Multiple sequence alignment - TraesCS7D01G335900

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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 TraesCS7D01G335900 chr7D 100.000 3881 0 0 966 4846 427631904 427628024 0.000000e+00 7167.0
1 TraesCS7D01G335900 chr7D 100.000 357 0 0 1 357 427632869 427632513 0.000000e+00 660.0
2 TraesCS7D01G335900 chr7B 94.099 2525 122 13 2071 4590 445422296 445419794 0.000000e+00 3812.0
3 TraesCS7D01G335900 chr7B 95.961 1114 33 4 966 2074 445423482 445422376 0.000000e+00 1797.0
4 TraesCS7D01G335900 chr7B 85.915 284 16 12 78 357 445423785 445423522 1.030000e-71 281.0
5 TraesCS7D01G335900 chr7B 96.875 32 1 0 2793 2824 688554298 688554329 2.000000e-03 54.7
6 TraesCS7D01G335900 chr7A 92.109 2129 111 20 2247 4342 505016939 505019043 0.000000e+00 2948.0
7 TraesCS7D01G335900 chr7A 89.574 1314 83 25 966 2246 505015614 505016906 0.000000e+00 1618.0
8 TraesCS7D01G335900 chr7A 87.008 254 21 3 4598 4839 505019233 505019486 4.780000e-70 276.0
9 TraesCS7D01G335900 chr7A 81.690 284 19 20 78 357 505015319 505015573 6.360000e-49 206.0
10 TraesCS7D01G335900 chr1D 88.095 84 10 0 3573 3656 291789621 291789538 3.090000e-17 100.0
11 TraesCS7D01G335900 chr1D 83.908 87 13 1 3581 3667 482932635 482932550 1.120000e-11 82.4
12 TraesCS7D01G335900 chr1A 87.013 77 10 0 3573 3649 363692915 363692839 2.400000e-13 87.9
13 TraesCS7D01G335900 chr5D 85.075 67 9 1 3573 3638 486478873 486478939 3.130000e-07 67.6


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 TraesCS7D01G335900 chr7D 427628024 427632869 4845 True 3913.500000 7167 100.000000 1 4846 2 chr7D.!!$R1 4845
1 TraesCS7D01G335900 chr7B 445419794 445423785 3991 True 1963.333333 3812 91.991667 78 4590 3 chr7B.!!$R1 4512
2 TraesCS7D01G335900 chr7A 505015319 505019486 4167 False 1262.000000 2948 87.595250 78 4839 4 chr7A.!!$F1 4761

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
217 229 3.491639 CACCACATGACACAAAGCAATTG 59.508 43.478 0.0 0.0 44.95 2.32 F
1344 1370 1.077644 CCTCCTCGTCTTCCTCCGA 60.078 63.158 0.0 0.0 0.00 4.55 F
2725 2890 0.663269 GGTAAACAAACGCCAGCAGC 60.663 55.000 0.0 0.0 38.52 5.25 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1483 1522 0.176680 GCACGGTGGAGTCATCTCAT 59.823 55.0 10.6 0.0 42.05 2.90 R
3167 3332 0.602106 CTGCTGGTGACTGGTGACTG 60.602 60.0 0.0 0.0 0.00 3.51 R
4600 4800 0.035820 GGCGGTTGGTGGATCAACTA 60.036 55.0 0.0 0.0 44.52 2.24 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
23 24 5.579718 TCTCGCTACTTGTACTAAATCAGC 58.420 41.667 0.00 0.00 0.00 4.26
24 25 4.677683 CGCTACTTGTACTAAATCAGCG 57.322 45.455 10.86 10.86 43.66 5.18
29 30 8.164058 GCTACTTGTACTAAATCAGCGATATC 57.836 38.462 0.00 0.00 0.00 1.63
30 31 8.024285 GCTACTTGTACTAAATCAGCGATATCT 58.976 37.037 0.34 0.00 0.00 1.98
36 37 9.983804 TGTACTAAATCAGCGATATCTAATACG 57.016 33.333 0.34 0.00 0.00 3.06
37 38 9.435802 GTACTAAATCAGCGATATCTAATACGG 57.564 37.037 0.34 0.00 0.00 4.02
38 39 8.277490 ACTAAATCAGCGATATCTAATACGGA 57.723 34.615 0.34 0.00 0.00 4.69
39 40 8.737175 ACTAAATCAGCGATATCTAATACGGAA 58.263 33.333 0.34 0.00 0.00 4.30
40 41 7.813852 AAATCAGCGATATCTAATACGGAAC 57.186 36.000 0.34 0.00 0.00 3.62
62 63 9.408069 GGAACGGAGTGAGTAGTATATTTTATG 57.592 37.037 0.00 0.00 45.00 1.90
71 72 9.419297 TGAGTAGTATATTTTATGATTCACCGC 57.581 33.333 0.00 0.00 0.00 5.68
72 73 8.773404 AGTAGTATATTTTATGATTCACCGCC 57.227 34.615 0.00 0.00 0.00 6.13
73 74 8.594550 AGTAGTATATTTTATGATTCACCGCCT 58.405 33.333 0.00 0.00 0.00 5.52
74 75 7.907214 AGTATATTTTATGATTCACCGCCTC 57.093 36.000 0.00 0.00 0.00 4.70
75 76 7.680730 AGTATATTTTATGATTCACCGCCTCT 58.319 34.615 0.00 0.00 0.00 3.69
76 77 8.157476 AGTATATTTTATGATTCACCGCCTCTT 58.843 33.333 0.00 0.00 0.00 2.85
77 78 7.823745 ATATTTTATGATTCACCGCCTCTTT 57.176 32.000 0.00 0.00 0.00 2.52
78 79 5.975693 TTTTATGATTCACCGCCTCTTTT 57.024 34.783 0.00 0.00 0.00 2.27
79 80 5.975693 TTTATGATTCACCGCCTCTTTTT 57.024 34.783 0.00 0.00 0.00 1.94
171 172 6.907206 ACATTTTGGAAATGCATAATTCCG 57.093 33.333 20.27 11.17 46.58 4.30
217 229 3.491639 CACCACATGACACAAAGCAATTG 59.508 43.478 0.00 0.00 44.95 2.32
240 252 9.762381 ATTGTAGGAATACAATTACCCTCAAAA 57.238 29.630 7.62 0.00 45.36 2.44
241 253 9.589461 TTGTAGGAATACAATTACCCTCAAAAA 57.411 29.630 0.00 0.00 35.27 1.94
1342 1368 1.758906 CCCCTCCTCGTCTTCCTCC 60.759 68.421 0.00 0.00 0.00 4.30
1344 1370 1.077644 CCTCCTCGTCTTCCTCCGA 60.078 63.158 0.00 0.00 0.00 4.55
1481 1520 9.990360 TCCTTTTAAGTTTGTTTGTTCTCTTTT 57.010 25.926 0.00 0.00 0.00 2.27
1508 1549 0.900182 TGACTCCACCGTGCTGATCT 60.900 55.000 0.00 0.00 0.00 2.75
1534 1575 8.896744 TGTAAATCCAGATTCAGATGAACAATC 58.103 33.333 0.00 0.00 36.80 2.67
1553 1594 6.611381 ACAATCGTTCCTGTCATTTACATTG 58.389 36.000 0.00 0.00 37.50 2.82
1643 1693 3.004734 GTCCACAGATGTTCCTTGTTTGG 59.995 47.826 0.00 0.00 0.00 3.28
1648 1698 3.068590 CAGATGTTCCTTGTTTGGCAGTT 59.931 43.478 0.00 0.00 0.00 3.16
1718 1768 5.523552 GGATGCTAGCTTTGTTTGTTTGTTT 59.476 36.000 17.23 0.00 0.00 2.83
1719 1769 5.776519 TGCTAGCTTTGTTTGTTTGTTTG 57.223 34.783 17.23 0.00 0.00 2.93
1722 1772 5.347364 GCTAGCTTTGTTTGTTTGTTTGTCA 59.653 36.000 7.70 0.00 0.00 3.58
1915 1965 3.135225 TGGTACGAAGACACACAATTGG 58.865 45.455 10.83 1.35 0.00 3.16
1929 1979 3.068024 CACAATTGGCACAGGTTGTTAGT 59.932 43.478 10.83 0.00 43.08 2.24
1941 1991 5.046304 ACAGGTTGTTAGTCATGTAGCTCAT 60.046 40.000 0.00 0.00 37.22 2.90
1989 2039 1.968493 TGTAGCTTCTTCCTGGTCGTT 59.032 47.619 0.00 0.00 0.00 3.85
2059 2109 4.708177 CCGTGTCCCTCATTTCATTCTAT 58.292 43.478 0.00 0.00 0.00 1.98
2105 2238 6.491714 ACCATACATGATTGAGTCTTAGCT 57.508 37.500 0.00 0.00 0.00 3.32
2111 2244 5.821470 ACATGATTGAGTCTTAGCTGAATGG 59.179 40.000 0.00 0.00 0.00 3.16
2153 2286 7.322664 TGCTTTATAAAGGAGCAATTTCAAGG 58.677 34.615 23.37 0.00 42.89 3.61
2165 2298 7.068716 GGAGCAATTTCAAGGGTCAATATAAGT 59.931 37.037 0.00 0.00 0.00 2.24
2177 2310 7.290481 AGGGTCAATATAAGTTACCTTCTCTCC 59.710 40.741 0.00 0.00 31.89 3.71
2238 2371 1.097547 GGGGCACTTCACCATGATCG 61.098 60.000 0.00 0.00 0.00 3.69
2242 2375 2.414559 GGCACTTCACCATGATCGTTTG 60.415 50.000 0.00 0.00 0.00 2.93
2432 2597 1.496429 CATAGAGGAAAGGGGCATGGT 59.504 52.381 0.00 0.00 0.00 3.55
2654 2819 1.436983 GCGTGCTGGGTAATGCTACC 61.437 60.000 0.00 0.00 46.24 3.18
2725 2890 0.663269 GGTAAACAAACGCCAGCAGC 60.663 55.000 0.00 0.00 38.52 5.25
2852 3017 4.287067 AGATACAGGAAGCTTTGTTCTCCA 59.713 41.667 8.99 0.00 0.00 3.86
3111 3276 9.743057 TTGAATCTGTTTGTTTGGTTATTACTG 57.257 29.630 0.00 0.00 0.00 2.74
3166 3331 1.270550 CACAAGCCAATGTTCCCTCAC 59.729 52.381 0.00 0.00 0.00 3.51
3167 3332 0.890683 CAAGCCAATGTTCCCTCACC 59.109 55.000 0.00 0.00 0.00 4.02
3168 3333 0.482446 AAGCCAATGTTCCCTCACCA 59.518 50.000 0.00 0.00 0.00 4.17
3169 3334 0.038744 AGCCAATGTTCCCTCACCAG 59.961 55.000 0.00 0.00 0.00 4.00
3170 3335 0.251341 GCCAATGTTCCCTCACCAGT 60.251 55.000 0.00 0.00 0.00 4.00
3171 3336 1.826385 CCAATGTTCCCTCACCAGTC 58.174 55.000 0.00 0.00 0.00 3.51
3172 3337 1.073763 CCAATGTTCCCTCACCAGTCA 59.926 52.381 0.00 0.00 0.00 3.41
3207 3372 0.407528 TGGGGTTGCAAATCAGGCTA 59.592 50.000 0.00 0.00 0.00 3.93
3215 3380 3.689347 TGCAAATCAGGCTAGACATTGT 58.311 40.909 0.00 0.00 0.00 2.71
3243 3408 3.052455 TGCTTCATTCGTTTGCCTCTA 57.948 42.857 0.00 0.00 0.00 2.43
3263 3434 0.249120 CGACTAGTGTCATGGCCCAA 59.751 55.000 0.00 0.00 43.06 4.12
3294 3465 4.922206 TGCTTGATTGATAACTTCACCCT 58.078 39.130 0.00 0.00 32.84 4.34
3355 3526 2.715046 AGTACAATGAGGTGCATGTGG 58.285 47.619 0.00 0.00 37.28 4.17
3550 3726 4.518970 TCATGTAAAGTTTGAAGGACTGCC 59.481 41.667 0.00 0.00 0.00 4.85
3567 3743 2.868583 CTGCCCTACAAATCTGACATCG 59.131 50.000 0.00 0.00 0.00 3.84
3609 3787 1.730064 TCGAGCGTCTTTTATGGCAAC 59.270 47.619 0.00 0.00 0.00 4.17
3638 3817 1.017387 CCGAGGATGGCAAGTTTAGC 58.983 55.000 0.00 0.00 0.00 3.09
3658 3837 1.065102 CTGGCAAGCATCTCAAATCCG 59.935 52.381 0.00 0.00 0.00 4.18
3667 3846 2.859165 TCTCAAATCCGGCTCAGTTT 57.141 45.000 0.00 0.00 0.00 2.66
3713 3892 4.251268 ACGTCAGACTTTTAGCATTACCC 58.749 43.478 0.00 0.00 0.00 3.69
3842 4031 3.678289 TCAATTGACATGACAGGTCCTG 58.322 45.455 17.88 17.88 37.52 3.86
3917 4109 6.897706 TCATGAGGAAGATCTAGATCAGTG 57.102 41.667 29.83 17.60 40.22 3.66
3925 4117 6.014669 GGAAGATCTAGATCAGTGGTGCTATT 60.015 42.308 29.83 14.08 40.22 1.73
3997 4189 0.729116 CCAGTTGTGCTAATCCTGCG 59.271 55.000 0.00 0.00 0.00 5.18
4001 4193 3.272334 GTGCTAATCCTGCGGCCG 61.272 66.667 24.05 24.05 0.00 6.13
4056 4250 2.202987 GGATCCAGCCAGCACTCG 60.203 66.667 6.95 0.00 0.00 4.18
4078 4272 4.559063 CCTGCTCCCCTGCCGATG 62.559 72.222 0.00 0.00 0.00 3.84
4187 4381 2.633488 GCTGTAAAAGAGTAGGCAGGG 58.367 52.381 0.00 0.00 0.00 4.45
4211 4405 2.614481 GGCAGACCGGTGTTCTAATCAA 60.614 50.000 14.63 0.00 0.00 2.57
4230 4424 1.098050 AGCCGACTTGATGCAAATCC 58.902 50.000 0.00 0.00 0.00 3.01
4236 4430 2.167075 GACTTGATGCAAATCCCCTTGG 59.833 50.000 0.00 0.00 0.00 3.61
4237 4431 2.181975 CTTGATGCAAATCCCCTTGGT 58.818 47.619 0.00 0.00 0.00 3.67
4238 4432 1.559368 TGATGCAAATCCCCTTGGTG 58.441 50.000 0.00 0.00 0.00 4.17
4289 4488 2.621055 GCGCTCCTCAATTCTCTCTCTA 59.379 50.000 0.00 0.00 0.00 2.43
4334 4534 4.269844 GCCTTCTTTCGCTTTATCTCTCTG 59.730 45.833 0.00 0.00 0.00 3.35
4376 4576 8.877779 CAAAAGTTCAAAACAACATAACATCCA 58.122 29.630 0.00 0.00 0.00 3.41
4377 4577 9.442047 AAAAGTTCAAAACAACATAACATCCAA 57.558 25.926 0.00 0.00 0.00 3.53
4382 4582 6.098982 TCAAAACAACATAACATCCAACCCTT 59.901 34.615 0.00 0.00 0.00 3.95
4415 4615 4.948341 TTTCACAGTACCTACTTGCTGA 57.052 40.909 0.00 0.00 33.46 4.26
4417 4617 4.252971 TCACAGTACCTACTTGCTGAAC 57.747 45.455 0.00 0.00 33.46 3.18
4434 4634 4.092968 GCTGAACGAAGTAATGTACCCTTG 59.907 45.833 0.00 0.00 45.00 3.61
4446 4646 8.161425 AGTAATGTACCCTTGAAGCTTTTTAGA 58.839 33.333 0.00 0.00 0.00 2.10
4468 4668 1.917872 AGCTACGAAAATTGGCCCAA 58.082 45.000 0.00 0.00 0.00 4.12
4510 4710 8.197592 AGTGACCCCATTTTGACGTATATATA 57.802 34.615 0.00 0.00 0.00 0.86
4597 4797 9.706691 ATATTACTGTTGTACTAAATCGATGGG 57.293 33.333 0.00 0.00 0.00 4.00
4599 4799 5.661458 ACTGTTGTACTAAATCGATGGGAG 58.339 41.667 0.00 0.00 0.00 4.30
4600 4800 5.187186 ACTGTTGTACTAAATCGATGGGAGT 59.813 40.000 0.00 5.53 0.00 3.85
4602 4802 6.802608 TGTTGTACTAAATCGATGGGAGTAG 58.197 40.000 12.28 6.66 0.00 2.57
4603 4803 6.379133 TGTTGTACTAAATCGATGGGAGTAGT 59.621 38.462 12.28 10.81 35.06 2.73
4623 4843 1.077787 GATCCACCAACCGCCATGA 60.078 57.895 0.00 0.00 0.00 3.07
4628 4848 0.602562 CACCAACCGCCATGACATTT 59.397 50.000 0.00 0.00 0.00 2.32
4646 4866 8.062065 TGACATTTATCATGTTTAAGGGTTCC 57.938 34.615 0.00 0.00 31.52 3.62
4648 4868 8.293699 ACATTTATCATGTTTAAGGGTTCCTC 57.706 34.615 0.00 0.00 30.89 3.71
4649 4869 6.995511 TTTATCATGTTTAAGGGTTCCTCG 57.004 37.500 0.00 0.00 30.89 4.63
4650 4870 2.706890 TCATGTTTAAGGGTTCCTCGC 58.293 47.619 0.00 0.00 30.89 5.03
4651 4871 2.039216 TCATGTTTAAGGGTTCCTCGCA 59.961 45.455 0.00 0.00 30.89 5.10
4652 4872 2.178912 TGTTTAAGGGTTCCTCGCAG 57.821 50.000 0.00 0.00 30.89 5.18
4653 4873 1.695242 TGTTTAAGGGTTCCTCGCAGA 59.305 47.619 0.00 0.00 30.89 4.26
4657 4877 1.207791 AAGGGTTCCTCGCAGATCAT 58.792 50.000 0.00 0.00 33.89 2.45
4658 4878 1.207791 AGGGTTCCTCGCAGATCATT 58.792 50.000 0.00 0.00 33.89 2.57
4667 4894 3.002042 CCTCGCAGATCATTTAAGCACTG 59.998 47.826 0.00 0.00 33.89 3.66
4668 4895 2.352651 TCGCAGATCATTTAAGCACTGC 59.647 45.455 0.00 0.00 44.48 4.40
4670 4897 2.424601 GCAGATCATTTAAGCACTGCCA 59.575 45.455 0.00 0.00 42.91 4.92
4681 4908 0.807496 GCACTGCCAAGGACATCTTC 59.193 55.000 0.00 0.00 32.41 2.87
4772 5004 3.873883 GCGAGCATGTGAGCTGCC 61.874 66.667 0.00 0.00 46.75 4.85
4773 5005 3.561213 CGAGCATGTGAGCTGCCG 61.561 66.667 0.00 0.00 46.75 5.69
4796 5028 1.735198 CCGCGTTAGACTTTCGGCA 60.735 57.895 4.92 0.00 33.36 5.69
4808 5040 4.036380 AGACTTTCGGCAAACAAAACTAGG 59.964 41.667 0.00 0.00 0.00 3.02
4818 5050 5.744490 CAAACAAAACTAGGTCCGTACAAG 58.256 41.667 0.00 0.00 0.00 3.16
4821 5053 3.975168 AAACTAGGTCCGTACAAGCAT 57.025 42.857 0.00 0.00 0.00 3.79
4844 5076 3.056328 GGCAACCTGAAGGCGGAC 61.056 66.667 0.00 0.00 39.32 4.79
4845 5077 3.056328 GCAACCTGAAGGCGGACC 61.056 66.667 0.00 0.00 39.32 4.46
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
1 2 5.874892 GCTGATTTAGTACAAGTAGCGAG 57.125 43.478 0.00 0.00 0.00 5.03
3 4 4.677683 CGCTGATTTAGTACAAGTAGCG 57.322 45.455 12.37 12.37 45.08 4.26
4 5 8.024285 AGATATCGCTGATTTAGTACAAGTAGC 58.976 37.037 0.00 0.00 0.00 3.58
10 11 9.983804 CGTATTAGATATCGCTGATTTAGTACA 57.016 33.333 0.00 0.00 0.00 2.90
11 12 9.435802 CCGTATTAGATATCGCTGATTTAGTAC 57.564 37.037 0.00 0.00 0.00 2.73
12 13 9.387257 TCCGTATTAGATATCGCTGATTTAGTA 57.613 33.333 0.00 0.00 0.00 1.82
13 14 8.277490 TCCGTATTAGATATCGCTGATTTAGT 57.723 34.615 0.00 0.00 0.00 2.24
14 15 9.011407 GTTCCGTATTAGATATCGCTGATTTAG 57.989 37.037 0.00 0.00 0.00 1.85
15 16 7.695201 CGTTCCGTATTAGATATCGCTGATTTA 59.305 37.037 0.00 0.00 0.00 1.40
16 17 6.527023 CGTTCCGTATTAGATATCGCTGATTT 59.473 38.462 0.00 0.00 0.00 2.17
17 18 6.028368 CGTTCCGTATTAGATATCGCTGATT 58.972 40.000 0.00 0.00 0.00 2.57
18 19 5.448768 CCGTTCCGTATTAGATATCGCTGAT 60.449 44.000 0.00 0.00 0.00 2.90
19 20 4.142752 CCGTTCCGTATTAGATATCGCTGA 60.143 45.833 0.00 0.00 0.00 4.26
20 21 4.096311 CCGTTCCGTATTAGATATCGCTG 58.904 47.826 0.00 0.00 0.00 5.18
21 22 4.005650 TCCGTTCCGTATTAGATATCGCT 58.994 43.478 0.00 0.00 0.00 4.93
22 23 4.142730 ACTCCGTTCCGTATTAGATATCGC 60.143 45.833 0.00 0.00 0.00 4.58
23 24 5.121298 TCACTCCGTTCCGTATTAGATATCG 59.879 44.000 0.00 0.00 0.00 2.92
24 25 6.149142 ACTCACTCCGTTCCGTATTAGATATC 59.851 42.308 0.00 0.00 0.00 1.63
25 26 6.002704 ACTCACTCCGTTCCGTATTAGATAT 58.997 40.000 0.00 0.00 0.00 1.63
26 27 5.371526 ACTCACTCCGTTCCGTATTAGATA 58.628 41.667 0.00 0.00 0.00 1.98
27 28 4.205587 ACTCACTCCGTTCCGTATTAGAT 58.794 43.478 0.00 0.00 0.00 1.98
28 29 3.614092 ACTCACTCCGTTCCGTATTAGA 58.386 45.455 0.00 0.00 0.00 2.10
29 30 4.574013 ACTACTCACTCCGTTCCGTATTAG 59.426 45.833 0.00 0.00 0.00 1.73
30 31 4.517285 ACTACTCACTCCGTTCCGTATTA 58.483 43.478 0.00 0.00 0.00 0.98
31 32 3.350833 ACTACTCACTCCGTTCCGTATT 58.649 45.455 0.00 0.00 0.00 1.89
32 33 2.996631 ACTACTCACTCCGTTCCGTAT 58.003 47.619 0.00 0.00 0.00 3.06
33 34 2.479566 ACTACTCACTCCGTTCCGTA 57.520 50.000 0.00 0.00 0.00 4.02
34 35 2.479566 TACTACTCACTCCGTTCCGT 57.520 50.000 0.00 0.00 0.00 4.69
35 36 5.686159 AATATACTACTCACTCCGTTCCG 57.314 43.478 0.00 0.00 0.00 4.30
36 37 9.408069 CATAAAATATACTACTCACTCCGTTCC 57.592 37.037 0.00 0.00 0.00 3.62
45 46 9.419297 GCGGTGAATCATAAAATATACTACTCA 57.581 33.333 0.00 0.00 0.00 3.41
46 47 8.870879 GGCGGTGAATCATAAAATATACTACTC 58.129 37.037 0.00 0.00 0.00 2.59
47 48 8.594550 AGGCGGTGAATCATAAAATATACTACT 58.405 33.333 0.00 0.00 0.00 2.57
48 49 8.773404 AGGCGGTGAATCATAAAATATACTAC 57.227 34.615 0.00 0.00 0.00 2.73
49 50 8.812972 AGAGGCGGTGAATCATAAAATATACTA 58.187 33.333 0.00 0.00 0.00 1.82
50 51 7.680730 AGAGGCGGTGAATCATAAAATATACT 58.319 34.615 0.00 0.00 0.00 2.12
51 52 7.907214 AGAGGCGGTGAATCATAAAATATAC 57.093 36.000 0.00 0.00 0.00 1.47
52 53 8.918202 AAAGAGGCGGTGAATCATAAAATATA 57.082 30.769 0.00 0.00 0.00 0.86
53 54 7.823745 AAAGAGGCGGTGAATCATAAAATAT 57.176 32.000 0.00 0.00 0.00 1.28
54 55 7.639113 AAAAGAGGCGGTGAATCATAAAATA 57.361 32.000 0.00 0.00 0.00 1.40
55 56 6.530019 AAAAGAGGCGGTGAATCATAAAAT 57.470 33.333 0.00 0.00 0.00 1.82
56 57 5.975693 AAAAGAGGCGGTGAATCATAAAA 57.024 34.783 0.00 0.00 0.00 1.52
57 58 5.975693 AAAAAGAGGCGGTGAATCATAAA 57.024 34.783 0.00 0.00 0.00 1.40
77 78 7.495934 TGGCAAATCCGTTATTCAAAAGAAAAA 59.504 29.630 0.00 0.00 37.80 1.94
78 79 6.986817 TGGCAAATCCGTTATTCAAAAGAAAA 59.013 30.769 0.00 0.00 37.80 2.29
79 80 6.422400 GTGGCAAATCCGTTATTCAAAAGAAA 59.578 34.615 0.00 0.00 37.80 2.52
80 81 5.923684 GTGGCAAATCCGTTATTCAAAAGAA 59.076 36.000 0.00 0.00 37.80 2.52
81 82 5.465935 GTGGCAAATCCGTTATTCAAAAGA 58.534 37.500 0.00 0.00 37.80 2.52
82 83 4.625311 GGTGGCAAATCCGTTATTCAAAAG 59.375 41.667 0.00 0.00 37.80 2.27
1342 1368 1.535462 AGCCACGGATTTTTCAACTCG 59.465 47.619 0.00 0.00 0.00 4.18
1344 1370 1.535462 CGAGCCACGGATTTTTCAACT 59.465 47.619 0.00 0.00 38.46 3.16
1481 1520 1.478105 CACGGTGGAGTCATCTCATCA 59.522 52.381 0.00 0.00 42.05 3.07
1482 1521 1.804372 GCACGGTGGAGTCATCTCATC 60.804 57.143 10.60 0.00 42.05 2.92
1483 1522 0.176680 GCACGGTGGAGTCATCTCAT 59.823 55.000 10.60 0.00 42.05 2.90
1508 1549 8.812513 ATTGTTCATCTGAATCTGGATTTACA 57.187 30.769 0.00 0.00 36.33 2.41
1534 1575 5.605564 TCACAATGTAAATGACAGGAACG 57.394 39.130 0.00 0.00 42.79 3.95
1538 1579 4.669965 CGTGCTCACAATGTAAATGACAGG 60.670 45.833 0.69 0.00 42.79 4.00
1553 1594 2.286294 CCTGAATAAGATGCGTGCTCAC 59.714 50.000 0.00 0.00 0.00 3.51
1643 1693 1.069227 GTTTCCACATGGACGAACTGC 60.069 52.381 0.00 0.00 45.39 4.40
1648 1698 1.600023 GTTGGTTTCCACATGGACGA 58.400 50.000 0.00 0.00 45.39 4.20
1718 1768 6.702282 TGTGATAACGAAACATAACAGTGACA 59.298 34.615 0.00 0.00 0.00 3.58
1719 1769 7.112528 TGTGATAACGAAACATAACAGTGAC 57.887 36.000 0.00 0.00 0.00 3.67
1722 1772 6.348213 GGCTTGTGATAACGAAACATAACAGT 60.348 38.462 0.00 0.00 0.00 3.55
1915 1965 3.125316 GCTACATGACTAACAACCTGTGC 59.875 47.826 0.00 0.00 0.00 4.57
1929 1979 4.763073 CCAGAAGACAATGAGCTACATGA 58.237 43.478 0.00 0.00 39.39 3.07
1941 1991 5.499004 AACTACCATTAGCCAGAAGACAA 57.501 39.130 0.00 0.00 0.00 3.18
2020 2070 5.332959 GGACACGGCAACAATTTTAACAATG 60.333 40.000 0.00 0.00 0.00 2.82
2105 2238 3.633525 GCATTATGTTCTCAGCCCATTCA 59.366 43.478 0.00 0.00 0.00 2.57
2111 2244 2.295885 AGCAGCATTATGTTCTCAGCC 58.704 47.619 0.00 0.00 0.00 4.85
2165 2298 4.416516 TCACAGATGTGGAGAGAAGGTAA 58.583 43.478 12.77 0.00 45.65 2.85
2177 2310 6.906659 AGAAGTGCTTAATTTCACAGATGTG 58.093 36.000 6.63 6.63 46.91 3.21
2238 2371 3.868077 CCAGATGTCTAGCTAGCACAAAC 59.132 47.826 18.83 18.72 0.00 2.93
2242 2375 1.410517 TGCCAGATGTCTAGCTAGCAC 59.589 52.381 18.83 14.54 31.80 4.40
2432 2597 1.272092 CCCAAGGCTTCCTCAATGACA 60.272 52.381 0.00 0.00 30.89 3.58
2654 2819 3.431912 TGAGCATACTTACTGCAAACACG 59.568 43.478 0.00 0.00 42.15 4.49
2725 2890 2.248248 TGTCGGCTCTCCTATATTGGG 58.752 52.381 3.23 0.00 0.00 4.12
2852 3017 4.729227 ACAAAACCGACCAAAACTCAAT 57.271 36.364 0.00 0.00 0.00 2.57
3111 3276 7.201644 CCAAGTTCATCACCATAGATGTTGTAC 60.202 40.741 0.00 0.00 44.46 2.90
3166 3331 1.302033 GCTGGTGACTGGTGACTGG 60.302 63.158 0.00 0.00 0.00 4.00
3167 3332 0.602106 CTGCTGGTGACTGGTGACTG 60.602 60.000 0.00 0.00 0.00 3.51
3168 3333 1.750930 CTGCTGGTGACTGGTGACT 59.249 57.895 0.00 0.00 0.00 3.41
3169 3334 1.963338 GCTGCTGGTGACTGGTGAC 60.963 63.158 0.00 0.00 0.00 3.67
3170 3335 2.142761 AGCTGCTGGTGACTGGTGA 61.143 57.895 0.00 0.00 0.00 4.02
3171 3336 1.964891 CAGCTGCTGGTGACTGGTG 60.965 63.158 21.71 0.00 43.76 4.17
3172 3337 2.429058 CAGCTGCTGGTGACTGGT 59.571 61.111 21.71 0.00 43.76 4.00
3193 3358 4.081406 ACAATGTCTAGCCTGATTTGCAA 58.919 39.130 0.00 0.00 0.00 4.08
3207 3372 4.520179 TGAAGCATAGCATCACAATGTCT 58.480 39.130 0.00 0.00 31.25 3.41
3215 3380 4.731483 GCAAACGAATGAAGCATAGCATCA 60.731 41.667 0.00 0.00 40.45 3.07
3267 3438 7.025963 GGTGAAGTTATCAATCAAGCAAAGAG 58.974 38.462 0.00 0.00 40.50 2.85
3294 3465 8.800370 TTTGGCTCAGTTATATACAAATCACA 57.200 30.769 0.00 0.00 0.00 3.58
3355 3526 2.424956 CTCAACCCTTTGAAGGCTATGC 59.575 50.000 4.19 0.00 45.10 3.14
3550 3726 6.683974 AAAATCCGATGTCAGATTTGTAGG 57.316 37.500 5.28 0.00 40.84 3.18
3593 3771 2.979813 CACAAGTTGCCATAAAAGACGC 59.020 45.455 1.81 0.00 0.00 5.19
3609 3787 0.523072 CCATCCTCGGCAAACACAAG 59.477 55.000 0.00 0.00 0.00 3.16
3638 3817 1.065102 CGGATTTGAGATGCTTGCCAG 59.935 52.381 0.00 0.00 0.00 4.85
3649 3828 2.426522 TCAAACTGAGCCGGATTTGAG 58.573 47.619 5.05 0.00 36.42 3.02
3658 3837 3.056322 AGCATGGAAAATCAAACTGAGCC 60.056 43.478 0.00 0.00 0.00 4.70
3667 3846 9.299963 CGTCATATTTTTAAGCATGGAAAATCA 57.700 29.630 0.00 0.00 35.36 2.57
3692 3871 4.250464 TGGGTAATGCTAAAAGTCTGACG 58.750 43.478 1.52 0.00 0.00 4.35
3713 3892 8.909708 TTTCACTGTAAACTGATTCAAACTTG 57.090 30.769 0.00 0.00 0.00 3.16
3917 4109 3.054802 CCCCTCATCCAGATAATAGCACC 60.055 52.174 0.00 0.00 0.00 5.01
3925 4117 3.344535 TTAGTGCCCCTCATCCAGATA 57.655 47.619 0.00 0.00 0.00 1.98
3966 4158 4.006319 AGCACAACTGGATTAGCTTCTTC 58.994 43.478 0.00 0.00 29.12 2.87
3997 4189 2.045926 ACTCCAGCATCAACGGCC 60.046 61.111 0.00 0.00 0.00 6.13
4001 4193 1.364626 CTGCCGACTCCAGCATCAAC 61.365 60.000 0.00 0.00 38.56 3.18
4056 4250 4.792804 GCAGGGGAGCAGGACAGC 62.793 72.222 0.00 0.00 0.00 4.40
4078 4272 3.070576 GAGGTGTTGGGCCATGGC 61.071 66.667 29.47 29.47 41.06 4.40
4187 4381 2.167398 TAGAACACCGGTCTGCCTGC 62.167 60.000 2.59 0.00 0.00 4.85
4211 4405 1.098050 GGATTTGCATCAAGTCGGCT 58.902 50.000 0.00 0.00 32.13 5.52
4230 4424 2.601367 CCCCAAGCACACCAAGGG 60.601 66.667 0.00 0.00 39.29 3.95
4236 4430 3.297620 CACAGCCCCCAAGCACAC 61.298 66.667 0.00 0.00 34.23 3.82
4289 4488 4.153655 GCGACGAAAGGAAAGGTAAAGATT 59.846 41.667 0.00 0.00 0.00 2.40
4351 4551 9.442047 TTGGATGTTATGTTGTTTTGAACTTTT 57.558 25.926 0.00 0.00 0.00 2.27
4352 4552 8.878769 GTTGGATGTTATGTTGTTTTGAACTTT 58.121 29.630 0.00 0.00 0.00 2.66
4353 4553 7.494298 GGTTGGATGTTATGTTGTTTTGAACTT 59.506 33.333 0.00 0.00 0.00 2.66
4354 4554 6.983890 GGTTGGATGTTATGTTGTTTTGAACT 59.016 34.615 0.00 0.00 0.00 3.01
4355 4555 6.201997 GGGTTGGATGTTATGTTGTTTTGAAC 59.798 38.462 0.00 0.00 0.00 3.18
4356 4556 6.098982 AGGGTTGGATGTTATGTTGTTTTGAA 59.901 34.615 0.00 0.00 0.00 2.69
4357 4557 5.600484 AGGGTTGGATGTTATGTTGTTTTGA 59.400 36.000 0.00 0.00 0.00 2.69
4358 4558 5.852827 AGGGTTGGATGTTATGTTGTTTTG 58.147 37.500 0.00 0.00 0.00 2.44
4359 4559 6.493189 AAGGGTTGGATGTTATGTTGTTTT 57.507 33.333 0.00 0.00 0.00 2.43
4363 4563 4.355543 CGAAGGGTTGGATGTTATGTTG 57.644 45.455 0.00 0.00 0.00 3.33
4382 4582 3.485463 ACTGTGAAAAGGATGAACCGA 57.515 42.857 0.00 0.00 44.74 4.69
4415 4615 4.694037 GCTTCAAGGGTACATTACTTCGTT 59.306 41.667 0.00 0.00 0.00 3.85
4417 4617 4.504858 AGCTTCAAGGGTACATTACTTCG 58.495 43.478 0.00 0.00 0.00 3.79
4446 4646 2.092323 GGGCCAATTTTCGTAGCTTCT 58.908 47.619 4.39 0.00 0.00 2.85
4452 4652 4.873746 TCATTTTGGGCCAATTTTCGTA 57.126 36.364 21.65 0.00 0.00 3.43
4454 4654 5.429957 TTTTCATTTTGGGCCAATTTTCG 57.570 34.783 21.65 7.52 0.00 3.46
4468 4668 6.263168 GGGGTCACTCGATATCATTTTCATTT 59.737 38.462 3.12 0.00 0.00 2.32
4571 4771 9.706691 CCCATCGATTTAGTACAACAGTAATAT 57.293 33.333 0.00 0.00 0.00 1.28
4572 4772 8.916062 TCCCATCGATTTAGTACAACAGTAATA 58.084 33.333 0.00 0.00 0.00 0.98
4577 4777 5.661458 ACTCCCATCGATTTAGTACAACAG 58.339 41.667 0.00 0.00 0.00 3.16
4578 4778 5.670792 ACTCCCATCGATTTAGTACAACA 57.329 39.130 0.00 0.00 0.00 3.33
4590 4790 2.693591 GTGGATCAACTACTCCCATCGA 59.306 50.000 0.00 0.00 0.00 3.59
4592 4792 2.771943 TGGTGGATCAACTACTCCCATC 59.228 50.000 0.00 0.00 0.00 3.51
4593 4793 2.845659 TGGTGGATCAACTACTCCCAT 58.154 47.619 0.00 0.00 0.00 4.00
4594 4794 2.304761 GTTGGTGGATCAACTACTCCCA 59.695 50.000 0.00 0.00 42.54 4.37
4596 4796 2.677037 CGGTTGGTGGATCAACTACTCC 60.677 54.545 0.00 0.00 44.52 3.85
4597 4797 2.618053 CGGTTGGTGGATCAACTACTC 58.382 52.381 0.00 0.00 44.52 2.59
4599 4799 1.084289 GCGGTTGGTGGATCAACTAC 58.916 55.000 0.00 0.00 44.52 2.73
4600 4800 0.035820 GGCGGTTGGTGGATCAACTA 60.036 55.000 0.00 0.00 44.52 2.24
4602 4802 0.965363 ATGGCGGTTGGTGGATCAAC 60.965 55.000 0.00 0.00 44.42 3.18
4603 4803 0.964860 CATGGCGGTTGGTGGATCAA 60.965 55.000 0.00 0.00 0.00 2.57
4623 4843 7.067008 CGAGGAACCCTTAAACATGATAAATGT 59.933 37.037 0.00 0.00 31.76 2.71
4628 4848 4.080807 TGCGAGGAACCCTTAAACATGATA 60.081 41.667 0.00 0.00 31.76 2.15
4636 4856 2.184533 TGATCTGCGAGGAACCCTTAA 58.815 47.619 0.00 0.00 31.76 1.85
4646 4866 3.545624 GCAGTGCTTAAATGATCTGCGAG 60.546 47.826 8.18 0.00 38.72 5.03
4648 4868 2.540361 GGCAGTGCTTAAATGATCTGCG 60.540 50.000 16.11 0.00 45.88 5.18
4649 4869 2.424601 TGGCAGTGCTTAAATGATCTGC 59.575 45.455 16.11 6.44 44.74 4.26
4650 4870 4.439700 CCTTGGCAGTGCTTAAATGATCTG 60.440 45.833 16.11 0.00 0.00 2.90
4651 4871 3.698040 CCTTGGCAGTGCTTAAATGATCT 59.302 43.478 16.11 0.00 0.00 2.75
4652 4872 3.696051 TCCTTGGCAGTGCTTAAATGATC 59.304 43.478 16.11 0.00 0.00 2.92
4653 4873 3.445096 GTCCTTGGCAGTGCTTAAATGAT 59.555 43.478 16.11 0.00 0.00 2.45
4657 4877 2.356665 TGTCCTTGGCAGTGCTTAAA 57.643 45.000 16.11 6.66 0.00 1.52
4658 4878 2.040278 AGATGTCCTTGGCAGTGCTTAA 59.960 45.455 16.11 9.87 0.00 1.85
4714 4945 2.813179 GCCCGCATCAACGCACTAG 61.813 63.158 0.00 0.00 0.00 2.57
4773 5005 1.967597 GAAAGTCTAACGCGGCAGCC 61.968 60.000 12.47 0.00 41.18 4.85
4796 5028 4.274214 GCTTGTACGGACCTAGTTTTGTTT 59.726 41.667 0.00 0.00 0.00 2.83
4808 5040 3.064931 GCCCTAATATGCTTGTACGGAC 58.935 50.000 0.00 0.00 0.00 4.79
4818 5050 2.887152 CCTTCAGGTTGCCCTAATATGC 59.113 50.000 0.00 0.00 39.89 3.14
4821 5053 1.134220 CGCCTTCAGGTTGCCCTAATA 60.134 52.381 0.00 0.00 39.89 0.98


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

AutoCloner maintained by Alex Coulton.