Multiple sequence alignment - TraesCS5D01G130300

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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 TraesCS5D01G130300 chr5D 100.000 4802 0 0 1 4802 205868911 205873712 0.000000e+00 8868
1 TraesCS5D01G130300 chr5A 96.943 2453 59 10 2068 4513 264091689 264094132 0.000000e+00 4100
2 TraesCS5D01G130300 chr5A 94.937 1343 38 7 731 2071 264083788 264085102 0.000000e+00 2076
3 TraesCS5D01G130300 chr5A 91.745 642 53 0 1 642 264082503 264083144 0.000000e+00 893
4 TraesCS5D01G130300 chr5B 95.489 2128 81 4 731 2850 206508379 206506259 0.000000e+00 3384
5 TraesCS5D01G130300 chr5B 98.415 820 12 1 2994 3813 206506217 206505399 0.000000e+00 1441
6 TraesCS5D01G130300 chr5B 90.486 988 55 16 3836 4800 206505410 206504439 0.000000e+00 1267
7 TraesCS5D01G130300 chr5B 79.361 407 62 15 177 578 75211358 75210969 2.850000e-67 267
8 TraesCS5D01G130300 chr6D 77.683 587 101 16 3 575 115579728 115580298 9.960000e-87 331
9 TraesCS5D01G130300 chr1D 81.793 368 53 13 179 543 353568786 353568430 3.630000e-76 296
10 TraesCS5D01G130300 chr4A 79.518 332 57 6 179 507 539124834 539125157 4.840000e-55 226
11 TraesCS5D01G130300 chr2B 75.298 336 81 2 179 513 58547189 58547523 4.970000e-35 159


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 TraesCS5D01G130300 chr5D 205868911 205873712 4801 False 8868.000000 8868 100.000000 1 4802 1 chr5D.!!$F1 4801
1 TraesCS5D01G130300 chr5A 264091689 264094132 2443 False 4100.000000 4100 96.943000 2068 4513 1 chr5A.!!$F1 2445
2 TraesCS5D01G130300 chr5A 264082503 264085102 2599 False 1484.500000 2076 93.341000 1 2071 2 chr5A.!!$F2 2070
3 TraesCS5D01G130300 chr5B 206504439 206508379 3940 True 2030.666667 3384 94.796667 731 4800 3 chr5B.!!$R2 4069
4 TraesCS5D01G130300 chr6D 115579728 115580298 570 False 331.000000 331 77.683000 3 575 1 chr6D.!!$F1 572

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
35 36 0.664761 CGTCCGCGATTTAGGGTCTA 59.335 55.000 8.23 0.00 41.33 2.59 F
656 1032 0.740516 CGGTATTGCGGTTTACGGGT 60.741 55.000 0.00 0.00 44.51 5.28 F
998 1580 1.002087 GAGTTTCGGAGAAGGCTTCCA 59.998 52.381 23.09 2.78 45.90 3.53 F
1262 1844 2.357034 GTTCAGCGCTTGGGACGA 60.357 61.111 7.50 0.00 0.00 4.20 F
1585 2167 2.734606 CCGTCTTTGCTGTGATAACGAA 59.265 45.455 0.00 0.00 0.00 3.85 F
2143 2727 4.101585 TGGGAGCTGTAACTATGGATCAAG 59.898 45.833 0.00 0.00 0.00 3.02 F
2869 3460 1.061967 ACCCCTACATTATGGGACGGA 60.062 52.381 0.00 0.00 46.15 4.69 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1180 1762 2.049475 GAGTCGAGCGCTGTACCGAT 62.049 60.000 18.48 7.72 33.47 4.18 R
1827 2409 3.763360 ACTCGCCAAAAATCATGAATCCA 59.237 39.130 0.00 0.00 0.00 3.41 R
2860 3451 0.186386 CTCTACTCCCTCCGTCCCAT 59.814 60.000 0.00 0.00 0.00 4.00 R
2862 3453 0.479378 ATCTCTACTCCCTCCGTCCC 59.521 60.000 0.00 0.00 0.00 4.46 R
2863 3454 2.638855 TCTATCTCTACTCCCTCCGTCC 59.361 54.545 0.00 0.00 0.00 4.79 R
3639 4231 0.861837 CTACCGGATCATTCGCAAGC 59.138 55.000 9.46 0.00 37.18 4.01 R
4650 5266 1.014352 GGCGTAATAGGTTGGTGCTG 58.986 55.000 0.00 0.00 0.00 4.41 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
35 36 0.664761 CGTCCGCGATTTAGGGTCTA 59.335 55.000 8.23 0.00 41.33 2.59
39 40 1.202336 CCGCGATTTAGGGTCTACGTT 60.202 52.381 8.23 0.00 0.00 3.99
43 44 2.467838 GATTTAGGGTCTACGTTCGCC 58.532 52.381 0.00 0.00 0.00 5.54
323 332 1.309950 CGCCTCCACGAGATCTTCTA 58.690 55.000 0.00 0.00 34.06 2.10
345 354 1.563173 GACGACCAAGCGTGTTCAC 59.437 57.895 0.00 0.00 45.72 3.18
473 482 0.745845 CTCGCCAACTCCTTGATGGG 60.746 60.000 0.00 0.00 38.83 4.00
615 625 7.801547 ATTGAATTTGATCATTTGTGTCGTC 57.198 32.000 0.00 0.00 0.00 4.20
645 655 4.647964 CCGCAAATATGATACGGTATTGC 58.352 43.478 10.39 10.39 39.05 3.56
654 1030 1.919918 TACGGTATTGCGGTTTACGG 58.080 50.000 0.00 0.00 44.51 4.02
656 1032 0.740516 CGGTATTGCGGTTTACGGGT 60.741 55.000 0.00 0.00 44.51 5.28
666 1042 4.542833 CGGTTTACGGGTCTGCAAGAGA 62.543 54.545 0.00 0.00 41.35 3.10
667 1043 5.781290 CGGTTTACGGGTCTGCAAGAGAT 62.781 52.174 0.00 0.00 41.35 2.75
684 1060 8.860088 TGCAAGAGATATATGCTCTAACAGTAA 58.140 33.333 12.32 0.00 41.66 2.24
708 1084 3.239587 TCGAGACCGAACAAATATGCA 57.760 42.857 0.00 0.00 42.51 3.96
709 1085 2.927477 TCGAGACCGAACAAATATGCAC 59.073 45.455 0.00 0.00 42.51 4.57
710 1086 2.930040 CGAGACCGAACAAATATGCACT 59.070 45.455 0.00 0.00 38.22 4.40
711 1087 3.000322 CGAGACCGAACAAATATGCACTC 60.000 47.826 0.00 0.00 38.22 3.51
712 1088 2.930040 AGACCGAACAAATATGCACTCG 59.070 45.455 0.00 0.00 0.00 4.18
713 1089 2.671396 GACCGAACAAATATGCACTCGT 59.329 45.455 0.00 0.00 0.00 4.18
817 1398 6.922980 TCGTAACGAGAAATACTCAAACTG 57.077 37.500 0.00 0.00 45.14 3.16
818 1399 5.344128 TCGTAACGAGAAATACTCAAACTGC 59.656 40.000 0.00 0.00 45.14 4.40
819 1400 5.118050 CGTAACGAGAAATACTCAAACTGCA 59.882 40.000 0.00 0.00 45.14 4.41
820 1401 6.346279 CGTAACGAGAAATACTCAAACTGCAA 60.346 38.462 0.00 0.00 45.14 4.08
821 1402 6.371809 AACGAGAAATACTCAAACTGCAAA 57.628 33.333 0.00 0.00 45.14 3.68
822 1403 5.990408 ACGAGAAATACTCAAACTGCAAAG 58.010 37.500 0.00 0.00 45.14 2.77
823 1404 5.527582 ACGAGAAATACTCAAACTGCAAAGT 59.472 36.000 0.00 0.00 45.14 2.66
824 1405 6.038271 ACGAGAAATACTCAAACTGCAAAGTT 59.962 34.615 0.00 0.00 45.14 2.66
825 1406 7.225931 ACGAGAAATACTCAAACTGCAAAGTTA 59.774 33.333 0.00 0.00 45.14 2.24
826 1407 8.230486 CGAGAAATACTCAAACTGCAAAGTTAT 58.770 33.333 0.00 0.00 45.14 1.89
869 1450 3.343941 AAGAAATACCACTAAGCCGCA 57.656 42.857 0.00 0.00 0.00 5.69
931 1513 2.996631 TCAGTACGTTACTCCCTCCTC 58.003 52.381 0.00 0.00 36.76 3.71
998 1580 1.002087 GAGTTTCGGAGAAGGCTTCCA 59.998 52.381 23.09 2.78 45.90 3.53
1262 1844 2.357034 GTTCAGCGCTTGGGACGA 60.357 61.111 7.50 0.00 0.00 4.20
1585 2167 2.734606 CCGTCTTTGCTGTGATAACGAA 59.265 45.455 0.00 0.00 0.00 3.85
1685 2267 6.360370 TCAACTCCTAAGCTTAGTGTCATT 57.640 37.500 27.54 13.89 0.00 2.57
1827 2409 6.092533 CACAAGTTTGCTTTTTGAAAGGACAT 59.907 34.615 2.95 0.00 31.49 3.06
1868 2450 5.533482 CGAGTTCTTAGAGGATGGTATTGG 58.467 45.833 0.00 0.00 0.00 3.16
1898 2480 6.672266 TTGAGGAAGTGATAAAGTCTGTCT 57.328 37.500 0.00 0.00 0.00 3.41
1961 2545 4.319984 CGCCATGTCACCAGATAATCAATG 60.320 45.833 0.00 0.00 0.00 2.82
2021 2605 5.369699 TGGCTAGAAATGTCCTAAAGGCTAT 59.630 40.000 0.00 0.00 34.44 2.97
2143 2727 4.101585 TGGGAGCTGTAACTATGGATCAAG 59.898 45.833 0.00 0.00 0.00 3.02
2165 2749 4.834496 AGGAATCAACATTTCTGCAAGGAA 59.166 37.500 0.00 0.00 34.64 3.36
2429 3020 7.587629 TGTTCTGAGCTTCAATTTCAAGTATG 58.412 34.615 0.00 0.00 0.00 2.39
2729 3320 7.464977 GCAGTGATTTTTAACATTCCATGCATC 60.465 37.037 0.00 0.00 0.00 3.91
2851 3442 8.448615 GTTGGAACAGTACAAATAGAACATACC 58.551 37.037 0.00 0.00 42.39 2.73
2854 3445 6.886178 ACAGTACAAATAGAACATACCCCT 57.114 37.500 0.00 0.00 0.00 4.79
2855 3446 7.983166 ACAGTACAAATAGAACATACCCCTA 57.017 36.000 0.00 0.00 0.00 3.53
2857 3448 7.400915 ACAGTACAAATAGAACATACCCCTACA 59.599 37.037 0.00 0.00 0.00 2.74
2858 3449 8.429641 CAGTACAAATAGAACATACCCCTACAT 58.570 37.037 0.00 0.00 0.00 2.29
2862 3453 9.793259 ACAAATAGAACATACCCCTACATTATG 57.207 33.333 0.00 0.00 0.00 1.90
2863 3454 9.231297 CAAATAGAACATACCCCTACATTATGG 57.769 37.037 0.00 0.00 0.00 2.74
2864 3455 5.843019 AGAACATACCCCTACATTATGGG 57.157 43.478 0.00 0.00 45.34 4.00
2866 3457 5.309806 AGAACATACCCCTACATTATGGGAC 59.690 44.000 0.00 0.00 46.15 4.46
2867 3458 3.581332 ACATACCCCTACATTATGGGACG 59.419 47.826 0.00 0.00 46.15 4.79
2869 3460 1.061967 ACCCCTACATTATGGGACGGA 60.062 52.381 0.00 0.00 46.15 4.69
2870 3461 1.623811 CCCCTACATTATGGGACGGAG 59.376 57.143 0.00 0.00 46.15 4.63
2871 3462 1.623811 CCCTACATTATGGGACGGAGG 59.376 57.143 0.00 0.00 46.15 4.30
2874 3465 1.424638 ACATTATGGGACGGAGGGAG 58.575 55.000 0.00 0.00 0.00 4.30
2875 3466 1.344087 ACATTATGGGACGGAGGGAGT 60.344 52.381 0.00 0.00 0.00 3.85
2876 3467 2.090943 ACATTATGGGACGGAGGGAGTA 60.091 50.000 0.00 0.00 0.00 2.59
2877 3468 2.376695 TTATGGGACGGAGGGAGTAG 57.623 55.000 0.00 0.00 0.00 2.57
2882 3473 1.704070 GGGACGGAGGGAGTAGAGATA 59.296 57.143 0.00 0.00 0.00 1.98
2982 3574 2.623416 GAGGTGTTTCTGTCCTTTTGGG 59.377 50.000 0.00 0.00 40.87 4.12
3093 3685 5.693104 GCACATGATGTCAAATTGTTTCTGT 59.307 36.000 0.00 0.00 0.00 3.41
3162 3754 1.669779 TGCATTGGTTTTGCACAAAGC 59.330 42.857 7.74 7.74 44.73 3.51
3639 4231 2.615447 ACTGGCATCATATGTGAAAGCG 59.385 45.455 12.01 4.70 39.16 4.68
3935 4527 3.347216 ACTTTGATCCAATGAGAACGGG 58.653 45.455 0.00 0.00 0.00 5.28
4011 4603 9.071276 GAAGTGGTCATATTATGGAATGTCAAT 57.929 33.333 3.89 0.00 0.00 2.57
4041 4633 0.608640 CTTCTAAGACCACACCGGCT 59.391 55.000 0.00 0.00 39.03 5.52
4292 4887 5.288015 TGTCAACACATTGCGAATCAATTT 58.712 33.333 0.00 0.00 42.48 1.82
4523 5129 6.102897 TCTTGAAAGACTTTCCACCTCTAG 57.897 41.667 22.23 6.48 38.90 2.43
4534 5140 4.569719 TCCACCTCTAGATTTTGGGAAC 57.430 45.455 12.31 0.00 0.00 3.62
4539 5145 5.001874 ACCTCTAGATTTTGGGAACGTTTC 58.998 41.667 0.46 0.00 0.00 2.78
4549 5165 3.207778 TGGGAACGTTTCGTCTCATTTT 58.792 40.909 0.46 0.00 39.99 1.82
4550 5166 3.249080 TGGGAACGTTTCGTCTCATTTTC 59.751 43.478 0.46 0.00 39.99 2.29
4579 5195 8.956426 GTGTTCCATTGGAGTTTAATTCTGATA 58.044 33.333 5.36 0.00 31.21 2.15
4580 5196 9.527157 TGTTCCATTGGAGTTTAATTCTGATAA 57.473 29.630 5.36 0.00 31.21 1.75
4587 5203 9.973661 TTGGAGTTTAATTCTGATAATCTTGGA 57.026 29.630 0.00 0.00 0.00 3.53
4588 5204 9.973661 TGGAGTTTAATTCTGATAATCTTGGAA 57.026 29.630 0.00 0.00 0.00 3.53
4635 5251 0.909623 ACTTCCATGGAACTACGGGG 59.090 55.000 23.63 13.90 0.00 5.73
4650 5266 3.283259 ACGGGGATTCATCTTTCCTTC 57.717 47.619 0.00 0.00 32.34 3.46
4656 5272 3.379688 GGATTCATCTTTCCTTCAGCACC 59.620 47.826 0.00 0.00 0.00 5.01
4658 5274 3.507162 TCATCTTTCCTTCAGCACCAA 57.493 42.857 0.00 0.00 0.00 3.67
4659 5275 3.149196 TCATCTTTCCTTCAGCACCAAC 58.851 45.455 0.00 0.00 0.00 3.77
4660 5276 1.981256 TCTTTCCTTCAGCACCAACC 58.019 50.000 0.00 0.00 0.00 3.77
4661 5277 1.494721 TCTTTCCTTCAGCACCAACCT 59.505 47.619 0.00 0.00 0.00 3.50
4662 5278 2.708861 TCTTTCCTTCAGCACCAACCTA 59.291 45.455 0.00 0.00 0.00 3.08
4663 5279 3.330701 TCTTTCCTTCAGCACCAACCTAT 59.669 43.478 0.00 0.00 0.00 2.57
4664 5280 3.806949 TTCCTTCAGCACCAACCTATT 57.193 42.857 0.00 0.00 0.00 1.73
4665 5281 4.919774 TTCCTTCAGCACCAACCTATTA 57.080 40.909 0.00 0.00 0.00 0.98
4667 5283 2.936498 CCTTCAGCACCAACCTATTACG 59.064 50.000 0.00 0.00 0.00 3.18
4710 5326 3.108144 GTTCCATTCCGCATTTCATTCG 58.892 45.455 0.00 0.00 0.00 3.34
4711 5327 1.065401 TCCATTCCGCATTTCATTCGC 59.935 47.619 0.00 0.00 0.00 4.70
4712 5328 1.480205 CATTCCGCATTTCATTCGCC 58.520 50.000 0.00 0.00 0.00 5.54
4713 5329 0.029300 ATTCCGCATTTCATTCGCCG 59.971 50.000 0.00 0.00 0.00 6.46
4714 5330 1.302383 TTCCGCATTTCATTCGCCGT 61.302 50.000 0.00 0.00 0.00 5.68
4715 5331 1.136565 CCGCATTTCATTCGCCGTT 59.863 52.632 0.00 0.00 0.00 4.44
4725 5341 2.229062 TCATTCGCCGTTGCCAAATTTA 59.771 40.909 0.00 0.00 0.00 1.40
4800 5416 7.555554 CCTTTATGGATGAAGATGTTGAACTCT 59.444 37.037 0.00 0.00 38.35 3.24
4801 5417 8.868522 TTTATGGATGAAGATGTTGAACTCTT 57.131 30.769 8.91 8.91 34.48 2.85
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
18 19 0.664761 CGTAGACCCTAAATCGCGGA 59.335 55.000 6.13 0.00 0.00 5.54
35 36 1.439679 GAAGGAGAAATGGCGAACGT 58.560 50.000 0.00 0.00 0.00 3.99
39 40 1.607612 GGGGAAGGAGAAATGGCGA 59.392 57.895 0.00 0.00 0.00 5.54
134 137 3.371097 GACATCGGGGCGAGCTTCA 62.371 63.158 0.00 0.00 39.91 3.02
135 138 2.586357 GACATCGGGGCGAGCTTC 60.586 66.667 0.00 0.00 39.91 3.86
177 180 2.483745 GTCTCGTCGTCATGGCGA 59.516 61.111 20.25 20.25 38.68 5.54
261 270 4.662961 CCACCGCTGCGAGTGTGA 62.663 66.667 28.51 0.00 31.88 3.58
473 482 0.527817 CTTGACGCCGAGATGGTACC 60.528 60.000 4.43 4.43 41.21 3.34
594 604 5.284660 GCAGACGACACAAATGATCAAATTC 59.715 40.000 0.00 0.00 0.00 2.17
604 614 1.425412 GTACCGCAGACGACACAAAT 58.575 50.000 0.00 0.00 43.93 2.32
631 641 3.737266 CGTAAACCGCAATACCGTATCAT 59.263 43.478 0.00 0.00 0.00 2.45
633 643 2.472488 CCGTAAACCGCAATACCGTATC 59.528 50.000 0.00 0.00 34.38 2.24
642 652 1.962306 GCAGACCCGTAAACCGCAA 60.962 57.895 0.00 0.00 34.38 4.85
644 654 1.908066 CTTGCAGACCCGTAAACCGC 61.908 60.000 0.00 0.00 34.38 5.68
645 655 0.320073 TCTTGCAGACCCGTAAACCG 60.320 55.000 0.00 0.00 0.00 4.44
654 1030 5.404466 AGAGCATATATCTCTTGCAGACC 57.596 43.478 8.19 0.00 37.63 3.85
656 1032 7.232330 ACTGTTAGAGCATATATCTCTTGCAGA 59.768 37.037 26.05 11.09 40.06 4.26
706 1082 3.218398 CGACAAGAAATGAAACGAGTGC 58.782 45.455 0.00 0.00 0.00 4.40
707 1083 3.493129 TCCGACAAGAAATGAAACGAGTG 59.507 43.478 0.00 0.00 0.00 3.51
708 1084 3.724374 TCCGACAAGAAATGAAACGAGT 58.276 40.909 0.00 0.00 0.00 4.18
709 1085 4.725556 TTCCGACAAGAAATGAAACGAG 57.274 40.909 0.00 0.00 0.00 4.18
710 1086 4.553938 GCTTTCCGACAAGAAATGAAACGA 60.554 41.667 0.00 0.00 35.30 3.85
711 1087 3.664025 GCTTTCCGACAAGAAATGAAACG 59.336 43.478 0.00 0.00 35.30 3.60
712 1088 3.981416 GGCTTTCCGACAAGAAATGAAAC 59.019 43.478 0.00 0.00 35.30 2.78
713 1089 3.888930 AGGCTTTCCGACAAGAAATGAAA 59.111 39.130 0.00 0.00 35.30 2.69
814 1395 5.010012 AGCTTTGCAGTTATAACTTTGCAGT 59.990 36.000 23.58 12.79 38.59 4.40
815 1396 5.464168 AGCTTTGCAGTTATAACTTTGCAG 58.536 37.500 23.58 17.43 38.59 4.41
816 1397 5.452078 AGCTTTGCAGTTATAACTTTGCA 57.548 34.783 22.00 22.00 37.08 4.08
817 1398 6.524586 CAGTAGCTTTGCAGTTATAACTTTGC 59.475 38.462 15.60 17.17 37.08 3.68
818 1399 6.524586 GCAGTAGCTTTGCAGTTATAACTTTG 59.475 38.462 15.60 7.84 41.17 2.77
819 1400 6.206634 TGCAGTAGCTTTGCAGTTATAACTTT 59.793 34.615 15.60 0.00 45.89 2.66
820 1401 5.705441 TGCAGTAGCTTTGCAGTTATAACTT 59.295 36.000 15.60 2.39 45.89 2.66
821 1402 5.245531 TGCAGTAGCTTTGCAGTTATAACT 58.754 37.500 18.35 12.50 45.89 2.24
822 1403 5.545658 TGCAGTAGCTTTGCAGTTATAAC 57.454 39.130 18.35 7.57 45.89 1.89
869 1450 8.043710 AGAAAACTATCGATGATGTTTCTTCCT 58.956 33.333 18.99 13.49 31.41 3.36
912 1493 2.022934 GGAGGAGGGAGTAACGTACTG 58.977 57.143 0.00 0.00 39.59 2.74
1180 1762 2.049475 GAGTCGAGCGCTGTACCGAT 62.049 60.000 18.48 7.72 33.47 4.18
1185 1767 2.745100 ACGGAGTCGAGCGCTGTA 60.745 61.111 18.48 0.00 29.74 2.74
1585 2167 7.341445 TGTAACAAAGAAATGCCACTTTACT 57.659 32.000 0.00 0.00 35.07 2.24
1685 2267 5.021033 ACATTTGCACCTTGTCAATTTGA 57.979 34.783 0.00 0.00 0.00 2.69
1827 2409 3.763360 ACTCGCCAAAAATCATGAATCCA 59.237 39.130 0.00 0.00 0.00 3.41
1837 2419 4.906618 TCCTCTAAGAACTCGCCAAAAAT 58.093 39.130 0.00 0.00 0.00 1.82
1868 2450 7.554476 AGACTTTATCACTTCCTCAATTTAGGC 59.446 37.037 0.34 0.00 36.51 3.93
1898 2480 7.750229 ACTTAAATCATTCTGCTCTGAACAA 57.250 32.000 0.00 0.00 0.00 2.83
2143 2727 4.789012 TCCTTGCAGAAATGTTGATTCC 57.211 40.909 0.00 0.00 0.00 3.01
2429 3020 8.915871 TTCATTCTCTGCAAAATATGTTAAGC 57.084 30.769 0.00 0.00 0.00 3.09
2684 3275 2.942376 TGCAAAGGCGATACATGTAAGG 59.058 45.455 10.14 5.93 45.35 2.69
2729 3320 7.156876 AGTAAAACATGGTTGGACATACATG 57.843 36.000 0.00 12.33 44.61 3.21
2851 3442 1.623811 CCTCCGTCCCATAATGTAGGG 59.376 57.143 0.00 0.00 46.90 3.53
2854 3445 2.090943 ACTCCCTCCGTCCCATAATGTA 60.091 50.000 0.00 0.00 0.00 2.29
2855 3446 1.344087 ACTCCCTCCGTCCCATAATGT 60.344 52.381 0.00 0.00 0.00 2.71
2857 3448 2.449730 TCTACTCCCTCCGTCCCATAAT 59.550 50.000 0.00 0.00 0.00 1.28
2858 3449 1.854939 TCTACTCCCTCCGTCCCATAA 59.145 52.381 0.00 0.00 0.00 1.90
2860 3451 0.186386 CTCTACTCCCTCCGTCCCAT 59.814 60.000 0.00 0.00 0.00 4.00
2861 3452 0.917821 TCTCTACTCCCTCCGTCCCA 60.918 60.000 0.00 0.00 0.00 4.37
2862 3453 0.479378 ATCTCTACTCCCTCCGTCCC 59.521 60.000 0.00 0.00 0.00 4.46
2863 3454 2.638855 TCTATCTCTACTCCCTCCGTCC 59.361 54.545 0.00 0.00 0.00 4.79
2864 3455 3.071312 TGTCTATCTCTACTCCCTCCGTC 59.929 52.174 0.00 0.00 0.00 4.79
2866 3457 3.773418 TGTCTATCTCTACTCCCTCCG 57.227 52.381 0.00 0.00 0.00 4.63
2867 3458 5.249780 TCATGTCTATCTCTACTCCCTCC 57.750 47.826 0.00 0.00 0.00 4.30
2869 3460 6.461577 TGATCATGTCTATCTCTACTCCCT 57.538 41.667 0.00 0.00 0.00 4.20
2870 3461 6.719370 ACTTGATCATGTCTATCTCTACTCCC 59.281 42.308 8.37 0.00 0.00 4.30
2871 3462 7.759489 ACTTGATCATGTCTATCTCTACTCC 57.241 40.000 8.37 0.00 0.00 3.85
2882 3473 8.072321 ACAGACAACTATACTTGATCATGTCT 57.928 34.615 16.80 15.97 45.05 3.41
2958 3550 2.938956 AAGGACAGAAACACCTCCAG 57.061 50.000 0.00 0.00 33.16 3.86
3093 3685 3.639561 TCTGACAGGTGTAGCACAAACTA 59.360 43.478 1.81 0.00 35.86 2.24
3162 3754 6.039829 TCGTATTATAGCAGGATGGATAGCAG 59.960 42.308 0.00 0.00 35.86 4.24
3639 4231 0.861837 CTACCGGATCATTCGCAAGC 59.138 55.000 9.46 0.00 37.18 4.01
3922 4514 2.679837 CAAGTCATCCCGTTCTCATTGG 59.320 50.000 0.00 0.00 0.00 3.16
3935 4527 4.232221 CAGACCATTTGTTGCAAGTCATC 58.768 43.478 14.43 0.00 0.00 2.92
4007 4599 9.147732 TGGTCTTAGAAGAATATCAGCTATTGA 57.852 33.333 0.00 0.00 37.18 2.57
4011 4603 7.201920 GGTGTGGTCTTAGAAGAATATCAGCTA 60.202 40.741 0.00 0.00 36.68 3.32
4292 4887 6.952773 AATGCCTAGTTTCTACACACAAAA 57.047 33.333 0.00 0.00 0.00 2.44
4514 5120 3.270877 CGTTCCCAAAATCTAGAGGTGG 58.729 50.000 10.75 10.75 0.00 4.61
4523 5129 3.249080 TGAGACGAAACGTTCCCAAAATC 59.751 43.478 0.00 0.00 41.37 2.17
4534 5140 3.247648 ACACCAGAAAATGAGACGAAACG 59.752 43.478 0.00 0.00 0.00 3.60
4539 5145 3.138304 TGGAACACCAGAAAATGAGACG 58.862 45.455 0.00 0.00 0.00 4.18
4579 5195 5.946486 AGAGGTGAAAAGACTTCCAAGATT 58.054 37.500 0.00 0.00 0.00 2.40
4580 5196 5.574970 AGAGGTGAAAAGACTTCCAAGAT 57.425 39.130 0.00 0.00 0.00 2.40
4582 5198 7.751768 ATTTAGAGGTGAAAAGACTTCCAAG 57.248 36.000 0.00 0.00 0.00 3.61
4583 5199 9.807921 AATATTTAGAGGTGAAAAGACTTCCAA 57.192 29.630 0.00 0.00 0.00 3.53
4584 5200 9.231297 CAATATTTAGAGGTGAAAAGACTTCCA 57.769 33.333 0.00 0.00 0.00 3.53
4585 5201 8.678199 CCAATATTTAGAGGTGAAAAGACTTCC 58.322 37.037 0.00 0.00 0.00 3.46
4586 5202 9.449719 TCCAATATTTAGAGGTGAAAAGACTTC 57.550 33.333 0.00 0.00 0.00 3.01
4587 5203 9.807921 TTCCAATATTTAGAGGTGAAAAGACTT 57.192 29.630 0.00 0.00 0.00 3.01
4588 5204 9.807921 TTTCCAATATTTAGAGGTGAAAAGACT 57.192 29.630 0.00 0.00 0.00 3.24
4625 5241 4.127907 GGAAAGATGAATCCCCGTAGTTC 58.872 47.826 0.00 0.00 0.00 3.01
4627 5243 3.385115 AGGAAAGATGAATCCCCGTAGT 58.615 45.455 0.00 0.00 36.31 2.73
4635 5251 4.012374 TGGTGCTGAAGGAAAGATGAATC 58.988 43.478 0.00 0.00 0.00 2.52
4650 5266 1.014352 GGCGTAATAGGTTGGTGCTG 58.986 55.000 0.00 0.00 0.00 4.41
4667 5283 4.030452 GCTGTGAGCACGTTGGGC 62.030 66.667 0.00 0.00 41.89 5.36
4710 5326 7.527084 TGTTATAAATAAATTTGGCAACGGC 57.473 32.000 0.00 0.00 42.51 5.68
4711 5327 8.926710 TGTTGTTATAAATAAATTTGGCAACGG 58.073 29.630 0.00 0.00 42.51 4.44


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

AutoCloner maintained by Alex Coulton.