Multiple sequence alignment - TraesCS7D01G252200

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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 TraesCS7D01G252200 chr7D 100.000 6125 0 0 1 6125 227175655 227169531 0.000000e+00 11311.0
1 TraesCS7D01G252200 chr7D 87.324 71 8 1 5881 5951 591219241 591219310 5.090000e-11 80.5
2 TraesCS7D01G252200 chr7B 96.759 2900 62 5 1975 4850 198941250 198938359 0.000000e+00 4806.0
3 TraesCS7D01G252200 chr7B 94.064 1988 103 12 1 1977 198943429 198941446 0.000000e+00 3003.0
4 TraesCS7D01G252200 chr7B 91.633 741 21 14 4846 5551 198938311 198937577 0.000000e+00 987.0
5 TraesCS7D01G252200 chr7B 88.172 372 17 7 5565 5936 198936017 198935673 9.500000e-113 418.0
6 TraesCS7D01G252200 chr7B 90.058 171 8 4 5960 6125 198935567 198935401 4.810000e-51 213.0
7 TraesCS7D01G252200 chr7B 91.304 46 4 0 5931 5976 198935626 198935581 5.130000e-06 63.9
8 TraesCS7D01G252200 chr7A 97.376 2172 48 5 2613 4775 239037183 239035012 0.000000e+00 3687.0
9 TraesCS7D01G252200 chr7A 94.679 1729 62 11 850 2567 239039187 239037478 0.000000e+00 2656.0
10 TraesCS7D01G252200 chr7A 91.029 758 51 11 11 755 239040397 239039644 0.000000e+00 1007.0
11 TraesCS7D01G252200 chr7A 88.227 739 27 14 4846 5551 239034986 239034275 0.000000e+00 828.0
12 TraesCS7D01G252200 chr7A 87.742 310 33 4 5552 5858 239034013 239033706 2.100000e-94 357.0
13 TraesCS7D01G252200 chr7A 89.759 166 5 5 2445 2609 239037477 239037323 1.040000e-47 202.0


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 TraesCS7D01G252200 chr7D 227169531 227175655 6124 True 11311.000000 11311 100.000000 1 6125 1 chr7D.!!$R1 6124
1 TraesCS7D01G252200 chr7B 198935401 198943429 8028 True 1581.816667 4806 91.998333 1 6125 6 chr7B.!!$R1 6124
2 TraesCS7D01G252200 chr7A 239033706 239040397 6691 True 1456.166667 3687 91.468667 11 5858 6 chr7A.!!$R1 5847

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
208 210 0.249120 AGGGTGCATCGATGAAACGA 59.751 50.000 29.20 3.65 46.04 3.85 F
759 773 1.378250 CCCCCAGCTCAAGCAAGAG 60.378 63.158 4.59 1.40 45.16 2.85 F
808 822 1.452108 GCGAATTCACCTCCCCCTG 60.452 63.158 6.22 0.00 0.00 4.45 F
978 1354 1.878522 CGAGGGAGTCCAATTCGCG 60.879 63.158 12.30 0.00 34.83 5.87 F
982 1358 2.032634 GGAGTCCAATTCGCGTGCA 61.033 57.895 5.77 0.00 0.00 4.57 F
1233 1609 2.202987 CCTGCTTAGCTGGCTCGG 60.203 66.667 16.82 10.12 40.48 4.63 F
1787 2167 2.287915 ACAAACACTTGCGTGATCACTC 59.712 45.455 22.95 16.27 43.97 3.51 F
3167 4001 1.863267 CTATTGAAGCCTCCTCAGCG 58.137 55.000 0.00 0.00 34.64 5.18 F
4000 4834 1.016653 GTGAGTTCCGCAGAGCCTTC 61.017 60.000 0.00 0.00 0.00 3.46 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1312 1688 1.026182 TTAGCAGCCGGTGATTGCAG 61.026 55.000 19.36 0.00 40.22 4.41 R
2170 2754 2.027745 CCCAGCTACTCTCTGCAGAAAA 60.028 50.000 18.85 8.06 0.00 2.29 R
2405 2989 2.978156 AAGCCAACCAGATTCCTTGA 57.022 45.000 0.00 0.00 0.00 3.02 R
2704 3538 3.572632 ATAGCTCATGCATTCCTGTGT 57.427 42.857 0.00 0.00 42.74 3.72 R
2918 3752 4.159321 TCATCAAGACTGTTAGCTCTGGAG 59.841 45.833 0.00 0.00 0.00 3.86 R
3167 4001 9.585099 TCAACAATGGAAAGCAAATGATATAAC 57.415 29.630 0.00 0.00 0.00 1.89 R
3742 4576 3.072915 TCTGCTGAAAGAATGACCCTTCA 59.927 43.478 0.00 0.00 34.07 3.02 R
4986 5895 1.226128 GCGATCTTGCTGAAACGCC 60.226 57.895 16.62 6.51 43.23 5.68 R
5174 6083 0.685785 TGCTGAGCTAGAGAGGGGTG 60.686 60.000 5.83 0.00 0.00 4.61 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
32 33 0.804989 CCTTCGACCAACCATTGCTC 59.195 55.000 0.00 0.00 0.00 4.26
45 46 5.629079 ACCATTGCTCTAACAAACTTAGC 57.371 39.130 0.00 0.00 32.27 3.09
64 66 8.894768 ACTTAGCATTATCATCTTACTTCACC 57.105 34.615 0.00 0.00 0.00 4.02
69 71 9.247861 AGCATTATCATCTTACTTCACCTTTTT 57.752 29.630 0.00 0.00 0.00 1.94
96 98 0.953471 TCCTCAAACCGTGAATGGCG 60.953 55.000 0.00 0.00 35.22 5.69
97 99 1.154225 CTCAAACCGTGAATGGCGC 60.154 57.895 0.00 0.00 35.22 6.53
98 100 1.577328 CTCAAACCGTGAATGGCGCT 61.577 55.000 7.64 0.00 35.22 5.92
99 101 0.320858 TCAAACCGTGAATGGCGCTA 60.321 50.000 7.64 0.00 31.51 4.26
117 119 2.699954 CTACAATCGCCACTTTCCACT 58.300 47.619 0.00 0.00 0.00 4.00
125 127 4.693283 TCGCCACTTTCCACTATGATTAG 58.307 43.478 0.00 0.00 0.00 1.73
132 134 3.961480 TCCACTATGATTAGCATCCGG 57.039 47.619 0.00 0.00 38.44 5.14
153 155 4.377021 GGCGGACTAATTGATACATGTCA 58.623 43.478 0.00 0.00 0.00 3.58
196 198 0.466555 AACGGCTAAACAAGGGTGCA 60.467 50.000 0.00 0.00 0.00 4.57
208 210 0.249120 AGGGTGCATCGATGAAACGA 59.751 50.000 29.20 3.65 46.04 3.85
226 228 3.549574 ACGAAACGACGAGTAAAGAGAC 58.450 45.455 0.00 0.00 37.03 3.36
275 277 2.805277 CGGTATCCGTATGGCGTTC 58.195 57.895 0.00 0.00 42.73 3.95
314 317 4.142687 CCGTTCCATCAAAATAGACCACAC 60.143 45.833 0.00 0.00 0.00 3.82
318 321 5.380900 TCCATCAAAATAGACCACACAACA 58.619 37.500 0.00 0.00 0.00 3.33
321 324 6.983307 CCATCAAAATAGACCACACAACAAAA 59.017 34.615 0.00 0.00 0.00 2.44
328 331 2.685897 GACCACACAACAAAAGGTAGCA 59.314 45.455 0.00 0.00 31.57 3.49
331 334 3.105203 CACACAACAAAAGGTAGCAACG 58.895 45.455 0.00 0.00 0.00 4.10
334 337 2.031191 ACAACAAAAGGTAGCAACGACG 59.969 45.455 0.00 0.00 0.00 5.12
424 427 6.530181 CCAAGCACCGATATTTCCTTTAAAAC 59.470 38.462 0.00 0.00 0.00 2.43
426 429 5.032220 GCACCGATATTTCCTTTAAAACCG 58.968 41.667 0.00 0.00 0.00 4.44
544 548 4.271807 TCCATCACCTCTCTCTTACCAT 57.728 45.455 0.00 0.00 0.00 3.55
600 607 7.461749 ACCTCTTCTATAGATTCTCTCTCCTG 58.538 42.308 2.58 0.00 35.28 3.86
694 702 3.344176 CTAACCCACCCCACCCCC 61.344 72.222 0.00 0.00 0.00 5.40
756 770 2.759114 CTCCCCCAGCTCAAGCAA 59.241 61.111 4.59 0.00 45.16 3.91
759 773 1.378250 CCCCCAGCTCAAGCAAGAG 60.378 63.158 4.59 1.40 45.16 2.85
777 791 2.047274 CGCCATTCCCGCGGATAT 60.047 61.111 30.73 16.71 45.80 1.63
791 805 2.425668 GCGGATATAGAAGAGGAGAGGC 59.574 54.545 0.00 0.00 0.00 4.70
808 822 1.452108 GCGAATTCACCTCCCCCTG 60.452 63.158 6.22 0.00 0.00 4.45
817 831 2.443016 CTCCCCCTGACCTCTCCG 60.443 72.222 0.00 0.00 0.00 4.63
848 1224 5.452341 AATCCTCCGAAAACCTAATCCTT 57.548 39.130 0.00 0.00 0.00 3.36
941 1317 2.668550 ACGTTTCTTGGCCTCCGC 60.669 61.111 3.32 0.00 0.00 5.54
978 1354 1.878522 CGAGGGAGTCCAATTCGCG 60.879 63.158 12.30 0.00 34.83 5.87
982 1358 2.032634 GGAGTCCAATTCGCGTGCA 61.033 57.895 5.77 0.00 0.00 4.57
1233 1609 2.202987 CCTGCTTAGCTGGCTCGG 60.203 66.667 16.82 10.12 40.48 4.63
1234 1610 2.894387 CTGCTTAGCTGGCTCGGC 60.894 66.667 5.60 5.65 35.73 5.54
1235 1611 4.819761 TGCTTAGCTGGCTCGGCG 62.820 66.667 5.60 0.00 41.21 6.46
1483 1860 8.486210 AGATTGGTGCTGTTACTGATCTATAAA 58.514 33.333 0.00 0.00 0.00 1.40
1532 1909 7.565680 TCCTTGCTATTTCTTTCTACCTAAGG 58.434 38.462 0.00 0.00 33.02 2.69
1545 1922 9.838339 CTTTCTACCTAAGGATGACATGTTTAT 57.162 33.333 0.00 0.00 0.00 1.40
1550 1927 8.650143 ACCTAAGGATGACATGTTTATTTTGT 57.350 30.769 0.00 0.00 0.00 2.83
1557 1934 8.170553 GGATGACATGTTTATTTTGTTTCATGC 58.829 33.333 0.00 0.00 36.96 4.06
1710 2087 7.480810 ACATGATCTTGTGAATTGTGATGATG 58.519 34.615 13.08 0.00 35.77 3.07
1733 2110 6.987386 TGACATGGTAAACAAATTACAAGGG 58.013 36.000 0.00 0.00 44.77 3.95
1787 2167 2.287915 ACAAACACTTGCGTGATCACTC 59.712 45.455 22.95 16.27 43.97 3.51
1886 2266 3.565482 AGTGGTGCTTGACAAGTGTTATG 59.435 43.478 16.39 0.00 0.00 1.90
2054 2638 5.009911 TGTGAATAGCTTGCTCACACAAAAT 59.990 36.000 16.78 0.00 43.36 1.82
2073 2657 8.891671 ACAAAATTGTGCACTTTTTCTATGAT 57.108 26.923 19.41 0.00 40.49 2.45
2074 2658 8.767085 ACAAAATTGTGCACTTTTTCTATGATG 58.233 29.630 19.41 12.66 40.49 3.07
2075 2659 8.980610 CAAAATTGTGCACTTTTTCTATGATGA 58.019 29.630 19.41 0.00 0.00 2.92
2076 2660 9.715121 AAAATTGTGCACTTTTTCTATGATGAT 57.285 25.926 19.41 0.00 0.00 2.45
2128 2712 3.073678 TGCTTGATACTTTGTGCGACAT 58.926 40.909 0.00 0.00 0.00 3.06
2405 2989 8.360390 AGAAGAAACAAAGTTCTCAAGTTGTTT 58.640 29.630 11.87 11.87 36.84 2.83
2429 3013 2.646798 AGGAATCTGGTTGGCTTTCTCT 59.353 45.455 0.00 0.00 0.00 3.10
2503 3087 5.117584 TGCACGAGACTAAGTTGGTAAAAA 58.882 37.500 0.00 0.00 0.00 1.94
2592 3290 7.041235 GCTTTGAGATCTCTTAATAGCAATGCT 60.041 37.037 22.95 13.92 43.41 3.79
2684 3518 6.572519 TCTTGTTTAATTGCTGAATATGGCC 58.427 36.000 0.00 0.00 0.00 5.36
2704 3538 3.495629 GCCTGACATATGGCTCATCTTGA 60.496 47.826 10.60 0.00 45.26 3.02
2918 3752 6.647895 ACAATGAAAATGATTCTGAAAGTGCC 59.352 34.615 0.00 0.00 33.76 5.01
3167 4001 1.863267 CTATTGAAGCCTCCTCAGCG 58.137 55.000 0.00 0.00 34.64 5.18
3306 4140 3.632604 CGGCCTCAGTGATCTCTTAGTAA 59.367 47.826 0.00 0.00 0.00 2.24
3356 4190 7.872993 TCCAATAGTATGCTGCTAAATAGTGAC 59.127 37.037 0.00 0.00 0.00 3.67
3636 4470 8.688151 AGTATGACAGAGTTAACAGTATTCTCC 58.312 37.037 8.61 0.00 0.00 3.71
3791 4625 7.781324 AATAAAGAAATCCTTGAGGCAGAAA 57.219 32.000 0.00 0.00 34.79 2.52
4000 4834 1.016653 GTGAGTTCCGCAGAGCCTTC 61.017 60.000 0.00 0.00 0.00 3.46
4076 4910 3.454858 ACTCAGCCCTCTAGAAAATCCA 58.545 45.455 0.00 0.00 0.00 3.41
4101 4935 1.078637 GTGCCAGCTGATGAGAGCA 60.079 57.895 17.39 12.35 41.83 4.26
4111 4945 3.057736 GCTGATGAGAGCACAACACAAAT 60.058 43.478 0.00 0.00 38.95 2.32
4307 5141 5.071384 TGAGTCATCCAGCTGTAATCATGAT 59.929 40.000 13.81 1.18 0.00 2.45
4651 5485 6.653020 TCCAGGTATATCATATGCAACATCC 58.347 40.000 0.00 0.00 0.00 3.51
4675 5518 7.229907 TCCTTTTGTGATACTTTTTGGTAGTCC 59.770 37.037 0.00 0.00 0.00 3.85
4782 5625 8.134202 TCTGAAGTCATTAGTGAAATACTCCA 57.866 34.615 0.00 0.00 40.89 3.86
4788 5631 7.287005 AGTCATTAGTGAAATACTCCATCCGTA 59.713 37.037 0.00 0.00 40.89 4.02
4794 5637 6.986817 AGTGAAATACTCCATCCGTATCAAAG 59.013 38.462 0.00 0.00 33.17 2.77
4801 5644 7.834881 ACTCCATCCGTATCAAAGTATAAGA 57.165 36.000 0.00 0.00 0.00 2.10
4879 5774 9.630098 CACAATTGTTCTGTATCTTTATTTGCT 57.370 29.630 8.77 0.00 0.00 3.91
4926 5829 6.218108 TCATGCCTATCTATGCATCACTAG 57.782 41.667 0.19 2.45 45.98 2.57
4986 5895 7.201359 GCAATGTAATTATAGGTGATCGAGTCG 60.201 40.741 6.09 6.09 32.46 4.18
5034 5943 0.537188 GCCCGATGGAGAACTTCTCA 59.463 55.000 18.56 7.13 45.12 3.27
5067 5976 1.966451 CGGCAAAGGACAGGTGACC 60.966 63.158 0.00 0.00 0.00 4.02
5070 5979 1.227823 CAAAGGACAGGTGACCGCA 60.228 57.895 0.00 0.00 35.05 5.69
5073 5982 2.668550 GGACAGGTGACCGCAACC 60.669 66.667 0.00 0.00 29.70 3.77
5171 6080 2.429930 CCGTCTGTTCCTGCCCAA 59.570 61.111 0.00 0.00 0.00 4.12
5172 6081 1.966451 CCGTCTGTTCCTGCCCAAC 60.966 63.158 0.00 0.00 0.00 3.77
5173 6082 1.966451 CGTCTGTTCCTGCCCAACC 60.966 63.158 0.00 0.00 0.00 3.77
5174 6083 1.603739 GTCTGTTCCTGCCCAACCC 60.604 63.158 0.00 0.00 0.00 4.11
5289 6214 9.823647 CTCCATATGTACATATAGGTTCCATTC 57.176 37.037 24.50 0.00 33.01 2.67
5292 6217 9.521503 CATATGTACATATAGGTTCCATTCGAG 57.478 37.037 24.50 6.81 33.01 4.04
5293 6218 6.971726 TGTACATATAGGTTCCATTCGAGT 57.028 37.500 0.00 0.00 0.00 4.18
5294 6219 6.978338 TGTACATATAGGTTCCATTCGAGTC 58.022 40.000 0.00 0.00 0.00 3.36
5360 6301 3.632333 ACTCCGATCAATCTAGGTGTCA 58.368 45.455 0.00 0.00 0.00 3.58
5389 6330 2.157738 ACGAGGCAGTAGTTTACGTCT 58.842 47.619 0.00 0.00 0.00 4.18
5516 6458 0.587768 TGTTGACGCATGTGCTGAAG 59.412 50.000 6.08 0.00 39.32 3.02
5629 8117 2.606519 TGGTCCAACGGAGGAGGG 60.607 66.667 0.00 0.00 38.64 4.30
5729 8220 5.073311 TGACCTTGACTACACAAGATAGC 57.927 43.478 9.55 0.00 46.85 2.97
5742 8233 3.187227 ACAAGATAGCGCAGTTTCAGTTG 59.813 43.478 11.47 4.55 0.00 3.16
5811 8302 3.429410 GCTAAACAGAATGAATGGTGCCC 60.429 47.826 0.00 0.00 39.69 5.36
5859 8350 8.603898 TCTCTCTATTCCAAACATAAGGTGTA 57.396 34.615 0.00 0.00 41.14 2.90
5860 8351 9.213777 TCTCTCTATTCCAAACATAAGGTGTAT 57.786 33.333 0.00 0.00 41.14 2.29
5861 8352 9.838339 CTCTCTATTCCAAACATAAGGTGTATT 57.162 33.333 0.00 0.00 41.14 1.89
5867 8358 9.975218 ATTCCAAACATAAGGTGTATTAGTCTT 57.025 29.630 0.00 0.00 41.14 3.01
5868 8359 9.802039 TTCCAAACATAAGGTGTATTAGTCTTT 57.198 29.630 0.00 0.00 41.14 2.52
5869 8360 9.802039 TCCAAACATAAGGTGTATTAGTCTTTT 57.198 29.630 0.00 0.00 41.14 2.27
5920 8411 9.083422 TGAACATCTCCAATACCAAATAAACAA 57.917 29.630 0.00 0.00 0.00 2.83
5966 8509 5.877031 TGAATCTAGCGATACGTATTAGGC 58.123 41.667 9.92 13.26 0.00 3.93
5970 8513 6.263516 TCTAGCGATACGTATTAGGCATTT 57.736 37.500 21.43 9.68 0.00 2.32
5972 8515 7.149973 TCTAGCGATACGTATTAGGCATTTTT 58.850 34.615 21.43 9.17 0.00 1.94
6035 8609 7.769044 AGAGCAGTTTGACTTCTGTAAAGTTAA 59.231 33.333 0.00 0.00 34.57 2.01
6039 8613 7.908601 CAGTTTGACTTCTGTAAAGTTAACACC 59.091 37.037 8.61 0.00 32.42 4.16
6072 8650 6.721571 TTGGAACAGAGTATTTCTTTAGCG 57.278 37.500 0.00 0.00 42.39 4.26
6074 8652 4.259850 GGAACAGAGTATTTCTTTAGCGCG 60.260 45.833 0.00 0.00 32.41 6.86
6094 8672 3.729762 GCGGAAAAGAAAGACACGTTGTT 60.730 43.478 0.00 0.00 0.00 2.83
6095 8673 3.783943 CGGAAAAGAAAGACACGTTGTTG 59.216 43.478 0.00 0.00 0.00 3.33
6096 8674 4.670735 CGGAAAAGAAAGACACGTTGTTGT 60.671 41.667 0.00 0.00 0.00 3.32
6122 8700 4.743493 ACATGGTGCAATCGTAAAAATCC 58.257 39.130 0.00 0.00 0.00 3.01
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
7 8 2.259266 TGGTTGGTCGAAGGGTTAAC 57.741 50.000 0.00 0.00 0.00 2.01
9 10 2.785562 CAATGGTTGGTCGAAGGGTTA 58.214 47.619 0.00 0.00 0.00 2.85
75 77 1.165270 CCATTCACGGTTTGAGGACC 58.835 55.000 0.00 0.00 34.94 4.46
96 98 1.130561 GTGGAAAGTGGCGATTGTAGC 59.869 52.381 0.00 0.00 0.00 3.58
97 99 2.699954 AGTGGAAAGTGGCGATTGTAG 58.300 47.619 0.00 0.00 0.00 2.74
98 100 2.851263 AGTGGAAAGTGGCGATTGTA 57.149 45.000 0.00 0.00 0.00 2.41
99 101 2.851263 TAGTGGAAAGTGGCGATTGT 57.149 45.000 0.00 0.00 0.00 2.71
117 119 1.067142 GTCCGCCGGATGCTAATCATA 60.067 52.381 10.04 0.00 38.05 2.15
125 127 0.531974 TCAATTAGTCCGCCGGATGC 60.532 55.000 10.04 0.00 32.73 3.91
132 134 5.984233 TTGACATGTATCAATTAGTCCGC 57.016 39.130 0.00 0.00 33.62 5.54
153 155 5.099042 AGGTTTACGGCTGAGTATGATTT 57.901 39.130 0.00 0.00 0.00 2.17
160 162 2.680577 CGTTTAGGTTTACGGCTGAGT 58.319 47.619 0.00 0.00 34.30 3.41
184 186 2.198827 TCATCGATGCACCCTTGTTT 57.801 45.000 20.81 0.00 0.00 2.83
196 198 2.587956 TCGTCGTTTCGTTTCATCGAT 58.412 42.857 0.00 0.00 39.57 3.59
208 210 3.567164 TCCTGTCTCTTTACTCGTCGTTT 59.433 43.478 0.00 0.00 0.00 3.60
226 228 1.019673 AGCATTGCACGCTATTCCTG 58.980 50.000 11.91 0.00 38.15 3.86
265 267 9.434559 GTTAAATAATGAAAGAGAACGCCATAC 57.565 33.333 0.00 0.00 0.00 2.39
268 270 6.402766 CGGTTAAATAATGAAAGAGAACGCCA 60.403 38.462 0.00 0.00 0.00 5.69
275 277 8.673711 TGATGGAACGGTTAAATAATGAAAGAG 58.326 33.333 0.00 0.00 0.00 2.85
314 317 2.031191 ACGTCGTTGCTACCTTTTGTTG 59.969 45.455 0.00 0.00 0.00 3.33
318 321 2.228138 TGACGTCGTTGCTACCTTTT 57.772 45.000 11.62 0.00 0.00 2.27
321 324 1.174783 AGATGACGTCGTTGCTACCT 58.825 50.000 12.40 0.00 0.00 3.08
328 331 1.000955 AGGAGCAAAGATGACGTCGTT 59.999 47.619 12.40 0.37 0.00 3.85
331 334 2.003301 GGAAGGAGCAAAGATGACGTC 58.997 52.381 9.11 9.11 0.00 4.34
334 337 3.055530 TGAGAGGAAGGAGCAAAGATGAC 60.056 47.826 0.00 0.00 0.00 3.06
544 548 2.833943 TGTTCTCTATTGGCAGAGCAGA 59.166 45.455 0.00 0.00 41.61 4.26
694 702 0.693767 ATGCTTGGAGGAGAGGGAGG 60.694 60.000 0.00 0.00 0.00 4.30
777 791 3.381908 GTGAATTCGCCTCTCCTCTTCTA 59.618 47.826 7.83 0.00 0.00 2.10
791 805 0.107654 GTCAGGGGGAGGTGAATTCG 60.108 60.000 0.04 0.00 0.00 3.34
808 822 1.486145 TTTTGGGGGACGGAGAGGTC 61.486 60.000 0.00 0.00 36.18 3.85
817 831 0.330267 TTCGGAGGATTTTGGGGGAC 59.670 55.000 0.00 0.00 0.00 4.46
936 1312 1.101049 AACAACAACCCACAGCGGAG 61.101 55.000 0.00 0.00 36.56 4.63
941 1317 4.320202 CCTCGAATTAACAACAACCCACAG 60.320 45.833 0.00 0.00 0.00 3.66
978 1354 2.991540 GGGCCCCTTCAGTTGCAC 60.992 66.667 12.23 0.00 0.00 4.57
1233 1609 2.566952 AATGAAAGCCATAACAGCGC 57.433 45.000 0.00 0.00 34.45 5.92
1234 1610 4.095410 TCAAATGAAAGCCATAACAGCG 57.905 40.909 0.00 0.00 34.45 5.18
1235 1611 6.335777 AGAATCAAATGAAAGCCATAACAGC 58.664 36.000 0.00 0.00 34.45 4.40
1236 1612 7.201496 GCAAGAATCAAATGAAAGCCATAACAG 60.201 37.037 0.00 0.00 34.45 3.16
1312 1688 1.026182 TTAGCAGCCGGTGATTGCAG 61.026 55.000 19.36 0.00 40.22 4.41
1339 1715 6.662865 TGTTCATATGACCACAACCAAATT 57.337 33.333 4.48 0.00 0.00 1.82
1532 1909 8.928733 AGCATGAAACAAAATAAACATGTCATC 58.071 29.630 0.00 0.00 37.83 2.92
1545 1922 5.971763 ACCTACAACAAGCATGAAACAAAA 58.028 33.333 0.00 0.00 0.00 2.44
1550 1927 6.892658 AACATACCTACAACAAGCATGAAA 57.107 33.333 0.00 0.00 0.00 2.69
1557 1934 7.360946 GCCTCAAACTAACATACCTACAACAAG 60.361 40.741 0.00 0.00 0.00 3.16
1710 2087 6.988522 ACCCTTGTAATTTGTTTACCATGTC 58.011 36.000 0.00 0.00 39.63 3.06
1733 2110 7.383102 ACAAGTCATCCATGTTCAAAGATAC 57.617 36.000 0.00 0.00 0.00 2.24
1787 2167 3.752747 TGCAGTACAAATCTGTGATGGTG 59.247 43.478 0.00 0.00 36.96 4.17
2018 2602 7.555554 AGCAAGCTATTCACACTCTGAATAATT 59.444 33.333 0.00 0.00 46.70 1.40
2074 2658 9.899226 GGAGGCTTTTGTTACATATCAATTATC 57.101 33.333 0.00 0.00 0.00 1.75
2075 2659 9.420118 TGGAGGCTTTTGTTACATATCAATTAT 57.580 29.630 0.00 0.00 0.00 1.28
2076 2660 8.815565 TGGAGGCTTTTGTTACATATCAATTA 57.184 30.769 0.00 0.00 0.00 1.40
2077 2661 7.716799 TGGAGGCTTTTGTTACATATCAATT 57.283 32.000 0.00 0.00 0.00 2.32
2078 2662 7.397192 ACTTGGAGGCTTTTGTTACATATCAAT 59.603 33.333 0.00 0.00 0.00 2.57
2079 2663 6.719370 ACTTGGAGGCTTTTGTTACATATCAA 59.281 34.615 0.00 0.00 0.00 2.57
2128 2712 5.768980 AGATGGAAACTTGGAATCAGAGA 57.231 39.130 0.00 0.00 0.00 3.10
2170 2754 2.027745 CCCAGCTACTCTCTGCAGAAAA 60.028 50.000 18.85 8.06 0.00 2.29
2371 2955 4.147219 ACTTTGTTTCTTCTACATGCGC 57.853 40.909 0.00 0.00 0.00 6.09
2405 2989 2.978156 AAGCCAACCAGATTCCTTGA 57.022 45.000 0.00 0.00 0.00 3.02
2429 3013 5.200483 ACCCATGAAGTTCTCAGTTGAAAA 58.800 37.500 4.17 0.00 37.52 2.29
2569 3267 6.709397 CCAGCATTGCTATTAAGAGATCTCAA 59.291 38.462 24.39 11.42 36.40 3.02
2592 3290 6.877322 GTCAAAAGATACTTTAGTGCTACCCA 59.123 38.462 0.00 0.00 0.00 4.51
2684 3518 4.510711 GTGTCAAGATGAGCCATATGTCAG 59.489 45.833 1.24 0.00 0.00 3.51
2704 3538 3.572632 ATAGCTCATGCATTCCTGTGT 57.427 42.857 0.00 0.00 42.74 3.72
2918 3752 4.159321 TCATCAAGACTGTTAGCTCTGGAG 59.841 45.833 0.00 0.00 0.00 3.86
3167 4001 9.585099 TCAACAATGGAAAGCAAATGATATAAC 57.415 29.630 0.00 0.00 0.00 1.89
3306 4140 3.443681 CAGGCGAAAACTTTGTCCCATAT 59.556 43.478 0.00 0.00 0.00 1.78
3320 4154 3.625764 GCATACTATTGGAACAGGCGAAA 59.374 43.478 0.00 0.00 42.39 3.46
3356 4190 5.317733 AGATCCGAAAGCTATATTCCTCG 57.682 43.478 0.00 0.00 0.00 4.63
3636 4470 4.160626 AGTTCTCGGAGGAGTTGAAATAGG 59.839 45.833 4.96 0.00 41.26 2.57
3742 4576 3.072915 TCTGCTGAAAGAATGACCCTTCA 59.927 43.478 0.00 0.00 34.07 3.02
3791 4625 3.967987 ACTCTGTCCTAGACAAACCAAGT 59.032 43.478 0.00 0.00 42.26 3.16
3956 4790 1.070758 GGCTCCTTGTGAGTTGAGACA 59.929 52.381 0.00 0.00 43.48 3.41
4000 4834 2.559840 CAGCTGCTCTTGGTTGCG 59.440 61.111 0.00 0.00 0.00 4.85
4101 4935 3.864583 GCACATTGTGTCATTTGTGTTGT 59.135 39.130 17.64 0.00 41.14 3.32
4111 4945 2.223548 GCTTCTGTTGCACATTGTGTCA 60.224 45.455 17.64 12.92 35.75 3.58
4307 5141 4.040339 TCTGAATCTTGAACACTACTGCCA 59.960 41.667 0.00 0.00 0.00 4.92
4344 5178 5.371526 TCCATCTGGATCTGCAGTTTTATC 58.628 41.667 14.67 9.05 39.78 1.75
4462 5296 1.300233 CCGCTACCCTTCTCGATGC 60.300 63.158 0.00 0.00 0.00 3.91
4651 5485 7.230712 AGGGACTACCAAAAAGTATCACAAAAG 59.769 37.037 0.00 0.00 43.89 2.27
4879 5774 8.103935 TGATCCAAGTTACACCATACATGTTTA 58.896 33.333 2.30 0.00 0.00 2.01
4926 5829 2.626266 TGATGAAGGCATGATCCATTGC 59.374 45.455 0.00 4.31 34.11 3.56
4986 5895 1.226128 GCGATCTTGCTGAAACGCC 60.226 57.895 16.62 6.51 43.23 5.68
5016 5925 3.003480 GTTTGAGAAGTTCTCCATCGGG 58.997 50.000 26.37 0.00 42.73 5.14
5034 5943 2.275380 GCCGCCCAGGATGTTGTTT 61.275 57.895 0.00 0.00 45.00 2.83
5070 5979 3.288308 CTCGGTCAGAGCTGCGGTT 62.288 63.158 0.00 0.00 40.54 4.44
5171 6080 1.311747 GAGCTAGAGAGGGGTGGGT 59.688 63.158 0.00 0.00 0.00 4.51
5172 6081 0.758685 CTGAGCTAGAGAGGGGTGGG 60.759 65.000 0.00 0.00 0.00 4.61
5173 6082 1.398958 GCTGAGCTAGAGAGGGGTGG 61.399 65.000 0.00 0.00 0.00 4.61
5174 6083 0.685785 TGCTGAGCTAGAGAGGGGTG 60.686 60.000 5.83 0.00 0.00 4.61
5289 6214 7.095607 GCCTTAATTAGTTACATGATGGACTCG 60.096 40.741 0.00 0.00 0.00 4.18
5292 6217 7.499232 AGTGCCTTAATTAGTTACATGATGGAC 59.501 37.037 0.00 0.00 0.00 4.02
5293 6218 7.573710 AGTGCCTTAATTAGTTACATGATGGA 58.426 34.615 0.00 0.00 0.00 3.41
5294 6219 7.807977 AGTGCCTTAATTAGTTACATGATGG 57.192 36.000 0.00 0.00 0.00 3.51
5389 6330 5.339008 AATACATCCTTCTAACGCTGACA 57.661 39.130 0.00 0.00 0.00 3.58
5629 8117 4.742438 TTGGAAATCGCAGTGTAGTTTC 57.258 40.909 0.00 0.36 0.00 2.78
5890 8381 9.913310 TTATTTGGTATTGGAGATGTTCACATA 57.087 29.630 0.00 0.00 36.57 2.29
5895 8386 9.921637 TTTGTTTATTTGGTATTGGAGATGTTC 57.078 29.630 0.00 0.00 0.00 3.18
5937 8480 5.629079 ACGTATCGCTAGATTCATCATGA 57.371 39.130 0.00 0.00 38.26 3.07
6035 8609 4.542525 TCTGTTCCAAAATATAGGGGGTGT 59.457 41.667 0.00 0.00 0.00 4.16
6039 8613 8.996651 AAATACTCTGTTCCAAAATATAGGGG 57.003 34.615 0.00 0.00 0.00 4.79
6072 8650 2.223180 ACAACGTGTCTTTCTTTTCCGC 60.223 45.455 0.00 0.00 0.00 5.54
6074 8652 4.729595 ACAACAACGTGTCTTTCTTTTCC 58.270 39.130 0.00 0.00 0.00 3.13
6094 8672 2.499197 ACGATTGCACCATGTTGTACA 58.501 42.857 0.00 0.00 0.00 2.90
6095 8673 4.671880 TTACGATTGCACCATGTTGTAC 57.328 40.909 0.00 0.00 0.00 2.90
6096 8674 5.690997 TTTTACGATTGCACCATGTTGTA 57.309 34.783 0.00 0.00 0.00 2.41


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

AutoCloner maintained by Alex Coulton.