Multiple sequence alignment - TraesCS1D01G287200

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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 TraesCS1D01G287200 chr1D 100.000 4489 0 0 1 4489 385617644 385622132 0.000000e+00 8290.0
1 TraesCS1D01G287200 chr1B 92.367 4559 195 54 1 4489 517903958 517908433 0.000000e+00 6349.0
2 TraesCS1D01G287200 chr1A 91.929 3023 129 49 1 2960 485339876 485342846 0.000000e+00 4124.0
3 TraesCS1D01G287200 chr1A 95.847 891 19 8 2958 3837 485342949 485343832 0.000000e+00 1424.0
4 TraesCS1D01G287200 chr1A 88.303 607 32 10 3884 4489 485343828 485344396 0.000000e+00 691.0
5 TraesCS1D01G287200 chr6B 97.727 44 1 0 4005 4048 409296787 409296744 4.820000e-10 76.8
6 TraesCS1D01G287200 chr2B 97.674 43 1 0 4004 4046 637044008 637044050 1.730000e-09 75.0
7 TraesCS1D01G287200 chr5B 95.556 45 1 1 4005 4048 249581809 249581853 2.240000e-08 71.3
8 TraesCS1D01G287200 chr5A 95.556 45 1 1 4005 4048 295728815 295728771 2.240000e-08 71.3
9 TraesCS1D01G287200 chr5A 100.000 32 0 0 4017 4048 313315136 313315105 4.850000e-05 60.2
10 TraesCS1D01G287200 chr3B 95.455 44 2 0 4002 4045 786966136 786966179 2.240000e-08 71.3
11 TraesCS1D01G287200 chr6A 95.349 43 2 0 4003 4045 213779491 213779533 8.060000e-08 69.4
12 TraesCS1D01G287200 chr3D 92.857 42 3 0 4005 4046 51440980 51441021 1.350000e-05 62.1


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 TraesCS1D01G287200 chr1D 385617644 385622132 4488 False 8290.000000 8290 100.000000 1 4489 1 chr1D.!!$F1 4488
1 TraesCS1D01G287200 chr1B 517903958 517908433 4475 False 6349.000000 6349 92.367000 1 4489 1 chr1B.!!$F1 4488
2 TraesCS1D01G287200 chr1A 485339876 485344396 4520 False 2079.666667 4124 92.026333 1 4489 3 chr1A.!!$F1 4488

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
673 683 0.033642 GCCCGTTAGTCTAGCCCATC 59.966 60.0 0.00 0.0 0.00 3.51 F
1018 1065 0.469917 GATGATCTGGCTTTCGGGGA 59.530 55.0 0.00 0.0 0.00 4.81 F
1803 1862 0.741221 GGCTCAAGGCTGGAGTTACG 60.741 60.0 19.88 0.0 41.46 3.18 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1528 1587 0.254178 TGGCCCTCTTTCTGATGCTC 59.746 55.0 0.0 0.0 0.00 4.26 R
2914 2976 0.466922 CCAGGAATCTCCATGCCACC 60.467 60.0 0.0 0.0 39.61 4.61 R
3592 3766 0.539669 GGCCAGCTAAACCCACTTGT 60.540 55.0 0.0 0.0 0.00 3.16 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
50 55 1.132640 GGTCATTTGCGTCGACTGC 59.867 57.895 20.46 20.46 0.00 4.40
58 63 3.103911 CGTCGACTGCAACCCGAC 61.104 66.667 14.70 19.10 46.27 4.79
93 98 3.313750 CGTAGGAATGAGCTGCGC 58.686 61.111 0.00 0.00 0.00 6.09
94 99 2.580470 CGTAGGAATGAGCTGCGCG 61.580 63.158 0.00 0.00 0.00 6.86
95 100 2.106938 TAGGAATGAGCTGCGCGG 59.893 61.111 13.18 13.18 0.00 6.46
96 101 2.721167 TAGGAATGAGCTGCGCGGT 61.721 57.895 19.23 11.01 0.00 5.68
97 102 2.238847 TAGGAATGAGCTGCGCGGTT 62.239 55.000 19.23 12.78 0.00 4.44
98 103 2.690778 GGAATGAGCTGCGCGGTTT 61.691 57.895 19.23 6.59 0.00 3.27
99 104 1.226128 GAATGAGCTGCGCGGTTTC 60.226 57.895 19.23 16.01 0.00 2.78
100 105 1.911293 GAATGAGCTGCGCGGTTTCA 61.911 55.000 22.03 22.03 0.00 2.69
101 106 1.514678 AATGAGCTGCGCGGTTTCAA 61.515 50.000 23.09 7.82 0.00 2.69
102 107 1.308069 ATGAGCTGCGCGGTTTCAAT 61.308 50.000 23.09 9.53 0.00 2.57
103 108 1.210155 GAGCTGCGCGGTTTCAATT 59.790 52.632 19.23 0.00 0.00 2.32
104 109 0.446222 GAGCTGCGCGGTTTCAATTA 59.554 50.000 19.23 0.00 0.00 1.40
105 110 0.447801 AGCTGCGCGGTTTCAATTAG 59.552 50.000 19.23 0.00 0.00 1.73
224 229 1.064296 CGCGCTCTTCACCTATCGT 59.936 57.895 5.56 0.00 0.00 3.73
235 240 4.639135 TCACCTATCGTTGAGATGACAG 57.361 45.455 0.00 0.00 40.40 3.51
245 250 4.849926 CGTTGAGATGACAGAAATGCAAAG 59.150 41.667 0.00 0.00 0.00 2.77
250 255 6.093633 TGAGATGACAGAAATGCAAAGATCAG 59.906 38.462 0.00 0.00 0.00 2.90
251 256 5.357314 AGATGACAGAAATGCAAAGATCAGG 59.643 40.000 0.00 0.00 0.00 3.86
259 264 5.382618 AATGCAAAGATCAGGAAGAACAC 57.617 39.130 0.00 0.00 0.00 3.32
262 267 3.994392 GCAAAGATCAGGAAGAACACGTA 59.006 43.478 0.00 0.00 0.00 3.57
264 269 4.457834 AAGATCAGGAAGAACACGTAGG 57.542 45.455 0.00 0.00 0.00 3.18
274 279 3.187700 AGAACACGTAGGAATCGAATGC 58.812 45.455 0.00 0.00 0.00 3.56
281 286 5.234329 CACGTAGGAATCGAATGCTGTTTAT 59.766 40.000 4.56 0.00 0.00 1.40
316 326 2.927477 GCATCAATCAACATTGCCACAG 59.073 45.455 0.00 0.00 39.56 3.66
317 327 3.367600 GCATCAATCAACATTGCCACAGA 60.368 43.478 0.00 0.00 39.56 3.41
318 328 4.679639 GCATCAATCAACATTGCCACAGAT 60.680 41.667 0.00 0.00 39.56 2.90
319 329 4.707030 TCAATCAACATTGCCACAGATC 57.293 40.909 0.00 0.00 39.56 2.75
347 357 5.544136 AGCAAAACAAAAATGTGAACACC 57.456 34.783 2.46 0.00 0.00 4.16
353 363 5.248870 ACAAAAATGTGAACACCAGAGAC 57.751 39.130 2.46 0.00 0.00 3.36
354 364 4.097892 ACAAAAATGTGAACACCAGAGACC 59.902 41.667 2.46 0.00 0.00 3.85
355 365 3.576078 AAATGTGAACACCAGAGACCA 57.424 42.857 2.46 0.00 0.00 4.02
356 366 2.550830 ATGTGAACACCAGAGACCAC 57.449 50.000 2.46 0.00 0.00 4.16
392 402 2.048222 TTCTGTCTTCTGCCGGCG 60.048 61.111 23.90 16.91 0.00 6.46
393 403 4.742201 TCTGTCTTCTGCCGGCGC 62.742 66.667 23.90 0.00 0.00 6.53
627 637 2.919494 GCAAACCCAGCCCACGAAG 61.919 63.158 0.00 0.00 0.00 3.79
636 646 2.328099 GCCCACGAAGCAACCTCAG 61.328 63.158 0.00 0.00 0.00 3.35
637 647 1.371183 CCCACGAAGCAACCTCAGA 59.629 57.895 0.00 0.00 0.00 3.27
644 654 1.708993 AAGCAACCTCAGAGCCCACA 61.709 55.000 0.00 0.00 0.00 4.17
646 656 1.757306 CAACCTCAGAGCCCACACT 59.243 57.895 0.00 0.00 0.00 3.55
649 659 1.298014 CCTCAGAGCCCACACTTCC 59.702 63.158 0.00 0.00 0.00 3.46
650 660 1.298014 CTCAGAGCCCACACTTCCC 59.702 63.158 0.00 0.00 0.00 3.97
651 661 2.046892 CAGAGCCCACACTTCCCG 60.047 66.667 0.00 0.00 0.00 5.14
652 662 3.322466 AGAGCCCACACTTCCCGG 61.322 66.667 0.00 0.00 0.00 5.73
673 683 0.033642 GCCCGTTAGTCTAGCCCATC 59.966 60.000 0.00 0.00 0.00 3.51
814 825 1.559065 CCGGAGGCCAAACCCTAGAA 61.559 60.000 5.01 0.00 46.14 2.10
818 829 1.354705 GAGGCCAAACCCTAGAACCTT 59.645 52.381 5.01 0.00 40.58 3.50
829 840 1.651240 TAGAACCTTCGTCTCCGCCG 61.651 60.000 0.00 0.00 0.00 6.46
875 917 2.590092 GCCCGTGCCTGAGGTATT 59.410 61.111 0.00 0.00 0.00 1.89
890 932 1.054978 GTATTTCGCCCTCCCCTCCT 61.055 60.000 0.00 0.00 0.00 3.69
913 955 2.031163 GGCGAGATCGATTGGGGG 59.969 66.667 6.39 0.00 43.02 5.40
1018 1065 0.469917 GATGATCTGGCTTTCGGGGA 59.530 55.000 0.00 0.00 0.00 4.81
1031 1078 4.928520 GGGGATGGAGGGAGGGGG 62.929 77.778 0.00 0.00 0.00 5.40
1166 1225 4.021925 GTTGCAGGGCGAGGAGGT 62.022 66.667 0.00 0.00 0.00 3.85
1264 1323 1.026182 TGCTGAAGCCGGTAAGCATG 61.026 55.000 15.46 0.00 40.59 4.06
1295 1354 4.508662 CCAGACTCTGGTTAGTTTGATCC 58.491 47.826 16.18 0.00 45.82 3.36
1298 1357 4.020128 AGACTCTGGTTAGTTTGATCCACC 60.020 45.833 0.00 0.00 0.00 4.61
1343 1402 1.860950 CCTTCGACTTGTATGGCATCG 59.139 52.381 1.65 0.48 32.57 3.84
1528 1587 1.035385 TGCATCTGAGCTGGCATTGG 61.035 55.000 0.00 0.00 34.99 3.16
1629 1688 2.227388 GCCTTTCATGGACAACTGTCTG 59.773 50.000 9.60 1.85 44.20 3.51
1743 1802 4.472833 AGTTGCTCTTGTCTCCCAGAATAT 59.527 41.667 0.00 0.00 0.00 1.28
1759 1818 5.481105 CAGAATATCTCTCTGAGAATGGCC 58.519 45.833 8.95 0.00 42.27 5.36
1803 1862 0.741221 GGCTCAAGGCTGGAGTTACG 60.741 60.000 19.88 0.00 41.46 3.18
2016 2075 1.753141 GCATGGGCAGAGGATGTCATT 60.753 52.381 0.00 0.00 40.72 2.57
2027 2086 2.816087 AGGATGTCATTGACACAACTGC 59.184 45.455 21.19 11.02 45.65 4.40
2204 2263 4.588951 AGAGTGTGGTGAAGTTGACATCTA 59.411 41.667 0.00 0.00 0.00 1.98
2511 2570 2.417933 GACATGTGCACCTTCATCAGAC 59.582 50.000 15.69 0.00 0.00 3.51
2841 2900 3.467803 CTCTTTTGGACCTTCACTTCGT 58.532 45.455 0.00 0.00 0.00 3.85
2850 2909 2.798847 ACCTTCACTTCGTAGTTTTCGC 59.201 45.455 0.00 0.00 30.26 4.70
2905 2967 8.958119 TGAATTGAATTATCCTAAGTTACGCT 57.042 30.769 0.00 0.00 0.00 5.07
2914 2976 5.250235 TCCTAAGTTACGCTCTGAAGATG 57.750 43.478 0.00 0.00 0.00 2.90
2917 2979 3.238108 AGTTACGCTCTGAAGATGGTG 57.762 47.619 0.00 0.00 0.00 4.17
3047 3218 0.389948 GTAGGGTGTCTGGAGTTGCG 60.390 60.000 0.00 0.00 0.00 4.85
3067 3238 1.917273 CTGGATTCTGCGCAAATTGG 58.083 50.000 13.05 0.00 0.00 3.16
3074 3245 0.098552 CTGCGCAAATTGGCATCGTA 59.901 50.000 13.05 0.00 38.69 3.43
3102 3273 4.130118 AGCTGACAAAGGTGAAACTGTAG 58.870 43.478 0.00 0.00 34.56 2.74
3150 3321 1.251251 GGTCAAGCTTGCAGGACAAT 58.749 50.000 21.99 0.00 37.72 2.71
3354 3525 0.540923 AGAAGAGACCAGCATGCCTC 59.459 55.000 15.66 13.63 35.44 4.70
3355 3526 0.809241 GAAGAGACCAGCATGCCTCG 60.809 60.000 15.66 4.23 38.65 4.63
3391 3562 6.538742 GCTCAAGCTTTTACTGGATATGTACA 59.461 38.462 0.00 0.00 38.21 2.90
3589 3763 3.370231 GCGACGGCCCAATTTGGT 61.370 61.111 14.26 0.00 35.17 3.67
3590 3764 2.566010 CGACGGCCCAATTTGGTG 59.434 61.111 14.26 7.05 35.17 4.17
3591 3765 2.969827 GACGGCCCAATTTGGTGG 59.030 61.111 14.26 5.54 35.17 4.61
3592 3766 1.605165 GACGGCCCAATTTGGTGGA 60.605 57.895 14.26 0.00 41.65 4.02
3593 3767 1.873270 GACGGCCCAATTTGGTGGAC 61.873 60.000 14.26 1.25 41.65 4.02
3594 3768 1.905843 CGGCCCAATTTGGTGGACA 60.906 57.895 14.26 0.00 41.65 4.02
3595 3769 1.467678 CGGCCCAATTTGGTGGACAA 61.468 55.000 14.26 0.00 41.65 3.18
3596 3770 0.321346 GGCCCAATTTGGTGGACAAG 59.679 55.000 14.26 0.00 41.65 3.16
3600 3774 1.344114 CCAATTTGGTGGACAAGTGGG 59.656 52.381 7.31 0.00 41.65 4.61
3601 3775 2.038659 CAATTTGGTGGACAAGTGGGT 58.961 47.619 0.00 0.00 40.82 4.51
3602 3776 2.433970 CAATTTGGTGGACAAGTGGGTT 59.566 45.455 0.00 0.00 40.82 4.11
3603 3777 2.239681 TTTGGTGGACAAGTGGGTTT 57.760 45.000 0.00 0.00 40.82 3.27
3609 3785 1.202879 TGGACAAGTGGGTTTAGCTGG 60.203 52.381 0.00 0.00 0.00 4.85
3836 4013 7.042456 GCACAACTGATTACTCGAACATCATAT 60.042 37.037 2.26 0.00 0.00 1.78
3837 4014 8.483218 CACAACTGATTACTCGAACATCATATC 58.517 37.037 2.26 0.00 0.00 1.63
3930 4107 7.933577 ACTGATGTTTCTCTTGTCATTTGACTA 59.066 33.333 11.67 3.74 44.99 2.59
3969 4146 6.725834 ACCCATCACCAAGATAGTGAAAAATT 59.274 34.615 0.00 0.00 46.67 1.82
3996 4173 4.410099 TGAATTTCTGCCTGGTGAGAAAT 58.590 39.130 20.94 20.94 46.28 2.17
4012 4189 6.993308 GGTGAGAAATTAGGAAATACTCCCTC 59.007 42.308 0.00 0.00 46.81 4.30
4014 4191 6.909158 TGAGAAATTAGGAAATACTCCCTCCT 59.091 38.462 0.00 0.00 46.81 3.69
4020 4197 8.871570 ATTAGGAAATACTCCCTCCTTAAAGA 57.128 34.615 0.00 0.00 46.81 2.52
4022 4199 7.773099 AGGAAATACTCCCTCCTTAAAGAAT 57.227 36.000 0.00 0.00 46.81 2.40
4096 4301 3.449018 AGGTATGAGTCGCATCTCAAACT 59.551 43.478 11.01 7.49 45.65 2.66
4107 4312 3.594134 CATCTCAAACTGAGTGGACTCC 58.406 50.000 4.34 0.00 44.58 3.85
4122 4327 1.747355 GACTCCGGTTTCTCATCCGTA 59.253 52.381 0.00 0.00 44.51 4.02
4125 4330 3.568853 ACTCCGGTTTCTCATCCGTATAG 59.431 47.826 0.00 0.00 44.51 1.31
4269 4475 9.869757 GTAATAAAGGCATATCCAACTTTTTGT 57.130 29.630 0.00 0.00 37.29 2.83
4329 4537 3.386237 GCTCCACTGCCGTCTCCT 61.386 66.667 0.00 0.00 0.00 3.69
4344 4552 1.866997 TCCTCCCCTTCCTCTCCCA 60.867 63.158 0.00 0.00 0.00 4.37
4402 4612 1.738099 GCAGCGAGTCCGACATTGT 60.738 57.895 0.40 0.00 38.22 2.71
4462 4672 2.504244 GGACGAGGAGTTCACGCG 60.504 66.667 3.53 3.53 0.00 6.01
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
54 59 1.664321 AATCCTCCCGTCTTCGTCGG 61.664 60.000 0.00 0.00 46.49 4.79
88 93 2.222953 GGTACTAATTGAAACCGCGCAG 60.223 50.000 8.75 0.00 0.00 5.18
89 94 1.733360 GGTACTAATTGAAACCGCGCA 59.267 47.619 8.75 0.00 0.00 6.09
90 95 2.004733 AGGTACTAATTGAAACCGCGC 58.995 47.619 0.00 0.00 36.02 6.86
91 96 2.222953 GCAGGTACTAATTGAAACCGCG 60.223 50.000 0.00 0.00 36.02 6.46
92 97 3.007635 AGCAGGTACTAATTGAAACCGC 58.992 45.455 0.00 1.76 36.02 5.68
93 98 4.454504 ACAAGCAGGTACTAATTGAAACCG 59.545 41.667 0.00 0.00 36.02 4.44
94 99 5.705905 AGACAAGCAGGTACTAATTGAAACC 59.294 40.000 0.00 0.00 36.02 3.27
95 100 6.803154 AGACAAGCAGGTACTAATTGAAAC 57.197 37.500 0.00 0.00 36.02 2.78
96 101 6.430000 GGAAGACAAGCAGGTACTAATTGAAA 59.570 38.462 0.00 0.00 36.02 2.69
97 102 5.938125 GGAAGACAAGCAGGTACTAATTGAA 59.062 40.000 0.00 0.00 36.02 2.69
98 103 5.248477 AGGAAGACAAGCAGGTACTAATTGA 59.752 40.000 0.00 0.00 36.02 2.57
99 104 5.491982 AGGAAGACAAGCAGGTACTAATTG 58.508 41.667 0.00 0.00 36.02 2.32
100 105 5.763876 AGGAAGACAAGCAGGTACTAATT 57.236 39.130 0.00 0.00 36.02 1.40
101 106 5.485708 AGAAGGAAGACAAGCAGGTACTAAT 59.514 40.000 0.00 0.00 36.02 1.73
102 107 4.838986 AGAAGGAAGACAAGCAGGTACTAA 59.161 41.667 0.00 0.00 36.02 2.24
103 108 4.417437 AGAAGGAAGACAAGCAGGTACTA 58.583 43.478 0.00 0.00 36.02 1.82
104 109 3.243724 AGAAGGAAGACAAGCAGGTACT 58.756 45.455 0.00 0.00 43.88 2.73
105 110 3.591023 GAGAAGGAAGACAAGCAGGTAC 58.409 50.000 0.00 0.00 0.00 3.34
224 229 6.431852 TGATCTTTGCATTTCTGTCATCTCAA 59.568 34.615 0.00 0.00 0.00 3.02
235 240 5.860716 GTGTTCTTCCTGATCTTTGCATTTC 59.139 40.000 0.00 0.00 0.00 2.17
245 250 4.451629 TTCCTACGTGTTCTTCCTGATC 57.548 45.455 0.00 0.00 0.00 2.92
250 255 3.498927 TCGATTCCTACGTGTTCTTCC 57.501 47.619 0.00 0.00 0.00 3.46
251 256 4.259850 GCATTCGATTCCTACGTGTTCTTC 60.260 45.833 0.00 0.00 0.00 2.87
259 264 5.333339 CCATAAACAGCATTCGATTCCTACG 60.333 44.000 0.00 0.00 0.00 3.51
262 267 3.316308 GCCATAAACAGCATTCGATTCCT 59.684 43.478 0.00 0.00 0.00 3.36
264 269 4.285292 CTGCCATAAACAGCATTCGATTC 58.715 43.478 0.00 0.00 0.00 2.52
274 279 4.168760 GCTAGTTTTGCTGCCATAAACAG 58.831 43.478 18.06 14.68 34.93 3.16
281 286 1.908344 TGATGCTAGTTTTGCTGCCA 58.092 45.000 0.00 0.00 0.00 4.92
316 326 5.569059 ACATTTTTGTTTTGCTCGATCGATC 59.431 36.000 19.78 15.57 0.00 3.69
317 327 5.343058 CACATTTTTGTTTTGCTCGATCGAT 59.657 36.000 19.78 0.00 0.00 3.59
318 328 4.674662 CACATTTTTGTTTTGCTCGATCGA 59.325 37.500 18.32 18.32 0.00 3.59
319 329 4.674662 TCACATTTTTGTTTTGCTCGATCG 59.325 37.500 9.36 9.36 0.00 3.69
392 402 2.336809 CATAGAGGACGAGCCGGC 59.663 66.667 21.89 21.89 43.43 6.13
393 403 2.336809 GCATAGAGGACGAGCCGG 59.663 66.667 0.00 0.00 43.43 6.13
394 404 2.336809 GGCATAGAGGACGAGCCG 59.663 66.667 0.00 0.00 43.43 5.52
395 405 2.336809 CGGCATAGAGGACGAGCC 59.663 66.667 0.00 0.00 43.61 4.70
396 406 1.008309 GACGGCATAGAGGACGAGC 60.008 63.158 0.00 0.00 43.61 5.03
397 407 1.158484 TCGACGGCATAGAGGACGAG 61.158 60.000 0.00 0.00 43.61 4.18
401 411 1.660355 GCATCGACGGCATAGAGGA 59.340 57.895 6.06 0.00 0.00 3.71
614 624 3.365265 GTTGCTTCGTGGGCTGGG 61.365 66.667 0.00 0.00 0.00 4.45
627 637 1.968540 GTGTGGGCTCTGAGGTTGC 60.969 63.158 6.83 0.00 0.00 4.17
636 646 4.410400 CCCGGGAAGTGTGGGCTC 62.410 72.222 18.48 0.00 35.82 4.70
651 661 2.804912 GGCTAGACTAACGGGCCCC 61.805 68.421 18.66 0.00 35.96 5.80
652 662 2.804912 GGGCTAGACTAACGGGCCC 61.805 68.421 13.57 13.57 46.55 5.80
665 675 2.923035 GCCGGGCTAGATGGGCTA 60.923 66.667 12.87 0.00 42.29 3.93
913 955 3.240631 GCGCAAATTAAAGCCTCGAAATC 59.759 43.478 0.30 0.00 0.00 2.17
1186 1245 1.525619 GTCGGCGGCAATATTCTGTAC 59.474 52.381 6.63 0.00 0.00 2.90
1295 1354 1.285641 GTGGAACCAACATGCGGTG 59.714 57.895 8.12 0.00 36.67 4.94
1343 1402 4.666928 TTACAAAAACCGATTAGTCCGC 57.333 40.909 0.00 0.00 0.00 5.54
1528 1587 0.254178 TGGCCCTCTTTCTGATGCTC 59.746 55.000 0.00 0.00 0.00 4.26
1629 1688 2.496899 TGCCTTGTTTCTCCATCTCC 57.503 50.000 0.00 0.00 0.00 3.71
1743 1802 1.829849 CACAGGCCATTCTCAGAGAGA 59.170 52.381 5.01 0.00 36.86 3.10
1759 1818 2.093306 TTCCCACGCAGATAACACAG 57.907 50.000 0.00 0.00 0.00 3.66
1803 1862 2.027100 AGCCTGGTTAACCTTAGAGCAC 60.027 50.000 24.78 8.97 36.82 4.40
2012 2071 1.317613 GGTGGCAGTTGTGTCAATGA 58.682 50.000 0.00 0.00 40.92 2.57
2016 2075 1.031235 CATTGGTGGCAGTTGTGTCA 58.969 50.000 0.00 0.00 35.32 3.58
2027 2086 0.896940 AGGCTGCACTTCATTGGTGG 60.897 55.000 0.50 0.00 35.47 4.61
2204 2263 3.243975 CCTTTTTGCTGGCTTCTTCACAT 60.244 43.478 0.00 0.00 0.00 3.21
2511 2570 4.576330 ATTCTGTACAGGGGAAGAAAGG 57.424 45.455 22.48 0.00 32.72 3.11
2595 2654 1.967779 TGGACCATCTTCTCGTCAACA 59.032 47.619 0.00 0.00 0.00 3.33
2850 2909 4.037208 AGAGAAAATGGCATATTCGCAAGG 59.963 41.667 0.00 0.00 38.47 3.61
2905 2967 1.211212 CTCCATGCCACCATCTTCAGA 59.789 52.381 0.00 0.00 0.00 3.27
2914 2976 0.466922 CCAGGAATCTCCATGCCACC 60.467 60.000 0.00 0.00 39.61 4.61
2917 2979 2.952310 GTTTACCAGGAATCTCCATGCC 59.048 50.000 0.00 0.00 39.61 4.40
3020 3191 4.215908 CTCCAGACACCCTACAAGCTATA 58.784 47.826 0.00 0.00 0.00 1.31
3021 3192 3.034635 CTCCAGACACCCTACAAGCTAT 58.965 50.000 0.00 0.00 0.00 2.97
3022 3193 2.225293 ACTCCAGACACCCTACAAGCTA 60.225 50.000 0.00 0.00 0.00 3.32
3047 3218 1.274596 CAATTTGCGCAGAATCCAGC 58.725 50.000 11.31 0.00 0.00 4.85
3067 3238 2.337583 TGTCAGCTTTGTCTACGATGC 58.662 47.619 0.00 0.99 0.00 3.91
3074 3245 3.281727 TCACCTTTGTCAGCTTTGTCT 57.718 42.857 0.00 0.00 0.00 3.41
3102 3273 3.191371 GTGTGTTCAACTGATGGATTCCC 59.809 47.826 0.00 0.00 0.00 3.97
3150 3321 1.411246 ACGCTCGGTATTGCCTTCATA 59.589 47.619 0.00 0.00 34.25 2.15
3341 3512 3.785859 TCCCGAGGCATGCTGGTC 61.786 66.667 18.92 11.05 0.00 4.02
3344 3515 3.790437 AGGTCCCGAGGCATGCTG 61.790 66.667 18.92 7.88 0.00 4.41
3354 3525 1.515020 CTTGAGCTCTCAGGTCCCG 59.485 63.158 16.19 0.00 41.77 5.14
3355 3526 1.220477 GCTTGAGCTCTCAGGTCCC 59.780 63.158 16.19 0.00 41.77 4.46
3391 3562 2.176798 TCATCCCCCACAGACTGTTTTT 59.823 45.455 5.04 0.00 0.00 1.94
3584 3758 2.239681 AAACCCACTTGTCCACCAAA 57.760 45.000 0.00 0.00 31.20 3.28
3586 3760 1.477923 GCTAAACCCACTTGTCCACCA 60.478 52.381 0.00 0.00 0.00 4.17
3587 3761 1.202891 AGCTAAACCCACTTGTCCACC 60.203 52.381 0.00 0.00 0.00 4.61
3588 3762 1.880027 CAGCTAAACCCACTTGTCCAC 59.120 52.381 0.00 0.00 0.00 4.02
3589 3763 1.202879 CCAGCTAAACCCACTTGTCCA 60.203 52.381 0.00 0.00 0.00 4.02
3590 3764 1.534729 CCAGCTAAACCCACTTGTCC 58.465 55.000 0.00 0.00 0.00 4.02
3591 3765 0.881796 GCCAGCTAAACCCACTTGTC 59.118 55.000 0.00 0.00 0.00 3.18
3592 3766 0.539669 GGCCAGCTAAACCCACTTGT 60.540 55.000 0.00 0.00 0.00 3.16
3593 3767 1.586154 CGGCCAGCTAAACCCACTTG 61.586 60.000 2.24 0.00 0.00 3.16
3594 3768 1.303317 CGGCCAGCTAAACCCACTT 60.303 57.895 2.24 0.00 0.00 3.16
3595 3769 1.774894 TTCGGCCAGCTAAACCCACT 61.775 55.000 2.24 0.00 0.00 4.00
3596 3770 1.302993 TTCGGCCAGCTAAACCCAC 60.303 57.895 2.24 0.00 0.00 4.61
3600 3774 4.390048 TGGTTCGGCCAGCTAAAC 57.610 55.556 2.24 0.00 43.61 2.01
3609 3785 3.877508 AGTTCAATATAAGCTGGTTCGGC 59.122 43.478 0.00 0.00 35.73 5.54
3836 4013 1.184970 TCCACTGATCACTGCACCGA 61.185 55.000 0.00 0.00 0.00 4.69
3837 4014 0.738762 CTCCACTGATCACTGCACCG 60.739 60.000 0.00 0.00 0.00 4.94
3930 4107 4.566907 GGTGATGGGTAAACACTACATGGT 60.567 45.833 0.00 0.00 35.28 3.55
3969 4146 5.104402 TCTCACCAGGCAGAAATTCATGATA 60.104 40.000 0.00 0.00 0.00 2.15
3996 4173 8.689707 TTCTTTAAGGAGGGAGTATTTCCTAA 57.310 34.615 0.00 0.00 45.98 2.69
4026 4203 7.571428 GCAAAACTTAGTGATCTAAACGCTCTT 60.571 37.037 0.00 0.00 35.98 2.85
4030 4207 5.928153 AGCAAAACTTAGTGATCTAAACGC 58.072 37.500 0.00 0.00 35.98 4.84
4044 4221 8.546597 ACAATAAACAAACAGAAGCAAAACTT 57.453 26.923 0.00 0.00 42.98 2.66
4096 4301 0.966920 GAGAAACCGGAGTCCACTCA 59.033 55.000 9.46 0.00 44.60 3.41
4122 4327 7.147846 CCATTGCACCCAAAGAATTTAGACTAT 60.148 37.037 0.00 0.00 35.03 2.12
4125 4330 5.170748 CCATTGCACCCAAAGAATTTAGAC 58.829 41.667 0.00 0.00 35.03 2.59
4282 4490 4.396790 GTCGAGAGAGTGAGGTTTGAGTAT 59.603 45.833 0.00 0.00 43.49 2.12
4285 4493 2.094957 GGTCGAGAGAGTGAGGTTTGAG 60.095 54.545 0.00 0.00 43.49 3.02
4323 4531 0.397957 GGAGAGGAAGGGGAGGAGAC 60.398 65.000 0.00 0.00 0.00 3.36
4329 4537 2.041265 GCTGGGAGAGGAAGGGGA 59.959 66.667 0.00 0.00 0.00 4.81
4344 4552 3.293379 AGGGGTGGGTAGAGGGCT 61.293 66.667 0.00 0.00 0.00 5.19
4442 4652 1.801332 CGTGAACTCCTCGTCCGAT 59.199 57.895 0.00 0.00 0.00 4.18


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

AutoCloner maintained by Alex Coulton.