Multiple sequence alignment - TraesCS1D01G410200

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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 TraesCS1D01G410200 chr1D 100.000 4056 0 0 1 4056 471838802 471842857 0.000000e+00 7491.0
1 TraesCS1D01G410200 chr1B 91.957 3643 203 48 1 3568 655846643 655850270 0.000000e+00 5022.0
2 TraesCS1D01G410200 chr1B 78.704 1080 123 59 9 1007 24503229 24504282 4.450000e-174 621.0
3 TraesCS1D01G410200 chr1B 92.542 295 17 2 3767 4056 655851630 655851924 6.270000e-113 418.0
4 TraesCS1D01G410200 chr1B 94.030 201 12 0 3561 3761 655850393 655850593 5.090000e-79 305.0
5 TraesCS1D01G410200 chr1A 91.958 3320 160 49 300 3568 566108936 566112199 0.000000e+00 4553.0
6 TraesCS1D01G410200 chr1A 96.070 229 8 1 1 228 566108765 566108993 4.950000e-99 372.0
7 TraesCS1D01G410200 chr1A 88.737 293 18 6 3767 4052 566118191 566118475 1.080000e-90 344.0
8 TraesCS1D01G410200 chr1A 93.605 172 11 0 3561 3732 566112312 566112483 1.450000e-64 257.0
9 TraesCS1D01G410200 chr5B 90.338 207 20 0 2533 2739 487222795 487223001 5.170000e-69 272.0
10 TraesCS1D01G410200 chr5D 89.855 207 21 0 2533 2739 406333758 406333964 2.400000e-67 267.0
11 TraesCS1D01G410200 chr5D 91.667 48 4 0 2423 2470 438448969 438449016 2.620000e-07 67.6
12 TraesCS1D01G410200 chr5A 89.855 207 21 0 2533 2739 511906069 511906275 2.400000e-67 267.0
13 TraesCS1D01G410200 chr2D 78.390 472 50 28 1 441 245678650 245679100 4.020000e-65 259.0
14 TraesCS1D01G410200 chr2D 91.667 48 2 1 2423 2470 423275684 423275729 9.410000e-07 65.8
15 TraesCS1D01G410200 chr6D 100.000 38 0 0 2433 2470 46838650 46838613 2.020000e-08 71.3
16 TraesCS1D01G410200 chr6D 97.500 40 1 0 2431 2470 22234212 22234251 7.270000e-08 69.4
17 TraesCS1D01G410200 chr3D 97.561 41 1 0 2430 2470 583101233 583101273 2.020000e-08 71.3
18 TraesCS1D01G410200 chr4B 91.489 47 3 1 2424 2470 89458246 89458291 3.380000e-06 63.9
19 TraesCS1D01G410200 chr2B 88.462 52 5 1 2419 2470 162868226 162868276 1.220000e-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 TraesCS1D01G410200 chr1D 471838802 471842857 4055 False 7491.000000 7491 100.000000 1 4056 1 chr1D.!!$F1 4055
1 TraesCS1D01G410200 chr1B 655846643 655851924 5281 False 1915.000000 5022 92.843000 1 4056 3 chr1B.!!$F2 4055
2 TraesCS1D01G410200 chr1B 24503229 24504282 1053 False 621.000000 621 78.704000 9 1007 1 chr1B.!!$F1 998
3 TraesCS1D01G410200 chr1A 566108765 566112483 3718 False 1727.333333 4553 93.877667 1 3732 3 chr1A.!!$F2 3731

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
656 729 0.250338 AGGCGTTCCAACCTTCAGTC 60.250 55.000 0.0 0.0 29.74 3.51 F
685 766 1.145738 CCCCCATGCTTTACTATGCCT 59.854 52.381 0.0 0.0 0.00 4.75 F
1066 1186 1.685421 GCTGAGCTGGAGAGGGAGT 60.685 63.158 0.0 0.0 0.00 3.85 F
2564 2698 2.031919 TGCGAGCCCGTGAACATT 59.968 55.556 0.0 0.0 38.24 2.71 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1840 1967 0.538287 AGAACCTGCAGGACCAAAGC 60.538 55.000 39.19 17.68 38.94 3.51 R
2564 2698 2.358957 CTCACCATTTCATCGCTTCCA 58.641 47.619 0.00 0.00 0.00 3.53 R
2669 2803 2.664851 TTGTCAGAGTTGCGGCCG 60.665 61.111 24.05 24.05 0.00 6.13 R
3568 3725 0.303493 CCCAATTTCGTATGACGCCG 59.697 55.000 0.00 0.00 42.21 6.46 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
60 61 4.816385 GTCAAAGGAGGATATCGCATTCAA 59.184 41.667 0.00 0.00 0.00 2.69
222 255 2.423538 ACCAACACACTGCAGAACTTTC 59.576 45.455 23.35 0.00 0.00 2.62
238 271 7.009179 AGAACTTTCTGTATCTCCATGTTCA 57.991 36.000 0.00 0.00 35.89 3.18
242 275 7.102346 ACTTTCTGTATCTCCATGTTCAGAAG 58.898 38.462 0.00 0.00 40.98 2.85
294 335 1.293924 CATCCGTCCATGAGACAAGC 58.706 55.000 12.80 0.00 46.69 4.01
297 338 0.389817 CCGTCCATGAGACAAGCGAA 60.390 55.000 12.80 0.00 46.69 4.70
349 390 5.104374 ACTGAACACACTGCAGAATTTTTG 58.896 37.500 23.35 9.62 33.94 2.44
587 660 3.003275 TGTTGTTCGAAGCAAGTTGGATC 59.997 43.478 4.75 0.00 0.00 3.36
609 682 4.041938 TCTTTTATTCCCTACGGTGTTGGT 59.958 41.667 0.00 0.00 0.00 3.67
618 691 0.466543 ACGGTGTTGGTCTGCAGTAA 59.533 50.000 14.67 5.20 0.00 2.24
619 692 1.071699 ACGGTGTTGGTCTGCAGTAAT 59.928 47.619 14.67 0.00 0.00 1.89
625 698 5.183140 GGTGTTGGTCTGCAGTAATGTTTAT 59.817 40.000 14.67 0.00 0.00 1.40
631 704 6.657117 TGGTCTGCAGTAATGTTTATTTAGCA 59.343 34.615 14.67 2.22 0.00 3.49
633 706 7.148239 GGTCTGCAGTAATGTTTATTTAGCAGT 60.148 37.037 14.67 0.00 40.77 4.40
641 714 5.539582 TGTTTATTTAGCAGTTGTAGGCG 57.460 39.130 0.00 0.00 34.54 5.52
656 729 0.250338 AGGCGTTCCAACCTTCAGTC 60.250 55.000 0.00 0.00 29.74 3.51
667 740 1.486726 ACCTTCAGTCGATGATTCCCC 59.513 52.381 0.00 0.00 37.89 4.81
685 766 1.145738 CCCCCATGCTTTACTATGCCT 59.854 52.381 0.00 0.00 0.00 4.75
686 767 2.375174 CCCCCATGCTTTACTATGCCTA 59.625 50.000 0.00 0.00 0.00 3.93
715 796 4.286297 CAGATCCCTGTAAAACCTGTCA 57.714 45.455 0.00 0.00 35.70 3.58
725 806 4.346709 TGTAAAACCTGTCAGGAGATGTGA 59.653 41.667 26.18 0.78 37.67 3.58
814 900 5.359009 ACATGACAAGGAATTAATGAGCAGG 59.641 40.000 0.00 0.00 0.00 4.85
861 972 7.093552 ACTGATGTACTCTGTTCAATCTTAGCT 60.094 37.037 0.00 0.00 32.62 3.32
1066 1186 1.685421 GCTGAGCTGGAGAGGGAGT 60.685 63.158 0.00 0.00 0.00 3.85
1299 1419 3.254060 CGTCGACCATGTCTTCAATCTT 58.746 45.455 10.58 0.00 0.00 2.40
1305 1425 2.477357 CCATGTCTTCAATCTTGCTGCG 60.477 50.000 0.00 0.00 0.00 5.18
1613 1739 7.201794 GGTGGTCTTTAGAAGCTTTGTTAAAGT 60.202 37.037 23.65 0.00 40.64 2.66
1624 1750 5.006941 AGCTTTGTTAAAGTTGCTTGCATTG 59.993 36.000 0.00 0.00 40.64 2.82
1713 1840 8.456471 ACCAAACTGAACTTAAGAAAACAGTAC 58.544 33.333 10.09 0.00 37.57 2.73
1716 1843 7.787725 ACTGAACTTAAGAAAACAGTACTGG 57.212 36.000 26.12 9.07 36.94 4.00
1722 1849 7.450903 ACTTAAGAAAACAGTACTGGTGCTAT 58.549 34.615 26.12 10.69 34.19 2.97
1727 1854 7.042335 AGAAAACAGTACTGGTGCTATGATAC 58.958 38.462 26.12 5.39 34.19 2.24
1728 1855 5.932619 AACAGTACTGGTGCTATGATACA 57.067 39.130 26.12 0.00 34.19 2.29
1730 1857 6.485830 ACAGTACTGGTGCTATGATACAAT 57.514 37.500 26.12 0.00 34.19 2.71
1765 1892 3.262135 TCCGTTCGAATTGTTTCAAGC 57.738 42.857 0.00 0.00 0.00 4.01
1775 1902 5.791974 CGAATTGTTTCAAGCACATGTCTAG 59.208 40.000 0.00 0.00 0.00 2.43
1791 1918 6.486657 ACATGTCTAGTTTGCAAGTACATTGT 59.513 34.615 0.00 0.00 41.29 2.71
1804 1931 6.363357 GCAAGTACATTGTCTCAAATCCAAAC 59.637 38.462 0.00 0.00 41.29 2.93
1813 1940 4.909880 GTCTCAAATCCAAACAACTTACGC 59.090 41.667 0.00 0.00 0.00 4.42
1840 1967 8.700722 TCCCATATTGATTCGATTTTGTTTTG 57.299 30.769 0.00 0.00 0.00 2.44
2209 2339 4.215109 TCGATCATAATGTCACCCTGAGA 58.785 43.478 0.00 0.00 0.00 3.27
2377 2507 3.066481 GTCGAGGGTGTTCTGAGGTATAC 59.934 52.174 0.00 0.00 0.00 1.47
2385 2515 5.826737 GGTGTTCTGAGGTATACAGCTACTA 59.173 44.000 5.01 0.00 36.41 1.82
2402 2532 6.865726 CAGCTACTAGTCACATTATCCACATC 59.134 42.308 0.00 0.00 0.00 3.06
2419 2549 5.719563 TCCACATCATACCAGACAGAACTAA 59.280 40.000 0.00 0.00 0.00 2.24
2421 2551 6.313905 CCACATCATACCAGACAGAACTAAAC 59.686 42.308 0.00 0.00 0.00 2.01
2486 2618 5.600898 ACCAATTAAAAACTACTGCCTTGGT 59.399 36.000 0.00 0.00 39.09 3.67
2503 2635 8.537728 TGCCTTGGTAGAAATGATAAATCAAT 57.462 30.769 0.00 0.00 40.69 2.57
2504 2636 8.415553 TGCCTTGGTAGAAATGATAAATCAATG 58.584 33.333 0.00 0.00 40.69 2.82
2564 2698 2.031919 TGCGAGCCCGTGAACATT 59.968 55.556 0.00 0.00 38.24 2.71
2612 2746 3.055530 ACGAGATGGCTGAGATTGTTCTT 60.056 43.478 0.00 0.00 30.30 2.52
2669 2803 4.083862 GGTCCAGAGGGTGTCCGC 62.084 72.222 0.00 0.00 38.33 5.54
2755 2889 7.477144 TCAAGGTAATGTAGCATAATTGTCG 57.523 36.000 0.00 0.00 0.00 4.35
2775 2910 2.878406 CGAACACTGACAATTCCAACCT 59.122 45.455 0.00 0.00 0.00 3.50
2783 2918 4.074259 TGACAATTCCAACCTCACATGAG 58.926 43.478 0.00 1.63 41.71 2.90
2792 2927 5.013079 TCCAACCTCACATGAGAATAACACT 59.987 40.000 10.55 0.00 44.74 3.55
2818 2953 7.555965 TGAAGCTCTTTACATTAGCACAGATA 58.444 34.615 0.00 0.00 38.75 1.98
2854 2989 7.015226 TGTTATGATGGCTTCAGTAAAATCG 57.985 36.000 9.09 0.00 37.89 3.34
2986 3125 1.040893 ACGTCGCCCTGTATGGATCA 61.041 55.000 0.00 0.00 38.35 2.92
3073 3215 3.551890 AGTAAACTATGCAGATCAACGCG 59.448 43.478 3.53 3.53 0.00 6.01
3076 3218 1.405463 ACTATGCAGATCAACGCGAGA 59.595 47.619 15.93 11.26 0.00 4.04
3077 3219 2.035193 ACTATGCAGATCAACGCGAGAT 59.965 45.455 15.93 16.17 0.00 2.75
3122 3266 2.159517 CGGATCCTTCCTTGCGAAAAAG 60.160 50.000 10.75 0.00 40.17 2.27
3134 3279 6.207417 TCCTTGCGAAAAAGATTCAGAGAATT 59.793 34.615 0.00 0.00 0.00 2.17
3150 3295 0.251742 AATTGCACAGCCTGCCCTAA 60.252 50.000 0.00 0.00 46.51 2.69
3162 3307 0.916845 TGCCCTAACTACCCCATGCA 60.917 55.000 0.00 0.00 0.00 3.96
3169 3315 2.038387 ACTACCCCATGCACGATTTC 57.962 50.000 0.00 0.00 0.00 2.17
3195 3341 5.049543 GCAGATTCAAGTGCTCCTATTCATC 60.050 44.000 0.00 0.00 36.71 2.92
3205 3351 1.745890 CTATTCATCGTCGCCCCCA 59.254 57.895 0.00 0.00 0.00 4.96
3207 3353 0.762418 TATTCATCGTCGCCCCCATT 59.238 50.000 0.00 0.00 0.00 3.16
3278 3424 7.517254 TGATTGGATGAAGAATAAGATCCCCTA 59.483 37.037 0.00 0.00 34.54 3.53
3463 3620 3.264450 AGTGGCAGTAGACCAGCTTAAAT 59.736 43.478 0.00 0.00 38.04 1.40
3552 3709 5.645624 TGAATAGAAGCTCTGAAGAACTCG 58.354 41.667 0.00 0.00 0.00 4.18
3579 3866 1.225637 GCAAACACGGCGTCATACG 60.226 57.895 10.85 0.00 45.88 3.06
3611 3898 6.751888 GGACTGAACCAAAAATAATTCATCCG 59.248 38.462 0.00 0.00 31.00 4.18
3613 3900 7.538575 ACTGAACCAAAAATAATTCATCCGAG 58.461 34.615 0.00 0.00 31.00 4.63
3761 4048 4.488879 CCCTTTTCATTGCAGAGTTAAGC 58.511 43.478 0.00 0.00 0.00 3.09
3762 4049 4.022068 CCCTTTTCATTGCAGAGTTAAGCA 60.022 41.667 0.00 0.00 39.32 3.91
3824 5145 5.923733 TTTGGAAACAGAGGCAACTTAAA 57.076 34.783 0.00 0.00 45.81 1.52
3839 5160 8.925161 GGCAACTTAAACAAATATAATGCTGA 57.075 30.769 0.00 0.00 0.00 4.26
3840 5161 8.807581 GGCAACTTAAACAAATATAATGCTGAC 58.192 33.333 0.00 0.00 0.00 3.51
3878 5199 7.646922 GGAAGCAGAAGCAATATTTTCTATGTG 59.353 37.037 2.75 0.00 45.49 3.21
3893 5214 4.546674 TCTATGTGAGTGCTCCTATTCCA 58.453 43.478 0.00 0.00 0.00 3.53
3894 5215 3.550437 ATGTGAGTGCTCCTATTCCAC 57.450 47.619 0.00 0.00 0.00 4.02
3917 5238 2.343758 GTGCGAGGAGAACCAGCA 59.656 61.111 0.00 0.00 44.80 4.41
3932 5253 1.270252 CCAGCAAACACAAACCCATCC 60.270 52.381 0.00 0.00 0.00 3.51
3938 5259 1.285641 CACAAACCCATCCGCACAC 59.714 57.895 0.00 0.00 0.00 3.82
3950 5271 0.038526 CCGCACACTTTAGGTCGACT 60.039 55.000 16.46 4.12 0.00 4.18
3953 5274 2.067013 GCACACTTTAGGTCGACTTCC 58.933 52.381 16.46 0.00 0.00 3.46
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
6 7 7.870954 TCGAAAACACAATAGTTAGACAGATGT 59.129 33.333 0.00 0.00 0.00 3.06
60 61 1.395826 GCCAGGAGTGTCGCCTCTAT 61.396 60.000 0.00 0.00 29.38 1.98
222 255 5.604758 TCCTTCTGAACATGGAGATACAG 57.395 43.478 0.00 0.00 0.00 2.74
228 261 3.760151 TGCAAATCCTTCTGAACATGGAG 59.240 43.478 0.00 0.00 31.59 3.86
229 262 3.765381 TGCAAATCCTTCTGAACATGGA 58.235 40.909 0.00 0.03 0.00 3.41
231 264 5.716094 TCATTGCAAATCCTTCTGAACATG 58.284 37.500 1.71 0.00 0.00 3.21
232 265 5.988310 TCATTGCAAATCCTTCTGAACAT 57.012 34.783 1.71 0.00 0.00 2.71
233 266 5.787953 TTCATTGCAAATCCTTCTGAACA 57.212 34.783 1.71 0.00 0.00 3.18
264 298 0.171007 GGACGGATGCATTGGTGTTG 59.829 55.000 0.00 0.00 0.00 3.33
267 301 0.382873 CATGGACGGATGCATTGGTG 59.617 55.000 0.00 0.00 34.04 4.17
609 682 7.921786 ACTGCTAAATAAACATTACTGCAGA 57.078 32.000 23.35 0.00 45.42 4.26
618 691 5.646360 ACGCCTACAACTGCTAAATAAACAT 59.354 36.000 0.00 0.00 0.00 2.71
619 692 4.998672 ACGCCTACAACTGCTAAATAAACA 59.001 37.500 0.00 0.00 0.00 2.83
625 698 2.224329 TGGAACGCCTACAACTGCTAAA 60.224 45.455 0.00 0.00 34.31 1.85
631 704 0.763035 AGGTTGGAACGCCTACAACT 59.237 50.000 11.76 0.00 42.93 3.16
633 706 1.141254 TGAAGGTTGGAACGCCTACAA 59.859 47.619 0.00 0.00 41.03 2.41
641 714 3.040147 TCATCGACTGAAGGTTGGAAC 57.960 47.619 0.00 0.00 0.00 3.62
667 740 3.181445 TGGTAGGCATAGTAAAGCATGGG 60.181 47.826 0.00 0.00 0.00 4.00
709 790 2.093075 AGCATTCACATCTCCTGACAGG 60.093 50.000 15.99 15.99 36.46 4.00
715 796 3.708403 TGTTCAGCATTCACATCTCCT 57.292 42.857 0.00 0.00 0.00 3.69
725 806 3.562973 CAGCCGAATCTATGTTCAGCATT 59.437 43.478 0.00 0.00 38.94 3.56
814 900 2.648059 ACACATCCATTGCTTAGAGGC 58.352 47.619 0.00 0.00 0.00 4.70
1066 1186 2.355108 GCTTCTCAGATGGCCAGTACAA 60.355 50.000 13.05 0.00 0.00 2.41
1299 1419 3.150949 CCTCCCATATCCGCAGCA 58.849 61.111 0.00 0.00 0.00 4.41
1305 1425 1.142688 ACCCCATGCCTCCCATATCC 61.143 60.000 0.00 0.00 31.47 2.59
1407 1527 7.639113 AAATGAAGTTACAAACCTCTTCACA 57.361 32.000 8.29 0.00 45.38 3.58
1486 1606 9.511272 AATAAACCGTTTCCAATAGACTTAGTT 57.489 29.630 0.00 0.00 0.00 2.24
1489 1610 8.732531 CCAAATAAACCGTTTCCAATAGACTTA 58.267 33.333 0.00 0.00 0.00 2.24
1504 1625 9.855021 AGTAATTTCTGAATTCCAAATAAACCG 57.145 29.630 2.27 0.00 36.82 4.44
1613 1739 7.554211 TGAATATATTTGTCCAATGCAAGCAA 58.446 30.769 0.00 0.00 0.00 3.91
1727 1854 8.225107 TCGAACGGAAAACAGAGTTAATTATTG 58.775 33.333 0.00 0.00 0.00 1.90
1728 1855 8.314143 TCGAACGGAAAACAGAGTTAATTATT 57.686 30.769 0.00 0.00 0.00 1.40
1730 1857 7.712264 TTCGAACGGAAAACAGAGTTAATTA 57.288 32.000 0.00 0.00 0.00 1.40
1748 1875 4.739716 ACATGTGCTTGAAACAATTCGAAC 59.260 37.500 0.00 0.00 38.46 3.95
1765 1892 5.922739 TGTACTTGCAAACTAGACATGTG 57.077 39.130 1.15 0.00 0.00 3.21
1775 1902 6.363357 GGATTTGAGACAATGTACTTGCAAAC 59.637 38.462 0.00 0.00 38.50 2.93
1791 1918 4.576873 TGCGTAAGTTGTTTGGATTTGAGA 59.423 37.500 0.00 0.00 41.68 3.27
1804 1931 5.947228 ATCAATATGGGATGCGTAAGTTG 57.053 39.130 0.00 0.00 41.68 3.16
1813 1940 8.876275 AAACAAAATCGAATCAATATGGGATG 57.124 30.769 0.00 0.00 0.00 3.51
1840 1967 0.538287 AGAACCTGCAGGACCAAAGC 60.538 55.000 39.19 17.68 38.94 3.51
2102 2232 3.585862 GCACTCGATGTCAAAGTCCTTA 58.414 45.455 0.00 0.00 0.00 2.69
2377 2507 6.149129 TGTGGATAATGTGACTAGTAGCTG 57.851 41.667 0.00 0.00 0.00 4.24
2385 2515 6.327365 TCTGGTATGATGTGGATAATGTGACT 59.673 38.462 0.00 0.00 0.00 3.41
2463 2595 6.096673 ACCAAGGCAGTAGTTTTTAATTGG 57.903 37.500 0.00 0.00 40.35 3.16
2507 2639 9.204570 GTCAATCTACAAAGTACAGTGTGTTAT 57.795 33.333 5.88 0.00 0.00 1.89
2509 2641 7.045416 TGTCAATCTACAAAGTACAGTGTGTT 58.955 34.615 5.88 0.00 0.00 3.32
2564 2698 2.358957 CTCACCATTTCATCGCTTCCA 58.641 47.619 0.00 0.00 0.00 3.53
2612 2746 3.914984 CTTCTTGTCCTCGAAGCCA 57.085 52.632 0.00 0.00 31.34 4.75
2669 2803 2.664851 TTGTCAGAGTTGCGGCCG 60.665 61.111 24.05 24.05 0.00 6.13
2755 2889 3.882888 TGAGGTTGGAATTGTCAGTGTTC 59.117 43.478 0.00 0.00 0.00 3.18
2775 2910 6.233434 AGCTTCAAGTGTTATTCTCATGTGA 58.767 36.000 0.00 0.00 0.00 3.58
2792 2927 6.230472 TCTGTGCTAATGTAAAGAGCTTCAA 58.770 36.000 0.00 0.00 37.12 2.69
2854 2989 6.038356 TGTTAATTATCTTCGACTTCCCGAC 58.962 40.000 0.00 0.00 38.39 4.79
3073 3215 2.028567 GGGCAGTGGCATAGTAGATCTC 60.029 54.545 19.48 0.00 43.71 2.75
3076 3218 1.806496 TGGGCAGTGGCATAGTAGAT 58.194 50.000 19.48 0.00 43.71 1.98
3077 3219 1.694150 GATGGGCAGTGGCATAGTAGA 59.306 52.381 19.48 0.00 43.71 2.59
3081 3223 0.179048 TTCGATGGGCAGTGGCATAG 60.179 55.000 19.48 10.25 43.71 2.23
3122 3266 3.015327 AGGCTGTGCAATTCTCTGAATC 58.985 45.455 0.00 0.00 0.00 2.52
3150 3295 1.280710 TGAAATCGTGCATGGGGTAGT 59.719 47.619 5.98 0.00 0.00 2.73
3162 3307 3.120060 GCACTTGAATCTGCTGAAATCGT 60.120 43.478 0.00 0.00 0.00 3.73
3169 3315 2.110901 AGGAGCACTTGAATCTGCTG 57.889 50.000 0.02 0.00 43.94 4.41
3195 3341 5.183228 AGATAATAATTAATGGGGGCGACG 58.817 41.667 0.00 0.00 0.00 5.12
3278 3424 7.693969 ATACAGCTCAGCTTCAAAGTAAAAT 57.306 32.000 0.00 0.00 36.40 1.82
3452 3609 8.807948 ATACATGTAAGAACATTTAAGCTGGT 57.192 30.769 10.14 0.00 44.07 4.00
3489 3646 8.893219 TTCAATGGAGCTACTATGTTTATCTG 57.107 34.615 0.00 0.00 0.00 2.90
3568 3725 0.303493 CCCAATTTCGTATGACGCCG 59.697 55.000 0.00 0.00 42.21 6.46
3579 3866 8.846943 ATTATTTTTGGTTCAGTCCCAATTTC 57.153 30.769 0.00 0.00 41.43 2.17
3611 3898 6.341316 TCCTTCATAGATTGTAACTGCACTC 58.659 40.000 0.00 0.00 0.00 3.51
3613 3900 6.763135 TCATCCTTCATAGATTGTAACTGCAC 59.237 38.462 0.00 0.00 0.00 4.57
3770 5088 8.045176 AGTCAATTATTTCAAACACTCTAGGC 57.955 34.615 0.00 0.00 0.00 3.93
3805 5123 4.911514 TGTTTAAGTTGCCTCTGTTTCC 57.088 40.909 0.00 0.00 0.00 3.13
3878 5199 1.202428 GGTCGTGGAATAGGAGCACTC 60.202 57.143 0.00 0.00 40.42 3.51
3894 5215 3.744719 TTCTCCTCGCACGGGTCG 61.745 66.667 0.00 0.00 0.00 4.79
3903 5224 0.868406 GTGTTTGCTGGTTCTCCTCG 59.132 55.000 0.00 0.00 34.23 4.63
3917 5238 0.387565 GTGCGGATGGGTTTGTGTTT 59.612 50.000 0.00 0.00 0.00 2.83
3932 5253 1.719780 GAAGTCGACCTAAAGTGTGCG 59.280 52.381 13.01 0.00 0.00 5.34
3938 5259 2.678336 GCAATGGGAAGTCGACCTAAAG 59.322 50.000 13.01 0.00 0.00 1.85


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

AutoCloner maintained by Alex Coulton.