Multiple sequence alignment - TraesCS3D01G060500

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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 TraesCS3D01G060500 chr3D 100.000 4793 0 0 1 4793 26300162 26304954 0.000000e+00 8852.0
1 TraesCS3D01G060500 chr3D 82.868 3257 520 27 514 3755 26290624 26293857 0.000000e+00 2889.0
2 TraesCS3D01G060500 chr3D 82.534 3252 510 37 538 3760 26270951 26274173 0.000000e+00 2806.0
3 TraesCS3D01G060500 chr3A 97.260 3394 60 12 1 3381 36299568 36302941 0.000000e+00 5722.0
4 TraesCS3D01G060500 chr3A 82.532 3286 514 42 538 3795 36246327 36249580 0.000000e+00 2833.0
5 TraesCS3D01G060500 chr3A 84.086 465 49 19 3497 3951 36302939 36303388 4.430000e-115 425.0
6 TraesCS3D01G060500 chr4D 82.899 3491 507 57 372 3806 1397865 1401321 0.000000e+00 3057.0
7 TraesCS3D01G060500 chrUn 82.819 3207 495 31 577 3757 75441437 75444613 0.000000e+00 2819.0
8 TraesCS3D01G060500 chrUn 81.981 3130 505 33 659 3757 245875185 245872084 0.000000e+00 2601.0
9 TraesCS3D01G060500 chrUn 81.733 3186 519 36 603 3757 260283682 260286835 0.000000e+00 2601.0
10 TraesCS3D01G060500 chrUn 75.664 226 41 12 4158 4379 245871861 245871646 3.050000e-17 100.0
11 TraesCS3D01G060500 chrUn 75.546 229 42 12 4155 4379 260287055 260287273 3.050000e-17 100.0
12 TraesCS3D01G060500 chr3B 82.189 3189 513 40 592 3755 43818566 43821724 0.000000e+00 2691.0
13 TraesCS3D01G060500 chr3B 93.884 1210 59 10 3590 4793 43937546 43938746 0.000000e+00 1810.0
14 TraesCS3D01G060500 chr3B 93.884 1210 59 10 3590 4793 44043026 44044226 0.000000e+00 1810.0
15 TraesCS3D01G060500 chr3B 94.769 497 12 5 1 493 43925423 43925909 0.000000e+00 761.0
16 TraesCS3D01G060500 chr3B 94.769 497 12 5 1 493 44031237 44031723 0.000000e+00 761.0
17 TraesCS3D01G060500 chr6D 82.044 3063 500 27 709 3742 387397 390438 0.000000e+00 2564.0
18 TraesCS3D01G060500 chr4A 84.845 1940 258 20 1931 3844 603384752 603382823 0.000000e+00 1921.0
19 TraesCS3D01G060500 chr7A 86.567 67 8 1 1 66 724652191 724652257 6.650000e-09 73.1
20 TraesCS3D01G060500 chr6A 84.848 66 8 2 1 64 608072691 608072626 1.110000e-06 65.8


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 TraesCS3D01G060500 chr3D 26300162 26304954 4792 False 8852.0 8852 100.0000 1 4793 1 chr3D.!!$F3 4792
1 TraesCS3D01G060500 chr3D 26290624 26293857 3233 False 2889.0 2889 82.8680 514 3755 1 chr3D.!!$F2 3241
2 TraesCS3D01G060500 chr3D 26270951 26274173 3222 False 2806.0 2806 82.5340 538 3760 1 chr3D.!!$F1 3222
3 TraesCS3D01G060500 chr3A 36299568 36303388 3820 False 3073.5 5722 90.6730 1 3951 2 chr3A.!!$F2 3950
4 TraesCS3D01G060500 chr3A 36246327 36249580 3253 False 2833.0 2833 82.5320 538 3795 1 chr3A.!!$F1 3257
5 TraesCS3D01G060500 chr4D 1397865 1401321 3456 False 3057.0 3057 82.8990 372 3806 1 chr4D.!!$F1 3434
6 TraesCS3D01G060500 chrUn 75441437 75444613 3176 False 2819.0 2819 82.8190 577 3757 1 chrUn.!!$F1 3180
7 TraesCS3D01G060500 chrUn 245871646 245875185 3539 True 1350.5 2601 78.8225 659 4379 2 chrUn.!!$R1 3720
8 TraesCS3D01G060500 chrUn 260283682 260287273 3591 False 1350.5 2601 78.6395 603 4379 2 chrUn.!!$F2 3776
9 TraesCS3D01G060500 chr3B 43818566 43821724 3158 False 2691.0 2691 82.1890 592 3755 1 chr3B.!!$F1 3163
10 TraesCS3D01G060500 chr3B 43937546 43938746 1200 False 1810.0 1810 93.8840 3590 4793 1 chr3B.!!$F3 1203
11 TraesCS3D01G060500 chr3B 44043026 44044226 1200 False 1810.0 1810 93.8840 3590 4793 1 chr3B.!!$F5 1203
12 TraesCS3D01G060500 chr6D 387397 390438 3041 False 2564.0 2564 82.0440 709 3742 1 chr6D.!!$F1 3033
13 TraesCS3D01G060500 chr4A 603382823 603384752 1929 True 1921.0 1921 84.8450 1931 3844 1 chr4A.!!$R1 1913

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
104 105 0.247460 CTTGCCGACACCATCTCTGA 59.753 55.000 0.00 0.0 0.00 3.27 F
179 180 0.385390 CCAAAGACCGGGCATAATGC 59.615 55.000 11.69 0.0 44.08 3.56 F
432 451 0.737715 CGCGTGGAAGAAGAGGAAGG 60.738 60.000 0.00 0.0 0.00 3.46 F
1324 1362 1.539388 CGGGTGCAAATCAGCTAACAA 59.461 47.619 0.00 0.0 42.57 2.83 F
2915 2957 1.019278 AGAAATGTGCGGCACCGTAG 61.019 55.000 28.57 0.0 42.09 3.51 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1551 1592 0.605319 GTTTGCTCATCGTGGTGGGA 60.605 55.0 0.00 0.0 0.00 4.37 R
1740 1781 2.540265 ACAGAGTCTGCTGGAGTTTG 57.460 50.0 20.31 0.0 40.20 2.93 R
2647 2689 0.321653 CTCTTGTGTTTCCCTCCCCG 60.322 60.0 0.00 0.0 0.00 5.73 R
3416 3496 0.261696 AGTTGAAACTTGGCCACCCT 59.738 50.0 3.88 0.0 35.21 4.34 R
4055 4154 0.462047 GTCGGATGGTGTTAGCCTGG 60.462 60.0 0.00 0.0 0.00 4.45 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
49 50 0.909623 ACCCTCTTACCCCGATGTTG 59.090 55.000 0.00 0.00 0.00 3.33
52 53 0.810031 CTCTTACCCCGATGTTGGCG 60.810 60.000 0.00 0.00 0.00 5.69
60 61 0.390603 CCGATGTTGGCGAGGTACAA 60.391 55.000 0.00 0.00 0.00 2.41
104 105 0.247460 CTTGCCGACACCATCTCTGA 59.753 55.000 0.00 0.00 0.00 3.27
128 129 4.286707 AGGTGGTACTATGTAGACATGCA 58.713 43.478 5.39 0.00 37.15 3.96
179 180 0.385390 CCAAAGACCGGGCATAATGC 59.615 55.000 11.69 0.00 44.08 3.56
215 216 6.090628 GCTAGCTAGCTAGTGCATTATTTCAG 59.909 42.308 39.05 20.92 45.67 3.02
224 225 4.009675 GTGCATTATTTCAGAGTGGACCA 58.990 43.478 0.00 0.00 0.00 4.02
253 257 4.613929 GCAGCAAGCTAGCAGAGT 57.386 55.556 18.83 0.00 41.15 3.24
254 258 3.748863 GCAGCAAGCTAGCAGAGTA 57.251 52.632 18.83 0.00 41.15 2.59
255 259 1.569708 GCAGCAAGCTAGCAGAGTAG 58.430 55.000 18.83 3.12 41.15 2.57
256 260 1.569708 CAGCAAGCTAGCAGAGTAGC 58.430 55.000 18.83 10.80 45.06 3.58
265 269 1.857965 AGCAGAGTAGCAGATCACCA 58.142 50.000 0.00 0.00 36.85 4.17
367 371 1.754621 CTCTCGCCTCTGCCCTACA 60.755 63.158 0.00 0.00 0.00 2.74
369 373 3.438017 CTCGCCTCTGCCCTACAGC 62.438 68.421 0.00 0.00 46.76 4.40
370 374 3.774528 CGCCTCTGCCCTACAGCA 61.775 66.667 0.00 0.00 46.76 4.41
432 451 0.737715 CGCGTGGAAGAAGAGGAAGG 60.738 60.000 0.00 0.00 0.00 3.46
461 480 2.063266 GGTTCGTACGCAATTCACAGA 58.937 47.619 11.24 0.00 0.00 3.41
591 618 5.365619 ACTGAAAACTAACTCGACCAACAT 58.634 37.500 0.00 0.00 0.00 2.71
656 688 4.851843 TCGGACAGTTACTCCTCTTGATA 58.148 43.478 0.00 0.00 0.00 2.15
732 764 4.439700 CCGTACATGGTAACGAGACAGATT 60.440 45.833 16.16 0.00 41.55 2.40
733 765 5.220912 CCGTACATGGTAACGAGACAGATTA 60.221 44.000 16.16 0.00 41.55 1.75
757 789 6.856761 TAGTTATCACTGCTTGGATTCAAGGG 60.857 42.308 15.71 0.00 41.20 3.95
979 1014 2.519780 ACTCGCCGGAGAGATCCC 60.520 66.667 37.54 1.35 43.27 3.85
980 1015 2.519541 CTCGCCGGAGAGATCCCA 60.520 66.667 29.23 0.00 43.27 4.37
981 1016 1.905843 CTCGCCGGAGAGATCCCAT 60.906 63.158 29.23 0.00 43.27 4.00
982 1017 2.152297 CTCGCCGGAGAGATCCCATG 62.152 65.000 29.23 0.42 43.27 3.66
1324 1362 1.539388 CGGGTGCAAATCAGCTAACAA 59.461 47.619 0.00 0.00 42.57 2.83
1543 1584 6.261158 TGATTTATCAACGAACAACTTCACCA 59.739 34.615 0.00 0.00 33.08 4.17
1624 1665 2.391616 TCAGCTCCAAGCACATAGTG 57.608 50.000 1.29 0.00 45.56 2.74
1740 1781 6.819397 AGTTCAATAGCTAACCTTTCCAAC 57.181 37.500 0.00 0.00 0.00 3.77
2551 2593 3.514645 GCATGTTTTGTTATGCCTCCAG 58.485 45.455 0.00 0.00 42.88 3.86
2655 2697 1.908483 CTTCTTTCTCCGGGGAGGG 59.092 63.158 14.50 1.11 42.20 4.30
2915 2957 1.019278 AGAAATGTGCGGCACCGTAG 61.019 55.000 28.57 0.00 42.09 3.51
3379 3444 8.256611 TCTATGTTAAGCAGTGAAGATGAAAC 57.743 34.615 0.00 0.00 0.00 2.78
3388 3453 5.350091 GCAGTGAAGATGAAACTAACTCCTC 59.650 44.000 0.00 0.00 0.00 3.71
3389 3454 5.872070 CAGTGAAGATGAAACTAACTCCTCC 59.128 44.000 0.00 0.00 0.00 4.30
3390 3455 5.046231 AGTGAAGATGAAACTAACTCCTCCC 60.046 44.000 0.00 0.00 0.00 4.30
3391 3456 4.225267 TGAAGATGAAACTAACTCCTCCCC 59.775 45.833 0.00 0.00 0.00 4.81
3396 3468 4.981812 TGAAACTAACTCCTCCCCTTTTC 58.018 43.478 0.00 0.00 0.00 2.29
3401 3481 5.105853 ACTAACTCCTCCCCTTTTCCATTA 58.894 41.667 0.00 0.00 0.00 1.90
3416 3496 7.441157 CCTTTTCCATTATGTAGAATACGCAGA 59.559 37.037 0.00 0.00 46.99 4.26
3423 3503 0.750850 TAGAATACGCAGAGGGTGGC 59.249 55.000 0.00 0.00 0.00 5.01
3489 3569 6.673106 TCTTCTCGAGATATTCATTCGAAGG 58.327 40.000 17.44 2.79 42.09 3.46
3574 3655 4.891992 CCTGATAGGGTATCGGTGATTT 57.108 45.455 2.80 0.00 39.42 2.17
3685 3775 1.068954 GCCTTTGCTGCACTAAGACAC 60.069 52.381 14.08 2.10 33.49 3.67
3777 3867 1.280746 CAGTGCCGTTGCTTCAGTG 59.719 57.895 0.00 0.00 38.71 3.66
3793 3887 4.471904 TCAGTGGCAGTACCTGAATAAG 57.528 45.455 3.31 0.00 40.22 1.73
3803 3897 7.360946 GGCAGTACCTGAATAAGTAACTTGTTG 60.361 40.741 0.00 0.00 32.44 3.33
3804 3898 7.172703 GCAGTACCTGAATAAGTAACTTGTTGT 59.827 37.037 0.00 0.00 32.44 3.32
3844 3943 0.469705 AACCATGCAAGCAAGGACCA 60.470 50.000 21.67 0.00 38.11 4.02
3847 3946 1.076192 ATGCAAGCAAGGACCAGCT 59.924 52.632 5.69 5.69 44.31 4.24
3893 3992 3.429410 CCTCTGATGTGTTACAGCATCGA 60.429 47.826 16.71 15.35 44.09 3.59
4003 4102 1.604604 TTGCCACACCTAACAGCTTC 58.395 50.000 0.00 0.00 0.00 3.86
4014 4113 6.546034 ACACCTAACAGCTTCAACTTTGTTAT 59.454 34.615 0.00 0.00 35.98 1.89
4016 4115 5.858581 CCTAACAGCTTCAACTTTGTTATGC 59.141 40.000 0.00 0.00 35.98 3.14
4034 4133 1.332375 TGCACACTTCGGCAAAACTAC 59.668 47.619 0.00 0.00 37.03 2.73
4055 4154 2.508526 CCCTGGACTAAATATGCCTGC 58.491 52.381 0.00 0.00 0.00 4.85
4074 4173 0.462047 CCAGGCTAACACCATCCGAC 60.462 60.000 0.00 0.00 0.00 4.79
4098 4197 1.337167 GCACTTGATTTCCCAGCAACC 60.337 52.381 0.00 0.00 0.00 3.77
4317 4417 1.750193 ATTTACCCTGGTGCACATCG 58.250 50.000 20.43 5.73 0.00 3.84
4381 4482 7.555554 ACACACAAAATGGAAAATGGAAAATGA 59.444 29.630 0.00 0.00 0.00 2.57
4491 4592 2.161012 GTCGTCTCGTAGTGGAACATCA 59.839 50.000 0.00 0.00 44.52 3.07
4508 4609 6.071952 GGAACATCAGTAAAATCTGCAAAGGA 60.072 38.462 0.00 0.00 35.63 3.36
4509 4610 6.899393 ACATCAGTAAAATCTGCAAAGGAA 57.101 33.333 0.00 0.00 35.63 3.36
4544 4645 5.988462 CAACATGACCTGGTGATGCCATAC 61.988 50.000 23.63 0.00 46.14 2.39
4596 4697 6.401903 CGACTGCAATCCTATTCATAGATTGC 60.402 42.308 23.27 23.27 43.87 3.56
4618 4719 8.948853 TTGCGATTGAATTGAAGTAGTTAAAG 57.051 30.769 0.00 0.00 0.00 1.85
4637 4738 9.448438 AGTTAAAGTTTCCTTTTTGCTCATTTT 57.552 25.926 0.00 0.00 41.18 1.82
4641 4742 8.648557 AAGTTTCCTTTTTGCTCATTTTAGTC 57.351 30.769 0.00 0.00 0.00 2.59
4664 4765 3.376234 CAGAATGGTGTGGCTAGAACATG 59.624 47.826 0.00 0.00 26.39 3.21
4678 4779 7.335924 TGGCTAGAACATGTTTTACATTAGGAC 59.664 37.037 13.36 1.41 36.53 3.85
4701 4802 4.096984 CCAGAGGTTTTAAGATGATGGCAC 59.903 45.833 0.00 0.00 0.00 5.01
4702 4803 4.946157 CAGAGGTTTTAAGATGATGGCACT 59.054 41.667 0.00 0.00 0.00 4.40
4703 4804 4.946157 AGAGGTTTTAAGATGATGGCACTG 59.054 41.667 0.00 0.00 0.00 3.66
4753 4854 6.152661 CCAAATATGTTAAGGTTTCAGGCAGA 59.847 38.462 0.00 0.00 0.00 4.26
4754 4855 7.309744 CCAAATATGTTAAGGTTTCAGGCAGAA 60.310 37.037 0.00 0.00 0.00 3.02
4755 4856 7.775053 AATATGTTAAGGTTTCAGGCAGAAA 57.225 32.000 0.44 0.44 43.71 2.52
4766 4867 6.764308 TTTCAGGCAGAAATTGGAGATAAG 57.236 37.500 0.44 0.00 41.17 1.73
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
9 10 0.242017 GCAAGCGAACCATCTTTGCT 59.758 50.000 0.66 0.00 39.10 3.91
13 14 1.244019 GGTGGCAAGCGAACCATCTT 61.244 55.000 9.80 0.00 38.46 2.40
49 50 2.869233 TACGGTAATTGTACCTCGCC 57.131 50.000 1.68 0.00 46.84 5.54
73 74 4.122776 GTGTCGGCAAGAGTCATCATAAT 58.877 43.478 0.00 0.00 0.00 1.28
74 75 3.521560 GTGTCGGCAAGAGTCATCATAA 58.478 45.455 0.00 0.00 0.00 1.90
83 84 0.534412 AGAGATGGTGTCGGCAAGAG 59.466 55.000 0.00 0.00 0.00 2.85
104 105 5.188948 TGCATGTCTACATAGTACCACCTTT 59.811 40.000 0.00 0.00 34.26 3.11
128 129 6.314648 TCGTTCACACTGTATTATCTCGTACT 59.685 38.462 0.00 0.00 0.00 2.73
215 216 1.003718 CCCGGTCTTTGGTCCACTC 60.004 63.158 0.00 0.00 0.00 3.51
224 225 3.790416 TTGCTGCTGCCCGGTCTTT 62.790 57.895 13.47 0.00 38.71 2.52
253 257 7.445121 CCTCACTTTATATTGGTGATCTGCTA 58.555 38.462 0.00 0.00 38.93 3.49
254 258 6.294473 CCTCACTTTATATTGGTGATCTGCT 58.706 40.000 0.00 0.00 38.93 4.24
255 259 5.471456 CCCTCACTTTATATTGGTGATCTGC 59.529 44.000 0.00 0.00 38.93 4.26
256 260 5.471456 GCCCTCACTTTATATTGGTGATCTG 59.529 44.000 0.00 0.00 38.93 2.90
432 451 1.749609 GCGTACGAACCTGCGGATTC 61.750 60.000 21.65 0.00 35.12 2.52
438 457 0.793861 TGAATTGCGTACGAACCTGC 59.206 50.000 21.65 0.00 0.00 4.85
461 480 4.399934 TCATGAAATGTACATGCATGTGCT 59.600 37.500 36.76 23.67 46.80 4.40
591 618 7.886970 GGCCGGGTATCTCTGTACATATATATA 59.113 40.741 2.18 0.00 0.00 0.86
732 764 6.115446 CCTTGAATCCAAGCAGTGATAACTA 58.885 40.000 0.00 0.00 46.42 2.24
733 765 4.946157 CCTTGAATCCAAGCAGTGATAACT 59.054 41.667 0.00 0.00 46.42 2.24
757 789 3.567797 GGTCGAGGCTGATTGCGC 61.568 66.667 0.00 0.00 44.05 6.09
979 1014 1.679680 GTGACCAAGGGATGATGCATG 59.320 52.381 2.46 0.00 0.00 4.06
980 1015 1.285667 TGTGACCAAGGGATGATGCAT 59.714 47.619 0.00 0.00 0.00 3.96
981 1016 0.697658 TGTGACCAAGGGATGATGCA 59.302 50.000 0.00 0.00 0.00 3.96
982 1017 1.679680 CATGTGACCAAGGGATGATGC 59.320 52.381 0.00 0.00 0.00 3.91
1324 1362 2.644798 AGATGGCTTGTGGAAACCTACT 59.355 45.455 0.00 0.00 0.00 2.57
1551 1592 0.605319 GTTTGCTCATCGTGGTGGGA 60.605 55.000 0.00 0.00 0.00 4.37
1624 1665 3.149981 CCAAAAACTCCCAGTCTTCTCC 58.850 50.000 0.00 0.00 0.00 3.71
1740 1781 2.540265 ACAGAGTCTGCTGGAGTTTG 57.460 50.000 20.31 0.00 40.20 2.93
2647 2689 0.321653 CTCTTGTGTTTCCCTCCCCG 60.322 60.000 0.00 0.00 0.00 5.73
2915 2957 6.183360 GCACACAGTTATTATAGGGACCAAAC 60.183 42.308 0.00 0.00 0.00 2.93
3379 3444 4.592997 AATGGAAAAGGGGAGGAGTTAG 57.407 45.455 0.00 0.00 0.00 2.34
3388 3453 6.072673 GCGTATTCTACATAATGGAAAAGGGG 60.073 42.308 0.00 0.00 30.61 4.79
3389 3454 6.485313 TGCGTATTCTACATAATGGAAAAGGG 59.515 38.462 0.00 0.00 30.61 3.95
3390 3455 7.441157 TCTGCGTATTCTACATAATGGAAAAGG 59.559 37.037 0.00 0.00 30.61 3.11
3391 3456 8.365399 TCTGCGTATTCTACATAATGGAAAAG 57.635 34.615 0.00 0.00 30.61 2.27
3396 3468 5.171476 CCCTCTGCGTATTCTACATAATGG 58.829 45.833 0.00 0.00 0.00 3.16
3401 3481 2.365617 CCACCCTCTGCGTATTCTACAT 59.634 50.000 0.00 0.00 0.00 2.29
3416 3496 0.261696 AGTTGAAACTTGGCCACCCT 59.738 50.000 3.88 0.00 35.21 4.34
3423 3503 0.318107 CTGCGGCAGTTGAAACTTGG 60.318 55.000 21.60 0.00 37.08 3.61
3489 3569 1.517257 CATGTCGTCAGTCGGCCTC 60.517 63.158 0.00 0.00 44.19 4.70
3566 3647 1.003112 TGGGGGTCGAAAATCACCG 60.003 57.895 0.00 0.00 32.89 4.94
3569 3650 0.322456 CAGCTGGGGGTCGAAAATCA 60.322 55.000 5.57 0.00 0.00 2.57
3574 3655 1.485294 TTTAGCAGCTGGGGGTCGAA 61.485 55.000 17.12 0.00 0.00 3.71
3893 3992 0.687354 CCAGAGTGCACTAGTTGGGT 59.313 55.000 25.83 3.98 0.00 4.51
3987 4086 2.851195 AGTTGAAGCTGTTAGGTGTGG 58.149 47.619 0.00 0.00 0.00 4.17
4003 4102 3.974401 CCGAAGTGTGCATAACAAAGTTG 59.026 43.478 0.00 0.00 41.57 3.16
4014 4113 1.332375 GTAGTTTTGCCGAAGTGTGCA 59.668 47.619 0.00 0.00 35.27 4.57
4016 4115 1.265905 GGGTAGTTTTGCCGAAGTGTG 59.734 52.381 0.00 0.00 0.00 3.82
4034 4133 2.815589 GCAGGCATATTTAGTCCAGGGG 60.816 54.545 0.00 0.00 0.00 4.79
4055 4154 0.462047 GTCGGATGGTGTTAGCCTGG 60.462 60.000 0.00 0.00 0.00 4.45
4074 4173 3.084039 TGCTGGGAAATCAAGTGCTTAG 58.916 45.455 0.00 0.00 0.00 2.18
4098 4197 9.219603 ACAAAGAATATATGTATCGGGTGAATG 57.780 33.333 0.00 0.00 0.00 2.67
4169 4268 7.464710 CGAATAGTACTGCCATGTTTTTCTCTC 60.465 40.741 5.39 0.00 0.00 3.20
4184 4283 9.021863 GGTTGATTTAGTTCTCGAATAGTACTG 57.978 37.037 5.39 0.00 36.59 2.74
4226 4325 6.285329 ACATAAATGAAGGAGAATGGGGAT 57.715 37.500 0.00 0.00 0.00 3.85
4317 4417 7.897800 GCGTGGTTCTTATTAATTTTTGCAATC 59.102 33.333 0.00 0.00 0.00 2.67
4418 4519 0.744771 GTAAGAGGAAAGCCGGCCAG 60.745 60.000 26.15 0.00 39.96 4.85
4546 4647 8.765219 CGATCGAAGGTTCTTGTATTTATGAAT 58.235 33.333 10.26 0.00 0.00 2.57
4547 4648 7.977293 TCGATCGAAGGTTCTTGTATTTATGAA 59.023 33.333 16.99 0.00 0.00 2.57
4548 4649 7.434307 GTCGATCGAAGGTTCTTGTATTTATGA 59.566 37.037 21.31 0.00 0.00 2.15
4549 4650 7.435488 AGTCGATCGAAGGTTCTTGTATTTATG 59.565 37.037 21.31 0.00 0.00 1.90
4550 4651 7.435488 CAGTCGATCGAAGGTTCTTGTATTTAT 59.565 37.037 21.31 0.00 0.00 1.40
4551 4652 6.750501 CAGTCGATCGAAGGTTCTTGTATTTA 59.249 38.462 21.31 0.00 0.00 1.40
4552 4653 5.577164 CAGTCGATCGAAGGTTCTTGTATTT 59.423 40.000 21.31 0.00 0.00 1.40
4618 4719 6.983890 TGGACTAAAATGAGCAAAAAGGAAAC 59.016 34.615 0.00 0.00 0.00 2.78
4624 4725 7.153985 CCATTCTGGACTAAAATGAGCAAAAA 58.846 34.615 0.00 0.00 40.96 1.94
4637 4738 1.656587 AGCCACACCATTCTGGACTA 58.343 50.000 0.00 0.00 40.96 2.59
4638 4739 1.556911 CTAGCCACACCATTCTGGACT 59.443 52.381 0.00 0.00 40.96 3.85
4639 4740 1.555075 TCTAGCCACACCATTCTGGAC 59.445 52.381 0.00 0.00 40.96 4.02
4641 4742 2.290260 TGTTCTAGCCACACCATTCTGG 60.290 50.000 0.00 0.00 45.02 3.86
4664 4765 7.520451 AAAACCTCTGGTCCTAATGTAAAAC 57.480 36.000 0.00 0.00 33.12 2.43
4678 4779 4.096984 GTGCCATCATCTTAAAACCTCTGG 59.903 45.833 0.00 0.00 0.00 3.86
4735 4836 5.221422 CCAATTTCTGCCTGAAACCTTAACA 60.221 40.000 0.00 0.00 46.08 2.41
4739 4840 3.575687 CTCCAATTTCTGCCTGAAACCTT 59.424 43.478 0.00 0.00 46.08 3.50
4742 4843 6.515272 TTATCTCCAATTTCTGCCTGAAAC 57.485 37.500 0.00 0.00 46.08 2.78
4749 4850 5.573337 AACTGCTTATCTCCAATTTCTGC 57.427 39.130 0.00 0.00 0.00 4.26
4753 4854 6.183347 AGTGCTAACTGCTTATCTCCAATTT 58.817 36.000 0.00 0.00 43.37 1.82
4754 4855 5.749462 AGTGCTAACTGCTTATCTCCAATT 58.251 37.500 0.00 0.00 43.37 2.32
4755 4856 5.365021 AGTGCTAACTGCTTATCTCCAAT 57.635 39.130 0.00 0.00 43.37 3.16
4766 4867 1.211190 GCAGGCAAGTGCTAACTGC 59.789 57.895 14.44 14.44 43.00 4.40


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

AutoCloner maintained by Alex Coulton.