Multiple sequence alignment - TraesCS7A01G054700

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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 TraesCS7A01G054700 chr7A 100.000 3880 0 0 1 3880 26415647 26419526 0.000000e+00 7166
1 TraesCS7A01G054700 chr7A 96.923 65 2 0 3345 3409 26424976 26425040 4.100000e-20 110
2 TraesCS7A01G054700 chr7A 96.923 65 2 0 3345 3409 95805670 95805606 4.100000e-20 110
3 TraesCS7A01G054700 chr4A 92.061 3930 192 46 1 3870 709893621 709897490 0.000000e+00 5419
4 TraesCS7A01G054700 chr7D 93.186 3405 151 37 1 3356 25399171 25402543 0.000000e+00 4927
5 TraesCS7A01G054700 chr7D 86.393 463 28 15 3409 3869 25402532 25402961 1.260000e-129 473
6 TraesCS7A01G054700 chr7D 98.462 65 1 0 3345 3409 25407646 25407710 8.810000e-22 115
7 TraesCS7A01G054700 chr7D 96.923 65 2 0 3345 3409 93505842 93505778 4.100000e-20 110
8 TraesCS7A01G054700 chr7B 98.246 57 1 0 3353 3409 46350458 46350402 2.470000e-17 100


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 TraesCS7A01G054700 chr7A 26415647 26419526 3879 False 7166 7166 100.0000 1 3880 1 chr7A.!!$F1 3879
1 TraesCS7A01G054700 chr4A 709893621 709897490 3869 False 5419 5419 92.0610 1 3870 1 chr4A.!!$F1 3869
2 TraesCS7A01G054700 chr7D 25399171 25402961 3790 False 2700 4927 89.7895 1 3869 2 chr7D.!!$F2 3868

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
370 382 0.241481 TTTTGTACATTTCCCGCGCC 59.759 50.0 0.00 0.00 0.0 6.53 F
371 383 0.606944 TTTGTACATTTCCCGCGCCT 60.607 50.0 0.00 0.00 0.0 5.52 F
1682 1710 0.181587 TTCCAAGACCGGTTTGCAGA 59.818 50.0 9.42 6.48 0.0 4.26 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1384 1411 0.176680 GCGTGTCCACATCCAGATCT 59.823 55.0 0.00 0.00 0.00 2.75 R
2221 2257 0.762418 TCTCCCGGTTTCTGAAAGCA 59.238 50.0 26.18 10.76 38.75 3.91 R
3213 3283 0.607112 CTCAGAGAGCAGGCTGTTCA 59.393 55.0 29.23 10.90 33.90 3.18 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
34 35 3.003480 GTTGGAGTATGCAGTGAACCTC 58.997 50.000 0.00 0.00 38.09 3.85
231 242 7.733773 AAAAGAAAGGAAGGAGGAAGAAAAA 57.266 32.000 0.00 0.00 0.00 1.94
331 343 4.780554 AGGAGGATTATCTTTAGGCCTAGC 59.219 45.833 13.36 0.00 0.00 3.42
370 382 0.241481 TTTTGTACATTTCCCGCGCC 59.759 50.000 0.00 0.00 0.00 6.53
371 383 0.606944 TTTGTACATTTCCCGCGCCT 60.607 50.000 0.00 0.00 0.00 5.52
372 384 1.022451 TTGTACATTTCCCGCGCCTC 61.022 55.000 0.00 0.00 0.00 4.70
373 385 1.153429 GTACATTTCCCGCGCCTCT 60.153 57.895 0.00 0.00 0.00 3.69
374 386 1.143183 TACATTTCCCGCGCCTCTC 59.857 57.895 0.00 0.00 0.00 3.20
375 387 2.306255 TACATTTCCCGCGCCTCTCC 62.306 60.000 0.00 0.00 0.00 3.71
376 388 4.176752 ATTTCCCGCGCCTCTCCC 62.177 66.667 0.00 0.00 0.00 4.30
507 522 9.152595 GTATATATAAGTAAGCACTTTGGAGGC 57.847 37.037 0.00 0.00 42.51 4.70
651 666 1.273606 CAGGCTCTGAAGAAACGGAGA 59.726 52.381 0.00 0.00 43.59 3.71
700 715 3.200825 TCCTCCTGTTCATGATTCTTCCC 59.799 47.826 0.00 0.00 0.00 3.97
707 722 2.863884 TCATGATTCTTCCCCCTTCCT 58.136 47.619 0.00 0.00 0.00 3.36
1298 1325 4.891037 GCCATGGGGAGAGCAGCC 62.891 72.222 15.13 0.00 35.59 4.85
1300 1327 3.790437 CATGGGGAGAGCAGCCGT 61.790 66.667 0.00 0.00 0.00 5.68
1345 1372 3.599730 ACTTCAGATGAACAGATCGCA 57.400 42.857 0.00 0.00 0.00 5.10
1348 1375 1.479730 TCAGATGAACAGATCGCAGCT 59.520 47.619 0.00 0.00 0.00 4.24
1384 1411 0.182061 GGATGCTGCAGGAGATGGAA 59.818 55.000 17.12 0.00 0.00 3.53
1545 1573 1.687612 CTGTGTGCCTTCCCCATCT 59.312 57.895 0.00 0.00 0.00 2.90
1557 1585 0.761187 CCCCATCTGACACCGATGAT 59.239 55.000 6.31 0.00 40.47 2.45
1566 1594 2.120232 GACACCGATGATGACGATGAC 58.880 52.381 0.00 0.00 0.00 3.06
1598 1626 7.751348 CGACGAAGAGGAGGTGATTTATTATAG 59.249 40.741 0.00 0.00 0.00 1.31
1604 1632 7.794683 AGAGGAGGTGATTTATTATAGGAACCA 59.205 37.037 0.00 0.00 0.00 3.67
1667 1695 6.424509 CAGCTTGCATCAAACTAAAAATTCCA 59.575 34.615 0.00 0.00 0.00 3.53
1682 1710 0.181587 TTCCAAGACCGGTTTGCAGA 59.818 50.000 9.42 6.48 0.00 4.26
1800 1828 5.451381 CCCACAGTTTCTTTTTCTGTTACCC 60.451 44.000 0.00 0.00 39.89 3.69
1848 1876 9.941664 CGAGATTTCTTTGTCAATAAATAGCAT 57.058 29.630 6.45 0.00 0.00 3.79
2061 2096 3.623906 AACCATGATGAGTGAGTCCAG 57.376 47.619 0.00 0.00 0.00 3.86
2221 2257 1.762957 ACTTGTACTGTGTGCCTGTCT 59.237 47.619 0.00 0.00 0.00 3.41
2252 2288 1.489230 ACCGGGAGAACATCATAACCC 59.511 52.381 6.32 0.00 0.00 4.11
2275 2311 3.194542 TGCCCTGCAAACATAATTACCAC 59.805 43.478 0.00 0.00 34.76 4.16
2317 2353 2.289945 GCTCAAGATCAACAGGGTGAGT 60.290 50.000 0.00 0.00 35.89 3.41
2413 2449 4.074259 TGCTGATATGTGCTCAACTGTTT 58.926 39.130 0.00 0.00 0.00 2.83
2617 2655 3.132111 TGTCAAAAGGAAGGAAAAGGCAC 59.868 43.478 0.00 0.00 0.00 5.01
2619 2657 3.132111 TCAAAAGGAAGGAAAAGGCACAC 59.868 43.478 0.00 0.00 0.00 3.82
2845 2902 1.202222 GCTATTGTGGTGCTGTGATGC 60.202 52.381 0.00 0.00 0.00 3.91
2886 2943 6.346477 TGATACTACTTATGATGACAGGCC 57.654 41.667 0.00 0.00 0.00 5.19
2897 2954 0.106708 TGACAGGCCACTCAAGTCAC 59.893 55.000 5.01 0.00 34.59 3.67
2915 2972 8.729756 TCAAGTCACACATGATAATAACAAAGG 58.270 33.333 0.00 0.00 37.14 3.11
3019 3085 3.838317 ACTACAGGGTTGAACTGCTATCA 59.162 43.478 0.00 0.00 39.55 2.15
3039 3105 3.641436 TCAAAGCCAACTCACACTCTCTA 59.359 43.478 0.00 0.00 0.00 2.43
3073 3139 6.672266 AGGTTTCACCGATATATGATCACT 57.328 37.500 0.00 0.00 44.90 3.41
3099 3169 7.047891 AGAATGTTCCAGCGAAACAAGATATA 58.952 34.615 5.84 0.00 39.84 0.86
3136 3206 9.461312 AGAAAAACATGTAGTAATCTAATGGCA 57.539 29.630 0.00 0.00 0.00 4.92
3143 3213 8.849168 CATGTAGTAATCTAATGGCAATTTCCA 58.151 33.333 0.00 0.00 40.97 3.53
3159 3229 7.983484 GGCAATTTCCAATCAATCATAACTCTT 59.017 33.333 0.00 0.00 0.00 2.85
3173 3243 7.297936 TCATAACTCTTGGAGTAGTCAAACA 57.702 36.000 0.00 0.00 42.59 2.83
3183 3253 4.564821 GGAGTAGTCAAACATAGGTTGGCA 60.565 45.833 2.01 0.00 37.30 4.92
3209 3279 2.425312 TGTGGTTTGTCACATGTTCCAC 59.575 45.455 16.29 16.29 42.05 4.02
3213 3283 1.603456 TTGTCACATGTTCCACGCAT 58.397 45.000 0.00 0.00 0.00 4.73
3214 3284 0.873721 TGTCACATGTTCCACGCATG 59.126 50.000 0.00 4.02 46.51 4.06
3222 3292 1.073025 TTCCACGCATGAACAGCCT 59.927 52.632 0.00 0.00 0.00 4.58
3234 3304 0.896923 AACAGCCTGCTCTCTGAGAG 59.103 55.000 26.58 26.58 45.04 3.20
3274 3344 1.141881 GAGATCGTCCATGCCGTGT 59.858 57.895 3.42 0.00 0.00 4.49
3308 3378 3.396260 TTGGAGTCAAACTTAGGTCGG 57.604 47.619 0.00 0.00 0.00 4.79
3348 3418 5.183713 TCACATGTTCCATGAAAATCCAGTC 59.816 40.000 10.96 0.00 0.00 3.51
3349 3419 5.184479 CACATGTTCCATGAAAATCCAGTCT 59.816 40.000 10.96 0.00 0.00 3.24
3350 3420 5.184479 ACATGTTCCATGAAAATCCAGTCTG 59.816 40.000 10.96 0.00 0.00 3.51
3351 3421 3.507233 TGTTCCATGAAAATCCAGTCTGC 59.493 43.478 0.00 0.00 0.00 4.26
3352 3422 3.726557 TCCATGAAAATCCAGTCTGCT 57.273 42.857 0.00 0.00 0.00 4.24
3353 3423 4.038271 TCCATGAAAATCCAGTCTGCTT 57.962 40.909 0.00 0.00 0.00 3.91
3354 3424 3.760151 TCCATGAAAATCCAGTCTGCTTG 59.240 43.478 0.00 0.00 0.00 4.01
3355 3425 3.119245 CCATGAAAATCCAGTCTGCTTGG 60.119 47.826 0.00 0.00 0.00 3.61
3356 3426 2.517959 TGAAAATCCAGTCTGCTTGGG 58.482 47.619 0.00 0.00 0.00 4.12
3357 3427 2.108075 TGAAAATCCAGTCTGCTTGGGA 59.892 45.455 0.00 0.00 0.00 4.37
3358 3428 3.245371 TGAAAATCCAGTCTGCTTGGGAT 60.245 43.478 0.00 0.00 41.80 3.85
3359 3429 4.018506 TGAAAATCCAGTCTGCTTGGGATA 60.019 41.667 0.00 0.00 39.17 2.59
3360 3430 3.853355 AATCCAGTCTGCTTGGGATAG 57.147 47.619 0.00 0.00 39.17 2.08
3361 3431 2.254152 TCCAGTCTGCTTGGGATAGT 57.746 50.000 0.00 0.00 0.00 2.12
3380 3450 0.837691 TTCTTCAGGCCCTCTGCAGA 60.838 55.000 17.19 17.19 42.48 4.26
3401 3471 7.545265 TGCAGATGAACAGGCAAAATATTAAAC 59.455 33.333 0.00 0.00 32.54 2.01
3402 3472 7.545265 GCAGATGAACAGGCAAAATATTAAACA 59.455 33.333 0.00 0.00 0.00 2.83
3422 3492 7.913674 AAACATTTAAAGTTTGACTTGGCAA 57.086 28.000 0.00 0.00 38.66 4.52
3423 3493 7.913674 AACATTTAAAGTTTGACTTGGCAAA 57.086 28.000 0.00 0.00 38.66 3.68
3424 3494 7.913674 ACATTTAAAGTTTGACTTGGCAAAA 57.086 28.000 2.93 0.00 38.66 2.44
3438 3508 7.015682 TGACTTGGCAAAATATTAACCAAAGGA 59.984 33.333 14.31 3.18 39.76 3.36
3514 3587 8.409358 AGCTACATTTTTAGAACCACAGAAAT 57.591 30.769 0.00 0.00 0.00 2.17
3587 3663 4.729868 AGTTTGAAAGAAGGTGCTATGGT 58.270 39.130 0.00 0.00 0.00 3.55
3615 3691 4.858850 TGAGGACTGCAATGAATTATGGT 58.141 39.130 0.00 0.00 0.00 3.55
3659 3735 4.152045 GTGTTCTGCATCTGAAGACTGAAG 59.848 45.833 7.08 0.00 34.52 3.02
3751 3827 2.757894 TGGTTGTTACACACCCCAAT 57.242 45.000 11.92 0.00 28.32 3.16
3758 3834 2.301583 GTTACACACCCCAATTGCCAAT 59.698 45.455 0.00 0.00 0.00 3.16
3774 3850 5.694231 TGCCAATGATCAGCAATATACAC 57.306 39.130 5.70 0.00 32.56 2.90
3775 3851 5.131784 TGCCAATGATCAGCAATATACACA 58.868 37.500 5.70 0.00 32.56 3.72
3776 3852 5.593502 TGCCAATGATCAGCAATATACACAA 59.406 36.000 5.70 0.00 32.56 3.33
3777 3853 5.916883 GCCAATGATCAGCAATATACACAAC 59.083 40.000 0.09 0.00 0.00 3.32
3778 3854 6.238842 GCCAATGATCAGCAATATACACAACT 60.239 38.462 0.09 0.00 0.00 3.16
3779 3855 7.682741 GCCAATGATCAGCAATATACACAACTT 60.683 37.037 0.09 0.00 0.00 2.66
3780 3856 8.839343 CCAATGATCAGCAATATACACAACTTA 58.161 33.333 0.09 0.00 0.00 2.24
3801 3877 7.175104 ACTTAACTAGAAAATGCCAGGAATCA 58.825 34.615 0.00 0.00 0.00 2.57
3843 3919 8.094798 TGTAGTAAACAGCTAAAAGAACCATG 57.905 34.615 0.00 0.00 33.01 3.66
3854 3930 0.963962 AGAACCATGTGCAGCCTTTG 59.036 50.000 0.00 0.00 0.00 2.77
3869 3945 5.222631 CAGCCTTTGAACCAAGTGTTAATC 58.777 41.667 0.00 0.00 37.29 1.75
3870 3946 4.280929 AGCCTTTGAACCAAGTGTTAATCC 59.719 41.667 0.00 0.00 37.29 3.01
3871 3947 4.560716 GCCTTTGAACCAAGTGTTAATCCC 60.561 45.833 0.00 0.00 37.29 3.85
3872 3948 4.021456 CCTTTGAACCAAGTGTTAATCCCC 60.021 45.833 0.00 0.00 37.29 4.81
3873 3949 3.885976 TGAACCAAGTGTTAATCCCCA 57.114 42.857 0.00 0.00 37.29 4.96
3874 3950 3.761897 TGAACCAAGTGTTAATCCCCAG 58.238 45.455 0.00 0.00 37.29 4.45
3875 3951 3.139397 TGAACCAAGTGTTAATCCCCAGT 59.861 43.478 0.00 0.00 37.29 4.00
3876 3952 3.154827 ACCAAGTGTTAATCCCCAGTG 57.845 47.619 0.00 0.00 0.00 3.66
3877 3953 1.818674 CCAAGTGTTAATCCCCAGTGC 59.181 52.381 0.00 0.00 0.00 4.40
3878 3954 2.513753 CAAGTGTTAATCCCCAGTGCA 58.486 47.619 0.00 0.00 0.00 4.57
3879 3955 3.091545 CAAGTGTTAATCCCCAGTGCAT 58.908 45.455 0.00 0.00 0.00 3.96
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
34 35 0.313043 CTTCACAGGTGGCAAGCAAG 59.687 55.000 0.00 0.00 0.00 4.01
181 182 9.826574 TTACCTCTACATATGTTAACCACATTC 57.173 33.333 14.77 0.00 44.40 2.67
201 204 5.877491 TCCTCCTTCCTTTCTTTTTACCTC 58.123 41.667 0.00 0.00 0.00 3.85
246 257 5.646793 TGAGGAGCTTTCATCTCAGATTTTG 59.353 40.000 0.00 0.00 33.07 2.44
267 278 3.815401 CCCCAACTGAACTAACTGTTGAG 59.185 47.826 15.91 6.53 45.62 3.02
331 343 5.428184 AAATGTGTAGAGGGAGAAAGAGG 57.572 43.478 0.00 0.00 0.00 3.69
409 421 1.608627 GGAGGCCCCGACGGTATAT 60.609 63.158 13.94 0.00 0.00 0.86
507 522 0.958822 GGTGGTTGGTTGGTTAGCTG 59.041 55.000 0.00 0.00 0.00 4.24
674 689 4.789807 AGAATCATGAACAGGAGGATTGG 58.210 43.478 0.00 0.00 0.00 3.16
700 715 1.562008 GAGGAGAAAAGGGAGGAAGGG 59.438 57.143 0.00 0.00 0.00 3.95
707 722 2.093447 GCGATGAAGAGGAGAAAAGGGA 60.093 50.000 0.00 0.00 0.00 4.20
767 782 3.180613 GAGGATCTTTCGTTCGGAAGAC 58.819 50.000 16.57 11.06 41.84 3.01
774 792 4.457834 TTCTGAGGAGGATCTTTCGTTC 57.542 45.455 0.00 0.00 33.73 3.95
782 800 7.449247 AGCAGTAATAATTTCTGAGGAGGATC 58.551 38.462 4.11 0.00 0.00 3.36
784 802 6.814954 AGCAGTAATAATTTCTGAGGAGGA 57.185 37.500 4.11 0.00 0.00 3.71
1065 1086 1.449601 ATCGTGGTTGGCATCGTCC 60.450 57.895 0.00 0.00 0.00 4.79
1074 1095 1.350193 CGAGGAAGTCATCGTGGTTG 58.650 55.000 7.18 0.00 44.02 3.77
1205 1232 4.082026 CAGGCCCTCCTAAGAAAACAAATG 60.082 45.833 0.00 0.00 41.93 2.32
1298 1325 2.545596 TTTCTGCTGCTGTGCCACG 61.546 57.895 0.00 0.00 0.00 4.94
1300 1327 2.195567 GGTTTCTGCTGCTGTGCCA 61.196 57.895 0.00 0.00 0.00 4.92
1345 1372 0.613260 TGGCGTATTTGAGGTCAGCT 59.387 50.000 0.00 0.00 0.00 4.24
1348 1375 1.271856 TCCTGGCGTATTTGAGGTCA 58.728 50.000 0.00 0.00 0.00 4.02
1384 1411 0.176680 GCGTGTCCACATCCAGATCT 59.823 55.000 0.00 0.00 0.00 2.75
1545 1573 1.748493 TCATCGTCATCATCGGTGTCA 59.252 47.619 0.00 0.00 39.89 3.58
1598 1626 5.576774 GCAAGCAACTACAAATATTGGTTCC 59.423 40.000 0.00 0.00 40.92 3.62
1604 1632 9.410556 CTTAACAAGCAAGCAACTACAAATATT 57.589 29.630 0.00 0.00 0.00 1.28
1667 1695 1.166531 GCAGTCTGCAAACCGGTCTT 61.167 55.000 20.16 1.26 44.26 3.01
1695 1723 3.798878 GTCGTCGTTGTCATCATCATCAT 59.201 43.478 0.00 0.00 0.00 2.45
1696 1724 3.179048 GTCGTCGTTGTCATCATCATCA 58.821 45.455 0.00 0.00 0.00 3.07
1697 1725 3.000674 GTGTCGTCGTTGTCATCATCATC 60.001 47.826 0.00 0.00 0.00 2.92
1738 1766 6.240894 ACAAACCTCATATGTCATGTTGTCT 58.759 36.000 1.90 0.00 0.00 3.41
1800 1828 0.890090 TTCCAAACGGGGCCTTTACG 60.890 55.000 0.84 5.36 37.22 3.18
1848 1876 3.127352 GAAACAACCAACCGCGGCA 62.127 57.895 28.58 0.00 0.00 5.69
1915 1950 1.149101 AGTTCCTGCCTTTCCTGGAA 58.851 50.000 4.68 4.68 39.55 3.53
2061 2096 9.741647 GGATTTCATATTTGATTGAGAAGGTTC 57.258 33.333 0.00 0.00 0.00 3.62
2221 2257 0.762418 TCTCCCGGTTTCTGAAAGCA 59.238 50.000 26.18 10.76 38.75 3.91
2252 2288 3.446873 TGGTAATTATGTTTGCAGGGCAG 59.553 43.478 0.00 0.00 40.61 4.85
2292 2328 1.004044 CCCTGTTGATCTTGAGCCAGT 59.996 52.381 0.00 0.00 0.00 4.00
2360 2396 3.540314 TGCACAAAGCCATGACTTTTT 57.460 38.095 4.02 0.00 44.83 1.94
2413 2449 0.257328 TGGGCAGGTCTGTTTCACAA 59.743 50.000 0.00 0.00 0.00 3.33
2573 2609 9.734620 TGACAGTGAAATCAAACTAAAATTCTG 57.265 29.630 0.00 0.00 0.00 3.02
2578 2614 9.364989 CCTTTTGACAGTGAAATCAAACTAAAA 57.635 29.630 6.84 0.00 42.87 1.52
2790 2833 9.520515 ACATGACAAGGACAGAAAAATATAAGT 57.479 29.630 0.00 0.00 0.00 2.24
2801 2858 4.102524 AGGTACAAACATGACAAGGACAGA 59.897 41.667 0.00 0.00 0.00 3.41
2845 2902 8.952278 GTAGTATCATATCCAAGAGAGGTGTAG 58.048 40.741 0.00 0.00 0.00 2.74
2886 2943 8.255394 TGTTATTATCATGTGTGACTTGAGTG 57.745 34.615 0.00 0.00 36.03 3.51
2915 2972 9.809096 TCTTAGACTGATGAAACATTCAGATAC 57.191 33.333 6.91 0.00 43.98 2.24
3019 3085 4.503991 CCTTAGAGAGTGTGAGTTGGCTTT 60.504 45.833 0.00 0.00 0.00 3.51
3058 3124 8.470002 TGGAACATTCTAGTGATCATATATCGG 58.530 37.037 0.00 0.00 0.00 4.18
3066 3132 3.447229 TCGCTGGAACATTCTAGTGATCA 59.553 43.478 14.94 0.00 46.03 2.92
3073 3139 4.637276 TCTTGTTTCGCTGGAACATTCTA 58.363 39.130 3.74 0.00 38.20 2.10
3118 3188 8.995027 TGGAAATTGCCATTAGATTACTACAT 57.005 30.769 0.00 0.00 31.66 2.29
3123 3193 9.768662 ATTGATTGGAAATTGCCATTAGATTAC 57.231 29.630 5.81 0.00 37.86 1.89
3130 3200 8.269317 AGTTATGATTGATTGGAAATTGCCATT 58.731 29.630 5.81 2.12 37.86 3.16
3136 3206 9.258629 TCCAAGAGTTATGATTGATTGGAAATT 57.741 29.630 1.43 0.00 41.17 1.82
3143 3213 8.762645 TGACTACTCCAAGAGTTATGATTGATT 58.237 33.333 2.05 0.00 40.28 2.57
3159 3229 4.564821 GCCAACCTATGTTTGACTACTCCA 60.565 45.833 0.00 0.00 30.42 3.86
3213 3283 0.607112 CTCAGAGAGCAGGCTGTTCA 59.393 55.000 29.23 10.90 33.90 3.18
3214 3284 0.894141 TCTCAGAGAGCAGGCTGTTC 59.106 55.000 22.06 22.06 33.90 3.18
3218 3288 1.185315 GAACTCTCAGAGAGCAGGCT 58.815 55.000 25.20 4.58 46.12 4.58
3222 3292 1.829849 CCCATGAACTCTCAGAGAGCA 59.170 52.381 25.20 16.86 46.12 4.26
3234 3304 3.209410 GACCATCTCATCACCCATGAAC 58.791 50.000 0.00 0.00 41.25 3.18
3274 3344 0.824109 CTCCAATGGCGGAGTCTGTA 59.176 55.000 0.00 0.00 46.48 2.74
3308 3378 2.672714 TGTGACAGACTGTGTTATCGC 58.327 47.619 14.14 5.35 40.56 4.58
3348 3418 3.539604 CCTGAAGAACTATCCCAAGCAG 58.460 50.000 0.00 0.00 0.00 4.24
3349 3419 2.356125 GCCTGAAGAACTATCCCAAGCA 60.356 50.000 0.00 0.00 0.00 3.91
3350 3420 2.293170 GCCTGAAGAACTATCCCAAGC 58.707 52.381 0.00 0.00 0.00 4.01
3351 3421 2.422093 GGGCCTGAAGAACTATCCCAAG 60.422 54.545 0.84 0.00 32.68 3.61
3352 3422 1.564348 GGGCCTGAAGAACTATCCCAA 59.436 52.381 0.84 0.00 32.68 4.12
3353 3423 1.213296 GGGCCTGAAGAACTATCCCA 58.787 55.000 0.84 0.00 32.68 4.37
3354 3424 1.418264 GAGGGCCTGAAGAACTATCCC 59.582 57.143 12.95 0.00 0.00 3.85
3355 3425 2.103941 CAGAGGGCCTGAAGAACTATCC 59.896 54.545 12.95 0.00 45.78 2.59
3356 3426 2.484594 GCAGAGGGCCTGAAGAACTATC 60.485 54.545 12.95 0.00 45.78 2.08
3357 3427 1.488393 GCAGAGGGCCTGAAGAACTAT 59.512 52.381 12.95 0.00 45.78 2.12
3358 3428 0.905357 GCAGAGGGCCTGAAGAACTA 59.095 55.000 12.95 0.00 45.78 2.24
3359 3429 1.130054 TGCAGAGGGCCTGAAGAACT 61.130 55.000 12.95 0.00 45.78 3.01
3360 3430 1.376466 TGCAGAGGGCCTGAAGAAC 59.624 57.895 12.95 0.00 45.78 3.01
3361 3431 3.905454 TGCAGAGGGCCTGAAGAA 58.095 55.556 12.95 0.00 45.78 2.52
3438 3508 6.182627 TGCTTTGTCCAGATGATCTGTTTAT 58.817 36.000 20.06 0.00 42.80 1.40
3450 3522 0.823356 GCAACCCTGCTTTGTCCAGA 60.823 55.000 0.00 0.00 45.74 3.86
3487 3559 7.817418 TCTGTGGTTCTAAAAATGTAGCTTT 57.183 32.000 0.00 0.00 0.00 3.51
3517 3590 1.616159 CACAATCCCCACCGTCTTTT 58.384 50.000 0.00 0.00 0.00 2.27
3533 3606 2.124768 TGGGCCCATCTCTCCACA 59.875 61.111 24.45 0.00 0.00 4.17
3534 3607 2.592308 GTGGGCCCATCTCTCCAC 59.408 66.667 31.45 8.65 42.11 4.02
3566 3639 6.569179 TTACCATAGCACCTTCTTTCAAAC 57.431 37.500 0.00 0.00 0.00 2.93
3587 3663 6.839124 AATTCATTGCAGTCCTCATGTTTA 57.161 33.333 0.00 0.00 0.00 2.01
3615 3691 7.759489 ACACCAAAGCTGATTAAATTGTAGA 57.241 32.000 0.00 0.00 0.00 2.59
3659 3735 6.401581 GCACTGAAACTGAAGTTACAGATAGC 60.402 42.308 0.00 0.00 40.63 2.97
3678 3754 3.881089 CCATTTGCTGATCTATGCACTGA 59.119 43.478 7.83 0.00 39.05 3.41
3721 3797 2.041081 TGTAACAACCAATCCCCCTCTG 59.959 50.000 0.00 0.00 0.00 3.35
3772 3848 6.206634 TCCTGGCATTTTCTAGTTAAGTTGTG 59.793 38.462 0.00 0.00 0.00 3.33
3773 3849 6.303839 TCCTGGCATTTTCTAGTTAAGTTGT 58.696 36.000 0.00 0.00 0.00 3.32
3774 3850 6.817765 TCCTGGCATTTTCTAGTTAAGTTG 57.182 37.500 0.00 0.00 0.00 3.16
3775 3851 7.669722 TGATTCCTGGCATTTTCTAGTTAAGTT 59.330 33.333 0.00 0.00 0.00 2.66
3776 3852 7.175104 TGATTCCTGGCATTTTCTAGTTAAGT 58.825 34.615 0.00 0.00 0.00 2.24
3777 3853 7.630242 TGATTCCTGGCATTTTCTAGTTAAG 57.370 36.000 0.00 0.00 0.00 1.85
3778 3854 8.415950 TTTGATTCCTGGCATTTTCTAGTTAA 57.584 30.769 0.00 0.00 0.00 2.01
3779 3855 7.362920 GCTTTGATTCCTGGCATTTTCTAGTTA 60.363 37.037 0.00 0.00 0.00 2.24
3780 3856 6.573094 GCTTTGATTCCTGGCATTTTCTAGTT 60.573 38.462 0.00 0.00 0.00 2.24
3781 3857 5.105595 GCTTTGATTCCTGGCATTTTCTAGT 60.106 40.000 0.00 0.00 0.00 2.57
3782 3858 5.105635 TGCTTTGATTCCTGGCATTTTCTAG 60.106 40.000 0.00 0.00 0.00 2.43
3801 3877 8.932791 GTTTACTACATATACACAGTGTGCTTT 58.067 33.333 23.21 10.42 36.98 3.51
3835 3911 0.963962 CAAAGGCTGCACATGGTTCT 59.036 50.000 0.50 0.00 0.00 3.01
3843 3919 0.746659 ACTTGGTTCAAAGGCTGCAC 59.253 50.000 0.50 0.00 0.00 4.57
3854 3930 3.506067 CACTGGGGATTAACACTTGGTTC 59.494 47.826 0.00 0.00 40.96 3.62


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

AutoCloner maintained by Alex Coulton.