0.00 0.00 3.86
167 189 0.954449 GACGAGACGAGGTGAGGTGA 60.954 60.000 0.00 0.00 0.00 4.02
168 190 1.502640 GACGAGACGAGGTGAGGTG 59.497 63.158 0.00 0.00 0.00 4.00
169 191 2.033755 CGACGAGACGAGGTGAGGT 61.034 63.158 0.00 0.00 35.09 3.85
271 349 2.674852 TCAGAATTTGCGAGAGATGCAC 59.325 45.455 0.00 0.00 43.10 4.57
281 359 0.798776 AGAAGCGGTCAGAATTTGCG 59.201 50.000 0.00 0.00 0.00 4.85
360 439 7.627088 GCCGAAAGATGAAAGATGAAAGATGAA 60.627 37.037 0.00 0.00 0.00 2.57
361 440 6.183360 GCCGAAAGATGAAAGATGAAAGATGA 60.183 38.462 0.00 0.00 0.00 2.92
362 441 5.970023 GCCGAAAGATGAAAGATGAAAGATG 59.030 40.000 0.00 0.00 0.00 2.90
363 442 5.220739 CGCCGAAAGATGAAAGATGAAAGAT 60.221 40.000 0.00 0.00 0.00 2.40
364 443 4.093408 CGCCGAAAGATGAAAGATGAAAGA 59.907 41.667 0.00 0.00 0.00 2.52
365 444 4.337763 CGCCGAAAGATGAAAGATGAAAG 58.662 43.478 0.00 0.00 0.00 2.62
366 445 3.126858 CCGCCGAAAGATGAAAGATGAAA 59.873 43.478 0.00 0.00 0.00 2.69
414 496 2.233271 CAGAGAGAGGGAGAGAGATGC 58.767 57.143 0.00 0.00 0.00 3.91
425 507 3.745458 GTGAACTCAAAAGCAGAGAGAGG 59.255 47.826 0.00 0.00 36.91 3.69
434 516 0.661483 GCTGCCGTGAACTCAAAAGC 60.661 55.000 0.00 0.00 0.00 3.51
435 517 0.384725 CGCTGCCGTGAACTCAAAAG 60.385 55.000 0.00 0.00 0.00 2.27
475 887 4.085466 GGAACGCGTGATTAAAAACCAAAC 60.085 41.667 14.98 0.00 0.00 2.93
482 894 4.273969 ACAGAAAGGAACGCGTGATTAAAA 59.726 37.500 14.98 0.00 0.00 1.52
519 931 0.179009 ACCTGCTTCACATGCACAGT 60.179 50.000 0.00 0.00 36.37 3.55
547 959 7.541122 AATTAGTAAAGGAAGAAGCGATCAC 57.459 36.000 0.00 0.00 0.00 3.06
806 1222 3.274067 GGCTAGTTTGTTGCCCCG 58.726 61.111 0.00 0.00 40.71 5.73
811 1227 3.254166 AGATTGCACAGGCTAGTTTGTTG 59.746 43.478 0.00 0.00 41.91 3.33
817 1234 3.423539 TTGAAGATTGCACAGGCTAGT 57.576 42.857 0.00 0.00 41.91 2.57
849 1266 0.475906 ATGCAGATAACTGGCCTCCC 59.524 55.000 3.32 0.00 43.62 4.30
850 1267 2.225467 GAATGCAGATAACTGGCCTCC 58.775 52.381 3.32 0.00 43.62 4.30
851 1268 2.923121 TGAATGCAGATAACTGGCCTC 58.077 47.619 3.32 0.00 43.62 4.70
852 1269 3.370840 TTGAATGCAGATAACTGGCCT 57.629 42.857 3.32 0.00 43.62 5.19
939 1359 2.681706 AGAGTGTGCGATTGTCTTGAG 58.318 47.619 0.00 0.00 0.00 3.02
946 1366 9.035607 AGAATAAATAGTAAGAGTGTGCGATTG 57.964 33.333 0.00 0.00 0.00 2.67
1010 1430 3.223661 GAGCAGGAGTGGTCTTGTG 57.776 57.895 0.00 0.00 46.01 3.33
1017 1437 0.397941 TGGTTCTTGAGCAGGAGTGG 59.602 55.000 0.00 0.00 0.00 4.00
1141 1565 2.577059 GTTGATGCGGAGGTCGGA 59.423 61.111 0.00 0.00 44.80 4.55
1483 1907 4.081030 CCGCGCATGATCATCCGC 62.081 66.667 29.82 29.82 42.71 5.54
1523 1947 0.249398 AAGCATGTCCCTGTCGTACC 59.751 55.000 0.00 0.00 0.00 3.34
1971 2395 0.179026 CCATGAGCTGGTCCATGAGG 60.179 60.000 13.26 0.00 41.88 3.86
1972 2396 3.398694 CCATGAGCTGGTCCATGAG 57.601 57.895 13.26 2.22 41.88 2.90
2116 2540 1.000163 CAGCTCGCCGTGGTATATTCT 60.000 52.381 0.00 0.00 0.00 2.40
2183 2607 0.602905 GGTGACCTTGACCTGAACGG 60.603 60.000 0.00 0.00 39.35 4.44
2187 2611 2.214216 CCCGGTGACCTTGACCTGA 61.214 63.158 0.00 0.00 0.00 3.86
2228 2652 4.459331 CGTTGACATTGGCGCCCG 62.459 66.667 26.77 15.34 0.00 6.13
2277 2701 2.922503 TCCGGCTTGAGCACCTCA 60.923 61.111 0.00 0.00 44.36 3.86
2940 3421 2.358247 TTGCCGTCCGCCTTCTTC 60.358 61.111 0.00 0.00 36.24 2.87
2981 3462 6.759497 ACTGTAATCCAAAAATGGTAGAGC 57.241 37.500 0.00 0.00 0.00 4.09
3079 3562 2.694065 GCAACTGCAGTGACAGACA 58.306 52.632 22.49 0.00 40.25 3.41
3210 3693 2.651361 CACCACGAGTCCGCTTCT 59.349 61.111 0.00 0.00 39.95 2.85
3217 3706 1.374758 CCCTGAAGCACCACGAGTC 60.375 63.158 0.00 0.00 0.00 3.36
3218 3707 2.743718 CCCTGAAGCACCACGAGT 59.256 61.111 0.00 0.00 0.00 4.18
3224 3713 2.045536 CAGCTCCCCTGAAGCACC 60.046 66.667 0.00 0.00 44.64 5.01
3239 3728 1.135024 CACCGGCATTCCAATTTCCAG 60.135 52.381 0.00 0.00 0.00 3.86
3245 3734 3.140141 CGGCACCGGCATTCCAAT 61.140 61.111 0.00 0.00 43.71 3.16
3246 3735 3.851897 TTCGGCACCGGCATTCCAA 62.852 57.895 9.58 0.00 43.71 3.53
3263 3752 3.825328 AGTTGATCAAAGGCACACTCTT 58.175 40.909 10.35 0.00 0.00 2.85
3288 3777 1.317613 GGTGATGCCACACAAGAACA 58.682 50.000 11.40 0.00 44.93 3.18
3292 3781 0.320683 TCTCGGTGATGCCACACAAG 60.321 55.000 11.40 8.43 44.93 3.16
3293 3782 0.602638 GTCTCGGTGATGCCACACAA 60.603 55.000 11.40 0.47 44.93 3.33
3295 3784 0.602638 TTGTCTCGGTGATGCCACAC 60.603 55.000 0.00 2.38 44.93 3.82
3447 3940 8.592809 TCTCTTGAAAATAGCTTCTTCTCTTCT 58.407 33.333 0.00 0.00 0.00 2.85
3448 3941 8.770438 TCTCTTGAAAATAGCTTCTTCTCTTC 57.230 34.615 0.00 0.00 0.00 2.87
3449 3942 8.592809 TCTCTCTTGAAAATAGCTTCTTCTCTT 58.407 33.333 0.00 0.00 0.00 2.85
3450 3943 8.034804 GTCTCTCTTGAAAATAGCTTCTTCTCT 58.965 37.037 0.00 0.00 0.00 3.10
3451 3944 8.034804 AGTCTCTCTTGAAAATAGCTTCTTCTC 58.965 37.037 0.00 0.00 0.00 2.87
3452 3945 7.906327 AGTCTCTCTTGAAAATAGCTTCTTCT 58.094 34.615 0.00 0.00 0.00 2.85
3507 4001 0.828343 ATAGCACTCCCCTCGTAGCC 60.828 60.000 0.00 0.00 0.00 3.93
3513 4007 1.137872 CAGACACATAGCACTCCCCTC 59.862 57.143 0.00 0.00 0.00 4.30
3545 4040 4.451150 GATCTGACGGCCCGCACA 62.451 66.667 1.23 2.83 0.00 4.57
3547 4042 4.147449 CAGATCTGACGGCCCGCA 62.147 66.667 18.34 0.84 0.00 5.69
3622 4117 3.067180 ACATGACCTCTGTTGCACAAAAG 59.933 43.478 0.00 0.00 0.00 2.27
3749 4253 2.079158 CAACTCAATGGTGCAGACGAT 58.921 47.619 0.00 0.00 0.00 3.73
3773 4277 4.609947 TCTGAAACATGTGAATGTTGTGC 58.390 39.130 0.00 0.20 43.29 4.57
3793 4298 3.861276 TGTAACACCGTCGATGATTCT 57.139 42.857 6.11 0.00 0.00 2.40
3811 4316 5.236478 CACACCGTAAGTCTCAAGATTTTGT 59.764 40.000 0.00 0.00 35.73 2.83
3828 4333 1.183676 GGACTAGTCCCACACACCGT 61.184 60.000 28.87 0.00 43.94 4.83
3862 4367 3.414700 GCGTCCACTGCGTTGAGG 61.415 66.667 0.00 0.00 0.00 3.86
3871 4376 1.320344 TTCTATGCTCCGCGTCCACT 61.320 55.000 4.92 0.00 0.00 4.00
3872 4377 0.249489 ATTCTATGCTCCGCGTCCAC 60.249 55.000 4.92 0.00 0.00 4.02
3932 4437 5.187772 TGGCTGAAGATGCTCTAAGACTAAA 59.812 40.000 0.00 0.00 0.00 1.85
3937 4442 4.256920 GTTTGGCTGAAGATGCTCTAAGA 58.743 43.478 0.00 0.00 0.00 2.10
3953 4458 2.289320 TGCCATGTTTGGTATGTTTGGC 60.289 45.455 4.14 4.14 45.57 4.52
3986 4491 2.221906 GACCGGGCACGTCTACATGT 62.222 60.000 7.97 2.69 38.78 3.21
4011 4516 2.614983 GGTTAACCAGTCACTTTTCGCA 59.385 45.455 20.12 0.00 35.64 5.10
4015 4520 4.513406 TGAGGGTTAACCAGTCACTTTT 57.487 40.909 25.71 0.00 43.89 2.27
4017 4522 4.513406 TTTGAGGGTTAACCAGTCACTT 57.487 40.909 25.71 2.35 43.89 3.16
4024 4529 2.785562 CCGTGATTTGAGGGTTAACCA 58.214 47.619 25.71 5.49 43.89 3.67
4041 4546 1.532868 GTATACGACTATGGACGCCGT 59.467 52.381 0.27 0.00 37.27 5.68
4058 4563 9.357161 GGATTTAGGATACGAGATATGAGGTAT 57.643 37.037 0.00 0.00 46.39 2.73
4088 4593 6.785191 ACTATCTTTCAATTTACATGCGTGG 58.215 36.000 11.36 0.00 0.00 4.94
4089 4594 8.387354 TGTACTATCTTTCAATTTACATGCGTG 58.613 33.333 3.82 3.82 0.00 5.34
4090 4595 8.487313 TGTACTATCTTTCAATTTACATGCGT 57.513 30.769 0.00 0.00 0.00 5.24
4151 4656 2.033424 GCTCTTTTGGTCCGGAATATGC 59.967 50.000 5.23 0.00 0.00 3.14
4156 4661 1.073125 TGATGCTCTTTTGGTCCGGAA 59.927 47.619 5.23 0.00 0.00 4.30
4226 4731 5.830457 GCTTGGCCCTCTCTATCTTTATTTT 59.170 40.000 0.00 0.00 0.00 1.82
4236 4741 2.375174 TGAAAAAGCTTGGCCCTCTCTA 59.625 45.455 0.00 0.00 0.00 2.43
4238 4743 1.620822 TGAAAAAGCTTGGCCCTCTC 58.379 50.000 0.00 0.00 0.00 3.20
4247 4752 3.823304 GTGAGGAGGTGATGAAAAAGCTT 59.177 43.478 0.00 0.00 0.00 3.74
4305 4811 1.113517 GCCTACGCCTACATGGAGGA 61.114 60.000 29.37 5.85 40.14 3.71
4329 4835 0.536915 GGCTACGACTACCCCGATCT 60.537 60.000 0.00 0.00 0.00 2.75
4332 4838 2.514592 CGGCTACGACTACCCCGA 60.515 66.667 0.00 0.00 44.60 5.14
4386 4893 4.844085 TGTCCCTCTCTGTCTTTATTTCCA 59.156 41.667 0.00 0.00 0.00 3.53
4407 4915 2.975489 AGGAGGTGATGAAGAAGTGTGT 59.025 45.455 0.00 0.00 0.00 3.72
4409 4917 3.007398 GTGAGGAGGTGATGAAGAAGTGT 59.993 47.826 0.00 0.00 0.00 3.55
4410 4918 3.594134 GTGAGGAGGTGATGAAGAAGTG 58.406 50.000 0.00 0.00 0.00 3.16
4411 4919 2.569404 GGTGAGGAGGTGATGAAGAAGT 59.431 50.000 0.00 0.00 0.00 3.01
4415 4923 0.176680 CCGGTGAGGAGGTGATGAAG 59.823 60.000 0.00 0.00 45.00 3.02


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

AutoCloner maintained by Alex Coulton.