Multiple sequence alignment - TraesCS6A01G118200

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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 TraesCS6A01G118200 chr6A 100.000 3977 0 0 1 3977 89294807 89298783 0.000000e+00 7345
1 TraesCS6A01G118200 chr6B 89.041 2409 172 41 715 3082 147011600 147013957 0.000000e+00 2902
2 TraesCS6A01G118200 chr6B 84.787 493 27 12 4 473 147010729 147011196 6.060000e-123 451
3 TraesCS6A01G118200 chr6D 90.154 1300 85 21 852 2125 72349606 72350888 0.000000e+00 1652
4 TraesCS6A01G118200 chr6D 93.848 894 53 2 3085 3977 454957043 454957935 0.000000e+00 1345
5 TraesCS6A01G118200 chr6D 91.290 930 55 12 2179 3082 72351081 72352010 0.000000e+00 1245
6 TraesCS6A01G118200 chr6D 85.731 855 49 19 3 831 72348812 72349619 0.000000e+00 835
7 TraesCS6A01G118200 chr1A 98.438 896 13 1 3083 3977 552336400 552337295 0.000000e+00 1576
8 TraesCS6A01G118200 chr5B 98.330 898 14 1 3081 3977 461691560 461692457 0.000000e+00 1574
9 TraesCS6A01G118200 chr7B 98.218 898 15 1 3081 3977 111939785 111940682 0.000000e+00 1568
10 TraesCS6A01G118200 chr2A 96.857 891 25 3 3088 3977 610112987 610113875 0.000000e+00 1487
11 TraesCS6A01G118200 chr1D 96.536 895 29 2 3085 3977 465462270 465463164 0.000000e+00 1480
12 TraesCS6A01G118200 chr7D 93.444 900 56 2 3081 3977 160558901 160558002 0.000000e+00 1332
13 TraesCS6A01G118200 chr4D 92.325 899 66 3 3080 3977 59602448 59603344 0.000000e+00 1275
14 TraesCS6A01G118200 chr2B 92.316 898 67 2 3081 3977 170932715 170931819 0.000000e+00 1275


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 TraesCS6A01G118200 chr6A 89294807 89298783 3976 False 7345.0 7345 100.000000 1 3977 1 chr6A.!!$F1 3976
1 TraesCS6A01G118200 chr6B 147010729 147013957 3228 False 1676.5 2902 86.914000 4 3082 2 chr6B.!!$F1 3078
2 TraesCS6A01G118200 chr6D 454957043 454957935 892 False 1345.0 1345 93.848000 3085 3977 1 chr6D.!!$F1 892
3 TraesCS6A01G118200 chr6D 72348812 72352010 3198 False 1244.0 1652 89.058333 3 3082 3 chr6D.!!$F2 3079
4 TraesCS6A01G118200 chr1A 552336400 552337295 895 False 1576.0 1576 98.438000 3083 3977 1 chr1A.!!$F1 894
5 TraesCS6A01G118200 chr5B 461691560 461692457 897 False 1574.0 1574 98.330000 3081 3977 1 chr5B.!!$F1 896
6 TraesCS6A01G118200 chr7B 111939785 111940682 897 False 1568.0 1568 98.218000 3081 3977 1 chr7B.!!$F1 896
7 TraesCS6A01G118200 chr2A 610112987 610113875 888 False 1487.0 1487 96.857000 3088 3977 1 chr2A.!!$F1 889
8 TraesCS6A01G118200 chr1D 465462270 465463164 894 False 1480.0 1480 96.536000 3085 3977 1 chr1D.!!$F1 892
9 TraesCS6A01G118200 chr7D 160558002 160558901 899 True 1332.0 1332 93.444000 3081 3977 1 chr7D.!!$R1 896
10 TraesCS6A01G118200 chr4D 59602448 59603344 896 False 1275.0 1275 92.325000 3080 3977 1 chr4D.!!$F1 897
11 TraesCS6A01G118200 chr2B 170931819 170932715 896 True 1275.0 1275 92.316000 3081 3977 1 chr2B.!!$R1 896

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
241 246 0.035439 AAATAGCCACACGTCCCCTG 60.035 55.0 0.0 0.0 0.00 4.45 F
530 562 0.108424 CCGCAAGTCCCAGAAGAGAG 60.108 60.0 0.0 0.0 0.00 3.20 F
1167 1419 0.321671 GGCTATGCCGCTTCATCCTA 59.678 55.0 0.0 0.0 39.62 2.94 F
1975 2252 0.179020 TTCTGTGTGGGAACTGCCTG 60.179 55.0 0.0 0.0 36.66 4.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1287 1539 0.098376 GGTCGACGTACAGCAGGTAG 59.902 60.0 9.92 0.0 31.13 3.18 R
1945 2222 0.675083 CACACAGAAGGCATGGCAAA 59.325 50.0 22.64 0.0 0.00 3.68 R
2783 3276 0.390860 GATCCCTAGCGTGACAGCAT 59.609 55.0 2.68 0.0 40.15 3.79 R
3232 3730 0.324368 TGCCTCCATACAGACCGAGT 60.324 55.0 0.00 0.0 0.00 4.18 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 5.046663 GGGGTTAGATTGGCAGAAAAATTGA 60.047 40.000 0.00 0.00 0.00 2.57
186 191 5.826601 TGACACAGATTACAAACAAAGCA 57.173 34.783 0.00 0.00 0.00 3.91
241 246 0.035439 AAATAGCCACACGTCCCCTG 60.035 55.000 0.00 0.00 0.00 4.45
301 306 1.375908 AATCGCAGCTGCTTCCGAA 60.376 52.632 34.22 14.03 39.32 4.30
312 317 0.799393 GCTTCCGAAACTCTTGCCTC 59.201 55.000 0.00 0.00 0.00 4.70
341 346 2.307098 AGAAAGGTAGCTGCATCTGGTT 59.693 45.455 3.61 0.00 0.00 3.67
351 356 1.875963 CATCTGGTTTCGCCGCTTT 59.124 52.632 0.00 0.00 41.21 3.51
416 444 2.167487 CTCTCCTCCTGCTTCAAGGTAC 59.833 54.545 0.00 0.00 38.58 3.34
457 485 6.900189 ACCGTATTCTTCAGTATCAGTATCG 58.100 40.000 0.00 0.00 0.00 2.92
479 507 1.305623 CTGATTGCCTTGCCTCCCT 59.694 57.895 0.00 0.00 0.00 4.20
481 509 0.323725 TGATTGCCTTGCCTCCCTTC 60.324 55.000 0.00 0.00 0.00 3.46
485 517 2.923910 GCCTTGCCTCCCTTCCCTT 61.924 63.158 0.00 0.00 0.00 3.95
494 526 1.303643 CCCTTCCCTTGCTGGTGTC 60.304 63.158 0.00 0.00 0.00 3.67
506 538 0.673644 CTGGTGTCGGATGTGTTCCC 60.674 60.000 0.00 0.00 42.06 3.97
523 555 2.435586 CAGCTCCGCAAGTCCCAG 60.436 66.667 0.00 0.00 0.00 4.45
530 562 0.108424 CCGCAAGTCCCAGAAGAGAG 60.108 60.000 0.00 0.00 0.00 3.20
587 626 2.224646 GGCAGGAACAGGGGATAGAATC 60.225 54.545 0.00 0.00 0.00 2.52
590 629 4.446889 GCAGGAACAGGGGATAGAATCAAT 60.447 45.833 0.00 0.00 0.00 2.57
605 644 9.125906 GATAGAATCAATACTGCAATTTGATGC 57.874 33.333 15.30 14.01 46.58 3.91
633 672 3.338249 GTCCTTGTTCTCTTATGCTGCA 58.662 45.455 4.13 4.13 0.00 4.41
638 677 1.336125 GTTCTCTTATGCTGCATGGCC 59.664 52.381 24.59 0.00 0.00 5.36
734 979 0.454600 TCACCGCTGGAACTCGATAC 59.545 55.000 1.50 0.00 0.00 2.24
740 985 1.756690 GCTGGAACTCGATACCCCCTA 60.757 57.143 0.00 0.00 0.00 3.53
750 995 3.000727 CGATACCCCCTAATGATTTCGC 58.999 50.000 0.00 0.00 0.00 4.70
807 1053 5.798434 CCCCGTTTCTTTGTATTCGAAATTC 59.202 40.000 0.00 0.00 0.00 2.17
907 1153 6.881065 TCTGAATGTTTCTCTGAATAACCCAG 59.119 38.462 0.00 0.00 0.00 4.45
914 1160 7.092623 TGTTTCTCTGAATAACCCAGCCTTATA 60.093 37.037 0.00 0.00 0.00 0.98
915 1161 6.420913 TCTCTGAATAACCCAGCCTTATAC 57.579 41.667 0.00 0.00 0.00 1.47
916 1162 5.903010 TCTCTGAATAACCCAGCCTTATACA 59.097 40.000 0.00 0.00 0.00 2.29
917 1163 6.042093 TCTCTGAATAACCCAGCCTTATACAG 59.958 42.308 0.00 0.00 0.00 2.74
993 1245 3.680786 TGAGCTCCCACCGACGTG 61.681 66.667 12.15 0.00 39.91 4.49
1167 1419 0.321671 GGCTATGCCGCTTCATCCTA 59.678 55.000 0.00 0.00 39.62 2.94
1170 1422 0.321671 TATGCCGCTTCATCCTAGCC 59.678 55.000 0.00 0.00 35.18 3.93
1615 1867 3.151022 GCGTGGAGAGGAGGAGGG 61.151 72.222 0.00 0.00 0.00 4.30
1665 1917 1.094073 GCATGTCGCTCAATCTGGCT 61.094 55.000 0.00 0.00 37.77 4.75
1706 1958 6.817140 GTCATTAACTCGGTTATTCTTCAGGT 59.183 38.462 0.00 0.00 0.00 4.00
1707 1959 6.816640 TCATTAACTCGGTTATTCTTCAGGTG 59.183 38.462 0.00 0.00 0.00 4.00
1708 1960 4.884668 AACTCGGTTATTCTTCAGGTGA 57.115 40.909 0.00 0.00 0.00 4.02
1709 1961 4.457834 ACTCGGTTATTCTTCAGGTGAG 57.542 45.455 0.00 0.00 0.00 3.51
1710 1962 4.087182 ACTCGGTTATTCTTCAGGTGAGA 58.913 43.478 0.00 0.00 0.00 3.27
1711 1963 4.158764 ACTCGGTTATTCTTCAGGTGAGAG 59.841 45.833 0.00 0.00 0.00 3.20
1746 2000 4.157840 GCCAGTTTAGGATAAACAACCCAG 59.842 45.833 13.29 0.00 32.81 4.45
1757 2011 2.664402 ACAACCCAGCTGAATTCTGT 57.336 45.000 17.39 8.10 0.00 3.41
1764 2018 4.702131 ACCCAGCTGAATTCTGTTTGTATC 59.298 41.667 17.39 0.00 0.00 2.24
1774 2028 7.602265 TGAATTCTGTTTGTATCGTCTGATTCA 59.398 33.333 7.05 0.00 35.99 2.57
1883 2160 2.710377 TCATCAACGGGGTTCATTCTG 58.290 47.619 0.00 0.00 0.00 3.02
1885 2162 2.178912 TCAACGGGGTTCATTCTGTC 57.821 50.000 0.00 0.00 0.00 3.51
1886 2163 1.418264 TCAACGGGGTTCATTCTGTCA 59.582 47.619 0.00 0.00 0.00 3.58
1891 2168 2.633488 GGGGTTCATTCTGTCACTAGC 58.367 52.381 0.00 0.00 0.00 3.42
1894 2171 3.265791 GGTTCATTCTGTCACTAGCCTG 58.734 50.000 0.00 0.00 0.00 4.85
1895 2172 3.307059 GGTTCATTCTGTCACTAGCCTGT 60.307 47.826 0.00 0.00 0.00 4.00
1896 2173 4.081642 GGTTCATTCTGTCACTAGCCTGTA 60.082 45.833 0.00 0.00 0.00 2.74
1945 2222 4.237018 TCCCCTTTCCTTTGTACTACAGT 58.763 43.478 0.00 0.00 0.00 3.55
1966 2243 2.345760 GCCATGCCTTCTGTGTGGG 61.346 63.158 0.00 0.00 0.00 4.61
1969 2246 0.883833 CATGCCTTCTGTGTGGGAAC 59.116 55.000 0.00 0.00 0.00 3.62
1975 2252 0.179020 TTCTGTGTGGGAACTGCCTG 60.179 55.000 0.00 0.00 36.66 4.85
2002 2279 4.034510 GCTACATGCATACCTGAAAGTGTC 59.965 45.833 0.00 0.00 42.31 3.67
2006 2283 4.019792 TGCATACCTGAAAGTGTCATGT 57.980 40.909 0.00 0.00 38.49 3.21
2056 2333 1.455248 GCCGGCTTTACCACATTGTA 58.545 50.000 22.15 0.00 39.03 2.41
2092 2370 6.795144 TTCAGGTAGTATGATTTTACCGGA 57.205 37.500 9.46 4.62 41.34 5.14
2151 2593 7.982354 AGGTACTACTGTTCAATTCATTAGCTC 59.018 37.037 0.00 0.00 36.02 4.09
2152 2594 6.893958 ACTACTGTTCAATTCATTAGCTCG 57.106 37.500 0.00 0.00 0.00 5.03
2153 2595 6.398918 ACTACTGTTCAATTCATTAGCTCGT 58.601 36.000 0.00 0.00 0.00 4.18
2154 2596 7.544622 ACTACTGTTCAATTCATTAGCTCGTA 58.455 34.615 0.00 0.00 0.00 3.43
2155 2597 6.648725 ACTGTTCAATTCATTAGCTCGTAC 57.351 37.500 0.00 0.00 0.00 3.67
2156 2598 6.163476 ACTGTTCAATTCATTAGCTCGTACA 58.837 36.000 0.00 0.00 0.00 2.90
2157 2599 6.649141 ACTGTTCAATTCATTAGCTCGTACAA 59.351 34.615 0.00 0.00 0.00 2.41
2158 2600 6.827641 TGTTCAATTCATTAGCTCGTACAAC 58.172 36.000 0.00 0.00 0.00 3.32
2159 2601 6.649141 TGTTCAATTCATTAGCTCGTACAACT 59.351 34.615 0.00 0.00 0.00 3.16
2160 2602 7.815549 TGTTCAATTCATTAGCTCGTACAACTA 59.184 33.333 0.00 0.00 0.00 2.24
2161 2603 8.653338 GTTCAATTCATTAGCTCGTACAACTAA 58.347 33.333 0.00 0.00 0.00 2.24
2162 2604 8.181487 TCAATTCATTAGCTCGTACAACTAAC 57.819 34.615 0.00 0.00 0.00 2.34
2163 2605 7.815549 TCAATTCATTAGCTCGTACAACTAACA 59.184 33.333 0.00 0.00 0.00 2.41
2164 2606 8.604035 CAATTCATTAGCTCGTACAACTAACAT 58.396 33.333 0.00 0.00 0.00 2.71
2165 2607 8.718102 ATTCATTAGCTCGTACAACTAACATT 57.282 30.769 0.00 0.00 0.00 2.71
2166 2608 7.751047 TCATTAGCTCGTACAACTAACATTC 57.249 36.000 0.00 0.00 0.00 2.67
2167 2609 7.544622 TCATTAGCTCGTACAACTAACATTCT 58.455 34.615 0.00 0.00 0.00 2.40
2168 2610 8.680001 TCATTAGCTCGTACAACTAACATTCTA 58.320 33.333 0.00 0.00 0.00 2.10
2169 2611 8.744011 CATTAGCTCGTACAACTAACATTCTAC 58.256 37.037 0.00 0.00 0.00 2.59
2170 2612 6.512342 AGCTCGTACAACTAACATTCTACT 57.488 37.500 0.00 0.00 0.00 2.57
2171 2613 6.553524 AGCTCGTACAACTAACATTCTACTC 58.446 40.000 0.00 0.00 0.00 2.59
2172 2614 6.374894 AGCTCGTACAACTAACATTCTACTCT 59.625 38.462 0.00 0.00 0.00 3.24
2173 2615 7.551974 AGCTCGTACAACTAACATTCTACTCTA 59.448 37.037 0.00 0.00 0.00 2.43
2174 2616 7.851963 GCTCGTACAACTAACATTCTACTCTAG 59.148 40.741 0.00 0.00 0.00 2.43
2202 2644 4.528206 TGAACCAGAGAAATGCTGTAGAGA 59.472 41.667 0.00 0.00 0.00 3.10
2207 2649 5.163322 CCAGAGAAATGCTGTAGAGATCCTT 60.163 44.000 0.00 0.00 0.00 3.36
2324 2781 2.912986 TGCCGTTAGAACAGCAGTG 58.087 52.632 0.00 0.00 37.40 3.66
2369 2826 3.563808 ACATAGTTCTTTCTTGCAACGCA 59.436 39.130 0.00 0.00 36.47 5.24
2438 2895 3.290776 GGATGTAAGCCTACGCCTG 57.709 57.895 0.00 0.00 41.12 4.85
2458 2915 5.452636 GCCTGTCCTCCTCTTATTGAGTTAG 60.453 48.000 0.00 0.00 41.11 2.34
2461 2918 6.017192 TGTCCTCCTCTTATTGAGTTAGTGT 58.983 40.000 0.00 0.00 41.11 3.55
2472 2930 9.760660 CTTATTGAGTTAGTGTCATAAAAGTGC 57.239 33.333 0.00 0.00 0.00 4.40
2492 2967 3.123804 GCCATTCACATAGTGTACTCCG 58.876 50.000 0.00 0.00 34.79 4.63
2503 2978 3.225104 AGTGTACTCCGTCACTAACCAA 58.775 45.455 0.00 0.00 42.13 3.67
2504 2979 3.830755 AGTGTACTCCGTCACTAACCAAT 59.169 43.478 0.00 0.00 42.13 3.16
2505 2980 4.082354 AGTGTACTCCGTCACTAACCAATC 60.082 45.833 0.00 0.00 42.13 2.67
2511 2986 4.250464 TCCGTCACTAACCAATCATCAAC 58.750 43.478 0.00 0.00 0.00 3.18
2603 3081 7.220030 TCCATCACTAGCCAGATATTTTTCTC 58.780 38.462 0.00 0.00 0.00 2.87
2620 3098 8.794335 ATTTTTCTCCAGGTCTTTATCTGTAC 57.206 34.615 0.00 0.00 31.30 2.90
2709 3202 2.436646 AGGACCATGAAAGCGCCG 60.437 61.111 2.29 0.00 0.00 6.46
2712 3205 2.033448 ACCATGAAAGCGCCGGAA 59.967 55.556 5.05 0.00 0.00 4.30
2730 3223 3.491447 CGGAAAATCAAAGGATGGATGGC 60.491 47.826 0.00 0.00 32.92 4.40
2756 3249 1.315257 GCGGCAACAAGGGATCACAT 61.315 55.000 0.00 0.00 0.00 3.21
2791 3284 2.672908 CCCTGAGGCATGCTGTCA 59.327 61.111 18.92 18.62 0.00 3.58
2852 3345 3.360758 GGAACATTCGACGAAAATGCAAC 59.639 43.478 15.22 4.74 37.58 4.17
2853 3346 3.896648 ACATTCGACGAAAATGCAACT 57.103 38.095 15.22 0.00 37.58 3.16
2856 3349 0.787787 TCGACGAAAATGCAACTCCG 59.212 50.000 0.00 0.00 0.00 4.63
2906 3399 2.749044 CAGTGGCAGGCGCAGAAT 60.749 61.111 10.83 0.00 41.24 2.40
2992 3485 4.262765 GGAGATAGATGATGGTGCATGTCA 60.263 45.833 0.00 0.00 0.00 3.58
2995 3488 2.640184 AGATGATGGTGCATGTCAGTG 58.360 47.619 0.00 0.00 0.00 3.66
3030 3526 5.989168 TGCGTCAGAAGTAGAAAAATTCAGA 59.011 36.000 0.00 0.00 0.00 3.27
3034 3530 8.499162 CGTCAGAAGTAGAAAAATTCAGACATT 58.501 33.333 10.04 0.00 38.59 2.71
3036 3532 9.559732 TCAGAAGTAGAAAAATTCAGACATTCA 57.440 29.630 0.00 0.00 0.00 2.57
3473 3972 4.583907 TGTCAATGATCAAAGACCAAAGCA 59.416 37.500 21.28 5.75 0.00 3.91
3633 4132 4.201910 CCAAGCGAAGAACTTGACTTTTGA 60.202 41.667 5.12 0.00 45.99 2.69
3699 4199 3.137360 ACCATCCCTAAGAATTGAGCCTC 59.863 47.826 0.00 0.00 0.00 4.70
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
1 2 3.432326 GCCAATCTAACCCCTAGACACTG 60.432 52.174 0.00 0.00 39.52 3.66
21 22 4.743057 AGGCCTAATCAATTTTTCTGCC 57.257 40.909 1.29 0.00 36.62 4.85
186 191 1.167851 CGCCAATCACTCCACATGTT 58.832 50.000 0.00 0.00 0.00 2.71
246 251 0.739813 GTCAAAGACGGGGGATCACG 60.740 60.000 0.00 0.00 0.00 4.35
257 262 3.877508 ACCTGCAACTACAAGTCAAAGAC 59.122 43.478 0.00 0.00 0.00 3.01
301 306 2.158957 TCTTTGTGTCGAGGCAAGAGTT 60.159 45.455 0.00 0.00 0.00 3.01
312 317 2.096218 GCAGCTACCTTTCTTTGTGTCG 60.096 50.000 0.00 0.00 0.00 4.35
351 356 2.031012 CCCAGACGAACAGCAGCA 59.969 61.111 0.00 0.00 0.00 4.41
416 444 2.233922 ACGGTTACTGGAGACATCTTGG 59.766 50.000 0.00 0.00 41.51 3.61
457 485 1.941999 GAGGCAAGGCAATCAGGTGC 61.942 60.000 0.00 0.00 44.14 5.01
479 507 1.488705 ATCCGACACCAGCAAGGGAA 61.489 55.000 0.04 0.00 43.89 3.97
481 509 1.746615 CATCCGACACCAGCAAGGG 60.747 63.158 0.04 0.00 43.89 3.95
485 517 0.602638 GAACACATCCGACACCAGCA 60.603 55.000 0.00 0.00 0.00 4.41
523 555 6.986904 AATCACCGAAATAAACCTCTCTTC 57.013 37.500 0.00 0.00 0.00 2.87
605 644 3.710209 AAGAGAACAAGGACCTCCATG 57.290 47.619 0.00 0.00 40.34 3.66
608 647 3.198853 AGCATAAGAGAACAAGGACCTCC 59.801 47.826 0.00 0.00 0.00 4.30
661 701 4.453478 TCAGCTGAGACAACTAATTGCAAG 59.547 41.667 13.74 0.00 39.66 4.01
734 979 1.841663 CGCGCGAAATCATTAGGGGG 61.842 60.000 28.94 0.00 32.84 5.40
740 985 2.450160 GGAAAATCGCGCGAAATCATT 58.550 42.857 38.07 23.14 0.00 2.57
750 995 0.801872 TGTGTGATGGGAAAATCGCG 59.198 50.000 0.00 0.00 39.46 5.87
807 1053 6.663523 ACTGGGGAAATGTTAAACTTAGGATG 59.336 38.462 0.00 0.00 0.00 3.51
813 1059 7.562088 TGAAGTTACTGGGGAAATGTTAAACTT 59.438 33.333 0.00 0.00 37.35 2.66
820 1066 4.447138 TGTGAAGTTACTGGGGAAATGT 57.553 40.909 0.00 0.00 0.00 2.71
993 1245 0.530650 ACGCGATGGACATCACATCC 60.531 55.000 15.93 0.00 41.22 3.51
994 1246 0.578683 CACGCGATGGACATCACATC 59.421 55.000 15.93 0.00 40.95 3.06
995 1247 1.431488 GCACGCGATGGACATCACAT 61.431 55.000 15.93 0.00 37.69 3.21
996 1248 2.100031 GCACGCGATGGACATCACA 61.100 57.895 15.93 0.00 37.69 3.58
997 1249 1.811266 AGCACGCGATGGACATCAC 60.811 57.895 15.93 2.00 37.69 3.06
998 1250 1.810853 CAGCACGCGATGGACATCA 60.811 57.895 15.93 0.00 37.69 3.07
1023 1275 1.113517 AGTACACGCACTCCACCACT 61.114 55.000 0.00 0.00 0.00 4.00
1158 1410 2.219458 TCGTAGACGGCTAGGATGAAG 58.781 52.381 16.57 0.00 36.78 3.02
1287 1539 0.098376 GGTCGACGTACAGCAGGTAG 59.902 60.000 9.92 0.00 31.13 3.18
1665 1917 1.153978 GACGTCGGCATAACGGACA 60.154 57.895 0.00 0.00 46.18 4.02
1706 1958 1.189752 GGCATGGAGTCTCACTCTCA 58.810 55.000 1.47 1.39 44.46 3.27
1707 1959 1.136695 CTGGCATGGAGTCTCACTCTC 59.863 57.143 1.47 0.00 44.46 3.20
1708 1960 1.193323 CTGGCATGGAGTCTCACTCT 58.807 55.000 1.47 0.00 44.46 3.24
1709 1961 0.901124 ACTGGCATGGAGTCTCACTC 59.099 55.000 1.47 0.00 44.32 3.51
1710 1962 1.356124 AACTGGCATGGAGTCTCACT 58.644 50.000 1.47 0.00 0.00 3.41
1711 1963 2.191128 AAACTGGCATGGAGTCTCAC 57.809 50.000 1.47 0.00 0.00 3.51
1746 2000 5.348724 TCAGACGATACAAACAGAATTCAGC 59.651 40.000 8.44 0.00 0.00 4.26
1757 2011 7.665561 TCAAACATGAATCAGACGATACAAA 57.334 32.000 0.00 0.00 0.00 2.83
1764 2018 9.986833 TGTAATTTATCAAACATGAATCAGACG 57.013 29.630 0.00 0.00 0.00 4.18
1864 2118 2.420022 GACAGAATGAACCCCGTTGATG 59.580 50.000 0.00 0.00 39.69 3.07
1883 2160 7.439655 CCTGAAAAGATATTACAGGCTAGTGAC 59.560 40.741 11.45 0.00 40.90 3.67
1885 2162 6.708054 CCCTGAAAAGATATTACAGGCTAGTG 59.292 42.308 16.09 4.09 44.43 2.74
1886 2163 6.387220 ACCCTGAAAAGATATTACAGGCTAGT 59.613 38.462 16.09 9.29 44.43 2.57
1891 2168 4.580580 GGCACCCTGAAAAGATATTACAGG 59.419 45.833 15.11 15.11 45.09 4.00
1922 2199 4.850386 ACTGTAGTACAAAGGAAAGGGGAT 59.150 41.667 4.21 0.00 0.00 3.85
1945 2222 0.675083 CACACAGAAGGCATGGCAAA 59.325 50.000 22.64 0.00 0.00 3.68
1966 2243 2.805099 GCATGTAGCTATCAGGCAGTTC 59.195 50.000 20.44 0.00 41.32 3.01
1969 2246 2.538512 TGCATGTAGCTATCAGGCAG 57.461 50.000 22.68 7.20 45.24 4.85
1975 2252 6.146837 CACTTTCAGGTATGCATGTAGCTATC 59.853 42.308 10.16 0.00 45.94 2.08
2002 2279 1.938577 CGCCTTGGATCTCTCAACATG 59.061 52.381 0.00 0.00 0.00 3.21
2006 2283 1.478510 GAGACGCCTTGGATCTCTCAA 59.521 52.381 11.71 0.00 36.69 3.02
2035 2312 2.043980 AATGTGGTAAAGCCGGCCG 61.044 57.895 26.15 21.04 41.21 6.13
2128 2407 7.544622 ACGAGCTAATGAATTGAACAGTAGTA 58.455 34.615 0.00 0.00 37.94 1.82
2129 2408 6.398918 ACGAGCTAATGAATTGAACAGTAGT 58.601 36.000 0.00 0.00 37.94 2.73
2130 2409 6.893958 ACGAGCTAATGAATTGAACAGTAG 57.106 37.500 0.00 0.00 38.43 2.57
2158 2600 9.953697 GGTTCACATACTAGAGTAGAATGTTAG 57.046 37.037 0.00 0.00 33.52 2.34
2159 2601 9.470399 TGGTTCACATACTAGAGTAGAATGTTA 57.530 33.333 0.00 0.00 33.52 2.41
2160 2602 8.362464 TGGTTCACATACTAGAGTAGAATGTT 57.638 34.615 0.00 0.00 33.52 2.71
2161 2603 7.834681 TCTGGTTCACATACTAGAGTAGAATGT 59.165 37.037 0.00 0.00 31.63 2.71
2162 2604 8.226819 TCTGGTTCACATACTAGAGTAGAATG 57.773 38.462 0.00 0.00 31.63 2.67
2163 2605 8.458573 CTCTGGTTCACATACTAGAGTAGAAT 57.541 38.462 0.00 0.00 44.28 2.40
2164 2606 7.867305 CTCTGGTTCACATACTAGAGTAGAA 57.133 40.000 0.00 0.00 44.28 2.10
2170 2612 6.155221 AGCATTTCTCTGGTTCACATACTAGA 59.845 38.462 0.00 0.00 34.87 2.43
2171 2613 6.257411 CAGCATTTCTCTGGTTCACATACTAG 59.743 42.308 0.00 0.00 0.00 2.57
2172 2614 6.108687 CAGCATTTCTCTGGTTCACATACTA 58.891 40.000 0.00 0.00 0.00 1.82
2173 2615 4.940046 CAGCATTTCTCTGGTTCACATACT 59.060 41.667 0.00 0.00 0.00 2.12
2174 2616 4.697352 ACAGCATTTCTCTGGTTCACATAC 59.303 41.667 0.00 0.00 35.94 2.39
2202 2644 6.994421 ACTAAAACCAAAATCACCAAGGAT 57.006 33.333 0.00 0.00 0.00 3.24
2207 2649 8.940952 CAAGAAAAACTAAAACCAAAATCACCA 58.059 29.630 0.00 0.00 0.00 4.17
2265 2722 6.088016 TCTGCAGCAGTTATTTCAACAAAT 57.912 33.333 22.10 0.00 33.34 2.32
2342 2799 3.433274 TGCAAGAAAGAACTATGTGCTCG 59.567 43.478 0.00 0.00 0.00 5.03
2369 2826 5.303589 CCAGATAATGGCATGGTCAGAAATT 59.696 40.000 0.00 0.00 43.83 1.82
2472 2930 4.386867 ACGGAGTACACTATGTGAATGG 57.613 45.455 4.61 0.00 41.94 3.16
2492 2967 3.684788 AGCGTTGATGATTGGTTAGTGAC 59.315 43.478 0.00 0.00 0.00 3.67
2503 2978 5.437289 TTTGAAACTTCAGCGTTGATGAT 57.563 34.783 19.58 7.07 38.61 2.45
2504 2979 4.891627 TTTGAAACTTCAGCGTTGATGA 57.108 36.364 19.58 0.00 38.61 2.92
2505 2980 5.036737 AGTTTTGAAACTTCAGCGTTGATG 58.963 37.500 12.61 12.61 46.52 3.07
2603 3081 4.631813 GCAACTGTACAGATAAAGACCTGG 59.368 45.833 29.30 2.15 34.85 4.45
2709 3202 3.491447 CGCCATCCATCCTTTGATTTTCC 60.491 47.826 0.00 0.00 0.00 3.13
2712 3205 3.017048 TCGCCATCCATCCTTTGATTT 57.983 42.857 0.00 0.00 0.00 2.17
2730 3223 2.426752 CTTGTTGCCGCGGTTTCG 60.427 61.111 28.70 6.96 39.81 3.46
2756 3249 4.399395 CCGCCTGCTGCTCCTCAA 62.399 66.667 0.00 0.00 38.05 3.02
2783 3276 0.390860 GATCCCTAGCGTGACAGCAT 59.609 55.000 2.68 0.00 40.15 3.79
2791 3284 1.109920 ACATCTGCGATCCCTAGCGT 61.110 55.000 0.00 0.00 36.72 5.07
2856 3349 4.925861 GATGCCTGGCGCTCCTCC 62.926 72.222 14.98 0.00 38.78 4.30
2906 3399 2.710377 CGATCCACTCATTCCAAACCA 58.290 47.619 0.00 0.00 0.00 3.67
2992 3485 1.935933 GACGCATAATTCCGTCCACT 58.064 50.000 12.52 0.00 45.81 4.00
3030 3526 7.969773 TGCACTGCATACCAAGAATTGAATGT 61.970 38.462 0.00 0.00 40.77 2.71
3034 3530 3.419943 TGCACTGCATACCAAGAATTGA 58.580 40.909 0.00 0.00 40.77 2.57
3232 3730 0.324368 TGCCTCCATACAGACCGAGT 60.324 55.000 0.00 0.00 0.00 4.18
3473 3972 1.130373 CAAATGCCGCTACACACGAAT 59.870 47.619 0.00 0.00 0.00 3.34
3580 4079 3.825328 ACAAGACAGAATTTGGACTGCT 58.175 40.909 0.00 0.00 37.61 4.24


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

AutoCloner maintained by Alex Coulton.