Multiple sequence alignment - TraesCS4B01G190600

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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 TraesCS4B01G190600 chr4B 100.000 4595 0 0 1 4595 413195266 413190672 0.000000e+00 8486.0
1 TraesCS4B01G190600 chr4B 95.722 1052 38 3 1 1045 413393146 413392095 0.000000e+00 1687.0
2 TraesCS4B01G190600 chr4B 95.247 1052 43 3 1 1045 413227495 413226444 0.000000e+00 1659.0
3 TraesCS4B01G190600 chr4B 95.152 1052 44 3 1 1045 413336142 413335091 0.000000e+00 1653.0
4 TraesCS4B01G190600 chr4B 97.064 579 12 2 4 577 413272974 413272396 0.000000e+00 970.0
5 TraesCS4B01G190600 chr4B 96.735 582 14 2 1 577 413303668 413303087 0.000000e+00 965.0
6 TraesCS4B01G190600 chr4A 93.536 2166 110 14 1612 3760 137891584 137893736 0.000000e+00 3197.0
7 TraesCS4B01G190600 chr4A 88.650 1304 97 27 330 1598 137890311 137891598 0.000000e+00 1541.0
8 TraesCS4B01G190600 chr4A 88.675 830 43 7 3789 4595 137894486 137895287 0.000000e+00 965.0
9 TraesCS4B01G190600 chr4A 84.821 336 34 5 1 329 137889946 137890271 5.730000e-84 322.0
10 TraesCS4B01G190600 chr4D 94.436 2049 86 9 1612 3640 335178756 335176716 0.000000e+00 3127.0
11 TraesCS4B01G190600 chr4D 89.653 1295 87 29 333 1598 335180018 335178742 0.000000e+00 1605.0
12 TraesCS4B01G190600 chr4D 93.627 408 9 4 4130 4537 335174759 335174369 1.100000e-165 593.0
13 TraesCS4B01G190600 chr4D 88.095 336 27 7 1 329 335180390 335180061 2.010000e-103 387.0
14 TraesCS4B01G190600 chr4D 90.361 166 15 1 3938 4102 335174913 335174748 2.780000e-52 217.0
15 TraesCS4B01G190600 chr4D 93.243 74 5 0 3628 3701 335176701 335176628 4.860000e-20 110.0
16 TraesCS4B01G190600 chr4D 86.111 72 3 1 4531 4595 335165561 335165490 2.290000e-08 71.3
17 TraesCS4B01G190600 chr7D 84.925 597 58 20 3961 4535 560576094 560576680 3.990000e-160 575.0
18 TraesCS4B01G190600 chr7D 85.455 385 37 7 3960 4326 560580294 560580677 2.590000e-102 383.0
19 TraesCS4B01G190600 chr7D 86.667 75 6 1 522 596 548151509 548151439 3.810000e-11 80.5
20 TraesCS4B01G190600 chr7A 83.798 574 55 18 3961 4514 644681519 644682074 1.140000e-140 510.0
21 TraesCS4B01G190600 chr7A 86.723 354 29 6 3986 4321 644706292 644706645 1.210000e-100 377.0
22 TraesCS4B01G190600 chr7B 84.270 534 59 16 3961 4476 608364285 608364811 8.880000e-137 497.0
23 TraesCS4B01G190600 chr7B 88.089 361 28 9 3987 4332 608375332 608375692 9.200000e-112 414.0
24 TraesCS4B01G190600 chr2A 80.172 116 20 2 505 619 702360379 702360492 2.950000e-12 84.2
25 TraesCS4B01G190600 chr3A 86.301 73 10 0 547 619 711531907 711531979 3.810000e-11 80.5
26 TraesCS4B01G190600 chr3D 84.211 76 12 0 547 622 410418775 410418700 1.770000e-09 75.0


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 TraesCS4B01G190600 chr4B 413190672 413195266 4594 True 8486.00 8486 100.000000 1 4595 1 chr4B.!!$R1 4594
1 TraesCS4B01G190600 chr4B 413392095 413393146 1051 True 1687.00 1687 95.722000 1 1045 1 chr4B.!!$R6 1044
2 TraesCS4B01G190600 chr4B 413226444 413227495 1051 True 1659.00 1659 95.247000 1 1045 1 chr4B.!!$R2 1044
3 TraesCS4B01G190600 chr4B 413335091 413336142 1051 True 1653.00 1653 95.152000 1 1045 1 chr4B.!!$R5 1044
4 TraesCS4B01G190600 chr4B 413272396 413272974 578 True 970.00 970 97.064000 4 577 1 chr4B.!!$R3 573
5 TraesCS4B01G190600 chr4B 413303087 413303668 581 True 965.00 965 96.735000 1 577 1 chr4B.!!$R4 576
6 TraesCS4B01G190600 chr4A 137889946 137895287 5341 False 1506.25 3197 88.920500 1 4595 4 chr4A.!!$F1 4594
7 TraesCS4B01G190600 chr4D 335174369 335180390 6021 True 1006.50 3127 91.569167 1 4537 6 chr4D.!!$R2 4536
8 TraesCS4B01G190600 chr7D 560576094 560580677 4583 False 479.00 575 85.190000 3960 4535 2 chr7D.!!$F1 575
9 TraesCS4B01G190600 chr7A 644681519 644682074 555 False 510.00 510 83.798000 3961 4514 1 chr7A.!!$F1 553
10 TraesCS4B01G190600 chr7B 608364285 608364811 526 False 497.00 497 84.270000 3961 4476 1 chr7B.!!$F1 515

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
419 474 2.391724 ATCGGCACAACCTTGTCCGT 62.392 55.000 19.46 10.6 44.52 4.69 F
1712 1804 2.223782 TGCTGACATGCTCAAAACCAAC 60.224 45.455 0.00 0.0 0.00 3.77 F
3318 3441 0.026803 GTTTATCTGCCGCTTGCTCG 59.973 55.000 0.00 0.0 42.00 5.03 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1749 1842 0.179018 AAGCAGCGTCTTCCACCTTT 60.179 50.000 0.00 0.0 0.00 3.11 R
3368 3491 0.478072 TGACACATTTCCAGGCCAGT 59.522 50.000 5.01 0.0 0.00 4.00 R
4326 6688 2.164673 CGTTGTTGTCGTCGTCGC 59.835 61.111 0.00 0.0 36.96 5.19 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
419 474 2.391724 ATCGGCACAACCTTGTCCGT 62.392 55.000 19.46 10.60 44.52 4.69
534 595 4.272489 AGCATAATCTTTGCAGCTTACCA 58.728 39.130 0.00 0.00 42.62 3.25
535 596 4.891756 AGCATAATCTTTGCAGCTTACCAT 59.108 37.500 0.00 0.00 42.62 3.55
645 706 4.263068 CCCAATCATAGCCTAATCGGACTT 60.263 45.833 0.00 0.00 33.16 3.01
701 782 2.500504 ACATCTTGCTGCTGAGATCAGA 59.499 45.455 13.98 0.00 46.59 3.27
777 860 2.413796 CAGCTTACGGTCGCAACAAATA 59.586 45.455 5.35 0.00 0.00 1.40
877 960 9.768662 AACTTTAGAATAAGACTCCGTTTACAA 57.231 29.630 0.00 0.00 0.00 2.41
961 1049 6.127730 CGCTGGACAAATTAAATTTAGGAGGT 60.128 38.462 0.00 0.00 0.00 3.85
1572 1663 3.700538 TGCCTCAAGCTGACCAAATTAT 58.299 40.909 0.00 0.00 44.23 1.28
1712 1804 2.223782 TGCTGACATGCTCAAAACCAAC 60.224 45.455 0.00 0.00 0.00 3.77
1749 1842 2.166459 GACGGTTGACCATCTGATCTGA 59.834 50.000 4.63 4.63 35.14 3.27
1774 1867 2.548480 GTGGAAGACGCTGCTTTAGTTT 59.452 45.455 0.00 0.00 0.00 2.66
1781 1874 3.326747 ACGCTGCTTTAGTTTAGTCCAG 58.673 45.455 0.00 0.00 0.00 3.86
1850 1943 6.070136 ACTGGAATTTTCTTCTAGGTACCTCC 60.070 42.308 20.32 9.57 32.20 4.30
1851 1944 5.788533 TGGAATTTTCTTCTAGGTACCTCCA 59.211 40.000 20.32 12.28 39.02 3.86
1852 1945 6.070194 TGGAATTTTCTTCTAGGTACCTCCAG 60.070 42.308 20.32 11.85 39.02 3.86
1853 1946 6.070136 GGAATTTTCTTCTAGGTACCTCCAGT 60.070 42.308 20.32 0.00 39.02 4.00
1854 1947 5.997384 TTTTCTTCTAGGTACCTCCAGTC 57.003 43.478 20.32 0.00 39.02 3.51
1855 1948 3.666345 TCTTCTAGGTACCTCCAGTCC 57.334 52.381 20.32 0.00 39.02 3.85
1856 1949 3.199671 TCTTCTAGGTACCTCCAGTCCT 58.800 50.000 20.32 0.00 39.02 3.85
1857 1950 3.202595 TCTTCTAGGTACCTCCAGTCCTC 59.797 52.174 20.32 0.00 39.02 3.71
1866 1959 1.981495 CCTCCAGTCCTCAAGGTCTTT 59.019 52.381 0.00 0.00 36.34 2.52
1907 2009 9.376075 ACAAGTATGATCTATGAAACACTCAAG 57.624 33.333 0.00 0.00 37.67 3.02
1925 2027 5.411669 ACTCAAGAAATGTCAATTACCGACC 59.588 40.000 0.00 0.00 32.15 4.79
2186 2300 2.528041 AACTTGAGTGTCCGTCTTCC 57.472 50.000 0.00 0.00 0.00 3.46
2310 2424 9.778741 ATCAAATCTGAATTAATAGTAGCGGAA 57.221 29.630 0.00 0.00 34.49 4.30
2348 2471 4.142600 GCTGTTAAATTGCAGTCTAGGTGG 60.143 45.833 0.00 0.00 35.33 4.61
2362 2485 4.226620 GTCTAGGTGGGGTTAAATCTGGAA 59.773 45.833 0.00 0.00 0.00 3.53
2389 2512 1.154225 GGCGATCTGTTTGGCAACG 60.154 57.895 0.00 0.00 42.51 4.10
2634 2757 3.667960 GCAAGATGAAAGTAGTTGTGCCG 60.668 47.826 0.00 0.00 0.00 5.69
2670 2793 4.094294 GCATACCAAAACGCATCAACTCTA 59.906 41.667 0.00 0.00 0.00 2.43
2772 2895 2.245159 TTATGGCTGAGCTGAATCCG 57.755 50.000 3.72 0.00 0.00 4.18
2784 2907 3.376546 AGCTGAATCCGATTTTGAGCTTC 59.623 43.478 13.56 0.00 31.27 3.86
2838 2961 2.505866 CTTTTCCAACTAATGTCGCGC 58.494 47.619 0.00 0.00 0.00 6.86
3114 3237 4.499183 ACAGCCTTTTAGACGAAGATCAG 58.501 43.478 0.00 0.00 0.00 2.90
3123 3246 4.039151 AGACGAAGATCAGCACAGTATG 57.961 45.455 0.00 0.00 46.00 2.39
3144 3267 2.346803 GCAAGCGGAAGTTATGACAGA 58.653 47.619 0.00 0.00 0.00 3.41
3168 3291 6.919721 ACACTATGGCATTTTTACGTTTGAT 58.080 32.000 4.78 0.00 0.00 2.57
3174 3297 3.367630 GCATTTTTACGTTTGATGGCCAG 59.632 43.478 13.05 0.00 0.00 4.85
3204 3327 2.586425 CATGTCAACTTGGGTCAAGGT 58.414 47.619 11.65 2.65 42.67 3.50
3208 3331 1.142870 TCAACTTGGGTCAAGGTCCTG 59.857 52.381 11.65 4.52 39.61 3.86
3222 3345 1.301716 TCCTGTGGCGCTCAAGAAC 60.302 57.895 7.64 0.00 0.00 3.01
3236 3359 0.036010 AAGAACGCTCTGGATGTGGG 60.036 55.000 0.00 0.00 30.03 4.61
3297 3420 7.234355 ACAAAGACCTATCCAATGTTTCTTCT 58.766 34.615 0.00 0.00 0.00 2.85
3303 3426 9.886132 GACCTATCCAATGTTTCTTCTAGTTTA 57.114 33.333 0.00 0.00 0.00 2.01
3318 3441 0.026803 GTTTATCTGCCGCTTGCTCG 59.973 55.000 0.00 0.00 42.00 5.03
3534 3657 0.522180 CTTCTGCTGCTGCTTCCTTG 59.478 55.000 17.00 0.97 40.48 3.61
3551 3674 2.738139 GCACCCAACATTTGCCGC 60.738 61.111 0.00 0.00 0.00 6.53
3569 3692 1.588404 CGCGCTGTGGATACTAGTTTG 59.412 52.381 5.56 0.00 37.61 2.93
3590 3713 6.716934 TTGGGTTTGCATTTACAGTTTAGA 57.283 33.333 0.00 0.00 0.00 2.10
3634 3784 3.200522 GGCTCGATTTGGGCCTTG 58.799 61.111 7.63 0.00 42.31 3.61
3671 3821 5.118990 GTGTCTCATGTAGCATGTGGTAAT 58.881 41.667 8.68 0.00 0.00 1.89
3675 3825 6.018425 GTCTCATGTAGCATGTGGTAATTCAG 60.018 42.308 8.68 0.00 0.00 3.02
3685 3835 5.304686 TGTGGTAATTCAGAAGTCTTGGT 57.695 39.130 0.00 0.00 0.00 3.67
3701 3851 3.625764 TCTTGGTGCACTGTCAAAACTAC 59.374 43.478 17.98 0.00 0.00 2.73
3705 3857 4.131596 GGTGCACTGTCAAAACTACCTAA 58.868 43.478 17.98 0.00 0.00 2.69
3712 3872 7.224949 GCACTGTCAAAACTACCTAATATCTCC 59.775 40.741 0.00 0.00 0.00 3.71
3716 3876 8.533657 TGTCAAAACTACCTAATATCTCCGAAA 58.466 33.333 0.00 0.00 0.00 3.46
3733 3893 4.023963 TCCGAAATTGTGCAAATTCGTACA 60.024 37.500 24.23 11.72 46.46 2.90
3734 3894 4.320690 CCGAAATTGTGCAAATTCGTACAG 59.679 41.667 24.23 11.85 46.46 2.74
3754 3914 2.555757 AGTACGTTGTACAGGACTCCAC 59.444 50.000 9.53 0.00 0.00 4.02
3760 4303 2.372264 TGTACAGGACTCCACGATACC 58.628 52.381 0.00 0.00 0.00 2.73
3763 4306 2.100989 ACAGGACTCCACGATACCTTC 58.899 52.381 0.00 0.00 0.00 3.46
3772 4315 2.945008 CCACGATACCTTCCACGTACTA 59.055 50.000 0.00 0.00 37.22 1.82
3773 4316 3.567164 CCACGATACCTTCCACGTACTAT 59.433 47.826 0.00 0.00 37.22 2.12
3774 4317 4.320057 CCACGATACCTTCCACGTACTATC 60.320 50.000 0.00 0.00 37.22 2.08
3775 4318 4.274214 CACGATACCTTCCACGTACTATCA 59.726 45.833 0.00 0.00 37.22 2.15
3776 4319 4.883585 ACGATACCTTCCACGTACTATCAA 59.116 41.667 0.00 0.00 37.22 2.57
3777 4320 5.210715 CGATACCTTCCACGTACTATCAAC 58.789 45.833 0.00 0.00 0.00 3.18
3778 4321 5.008415 CGATACCTTCCACGTACTATCAACT 59.992 44.000 0.00 0.00 0.00 3.16
3779 4322 6.203530 CGATACCTTCCACGTACTATCAACTA 59.796 42.308 0.00 0.00 0.00 2.24
3780 4323 5.573337 ACCTTCCACGTACTATCAACTAC 57.427 43.478 0.00 0.00 0.00 2.73
3781 4324 4.095483 ACCTTCCACGTACTATCAACTACG 59.905 45.833 0.00 0.00 41.24 3.51
3783 4326 3.872696 TCCACGTACTATCAACTACGGA 58.127 45.455 0.00 0.00 40.06 4.69
3784 4327 4.454678 TCCACGTACTATCAACTACGGAT 58.545 43.478 0.00 0.00 40.06 4.18
3785 4328 4.883585 TCCACGTACTATCAACTACGGATT 59.116 41.667 0.00 0.00 40.06 3.01
3786 4329 5.357878 TCCACGTACTATCAACTACGGATTT 59.642 40.000 0.00 0.00 40.06 2.17
3787 4330 6.038356 CCACGTACTATCAACTACGGATTTT 58.962 40.000 0.00 0.00 40.06 1.82
3807 4699 0.883370 GGGATCACGCCCCGATTAAC 60.883 60.000 0.00 0.00 42.62 2.01
3815 4707 2.081462 CGCCCCGATTAACTTTCTGTT 58.919 47.619 0.00 0.00 42.31 3.16
3837 4729 8.234136 TGTTGATAGAGTAACATACGAAGGAT 57.766 34.615 0.00 0.00 32.30 3.24
3868 4766 6.028987 GGGCAACGCGTTTAATTAAGATAAA 58.971 36.000 24.21 0.00 37.60 1.40
3913 4828 1.155889 TCGCTTACCTGACGTTACGA 58.844 50.000 13.03 0.00 0.00 3.43
3997 6350 4.054671 GACCTAAGATCATGGCTTCTTCG 58.945 47.826 8.97 4.86 34.22 3.79
4010 6363 0.333312 TTCTTCGGGCTCTCTCCTCT 59.667 55.000 0.00 0.00 0.00 3.69
4015 6368 2.124693 GGGCTCTCTCCTCTCCACG 61.125 68.421 0.00 0.00 0.00 4.94
4344 6712 2.287965 GCGACGACGACAACAACGA 61.288 57.895 12.29 0.00 42.66 3.85
4480 6866 3.573491 GGTGCGCCGTTAGATGGC 61.573 66.667 4.18 1.02 46.71 4.40
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
20 21 3.253230 GCTTCGCCAAATGCTTGTAAAT 58.747 40.909 0.00 0.00 38.05 1.40
419 474 0.251386 TTCCTGGTTTGCCGGCAATA 60.251 50.000 40.32 27.30 39.86 1.90
645 706 1.283029 AGCTAAGCAATGCCTTGGAGA 59.717 47.619 0.00 0.00 32.72 3.71
821 904 7.093684 GGATTACAGTCAAGAGGTAAGAGTTCT 60.094 40.741 0.00 0.00 31.26 3.01
883 966 5.129485 TGGTTCAAAATGCTCCTTTAAACCA 59.871 36.000 8.54 8.54 39.38 3.67
924 1012 1.001181 TGTCCAGCGGTTTACACTACC 59.999 52.381 0.00 0.00 0.00 3.18
1045 1133 1.210722 GAGGAAAAGGAGAAGCGGGAT 59.789 52.381 0.00 0.00 0.00 3.85
1464 1554 0.817013 GCCCCTTCGCATTTCATGAA 59.183 50.000 3.38 3.38 0.00 2.57
1616 1708 9.088512 CGGTGCCAATAGAGACTATAATATTTC 57.911 37.037 0.00 0.00 0.00 2.17
1617 1709 8.041323 CCGGTGCCAATAGAGACTATAATATTT 58.959 37.037 0.00 0.00 0.00 1.40
1618 1710 7.399191 TCCGGTGCCAATAGAGACTATAATATT 59.601 37.037 0.00 0.00 0.00 1.28
1619 1711 6.895756 TCCGGTGCCAATAGAGACTATAATAT 59.104 38.462 0.00 0.00 0.00 1.28
1620 1712 6.250711 TCCGGTGCCAATAGAGACTATAATA 58.749 40.000 0.00 0.00 0.00 0.98
1621 1713 5.084519 TCCGGTGCCAATAGAGACTATAAT 58.915 41.667 0.00 0.00 0.00 1.28
1622 1714 4.476297 TCCGGTGCCAATAGAGACTATAA 58.524 43.478 0.00 0.00 0.00 0.98
1623 1715 4.108501 TCCGGTGCCAATAGAGACTATA 57.891 45.455 0.00 0.00 0.00 1.31
1624 1716 2.958818 TCCGGTGCCAATAGAGACTAT 58.041 47.619 0.00 0.00 0.00 2.12
1625 1717 2.447408 TCCGGTGCCAATAGAGACTA 57.553 50.000 0.00 0.00 0.00 2.59
1628 1720 1.788229 TCATCCGGTGCCAATAGAGA 58.212 50.000 0.00 0.00 0.00 3.10
1690 1782 1.337703 TGGTTTTGAGCATGTCAGCAC 59.662 47.619 0.00 0.00 36.21 4.40
1712 1804 7.186804 GTCAACCGTCAACATTATTAAGGATG 58.813 38.462 0.00 0.00 0.00 3.51
1749 1842 0.179018 AAGCAGCGTCTTCCACCTTT 60.179 50.000 0.00 0.00 0.00 3.11
1774 1867 4.974645 ATTGAAGTCAACCACTGGACTA 57.025 40.909 0.71 0.00 43.26 2.59
1866 1959 9.474920 GATCATACTTGTTTGTTCCATGAAAAA 57.525 29.630 0.00 0.00 0.00 1.94
1907 2009 3.689649 AGCAGGTCGGTAATTGACATTTC 59.310 43.478 0.00 0.00 38.10 2.17
1925 2027 7.997482 TGTAGAGAATAAACACCTACTAGCAG 58.003 38.462 0.00 0.00 33.01 4.24
2186 2300 2.974165 GCCAGAAGCGAAATATCAACG 58.026 47.619 0.00 0.00 0.00 4.10
2310 2424 9.077885 CAATTTAACAGCCATATTACCCTACAT 57.922 33.333 0.00 0.00 0.00 2.29
2348 2471 4.023291 TGCCTCAATTCCAGATTTAACCC 58.977 43.478 0.00 0.00 0.00 4.11
2362 2485 0.254178 AACAGATCGCCTGCCTCAAT 59.746 50.000 4.84 0.00 46.81 2.57
2389 2512 8.524870 ACATGAAACAGAACAAATTAAGCATC 57.475 30.769 0.00 0.00 0.00 3.91
2634 2757 3.459232 TGGTATGCATCAGAGCTACAC 57.541 47.619 0.19 0.00 34.99 2.90
2670 2793 3.665190 CCTGAAGTAAGCTTTCGAAGGT 58.335 45.455 3.20 1.60 41.85 3.50
2751 2874 3.144506 CGGATTCAGCTCAGCCATAAAT 58.855 45.455 0.00 0.00 0.00 1.40
2759 2882 3.242673 GCTCAAAATCGGATTCAGCTCAG 60.243 47.826 16.31 5.45 0.00 3.35
2760 2883 2.679837 GCTCAAAATCGGATTCAGCTCA 59.320 45.455 16.31 0.00 0.00 4.26
2784 2907 7.067859 TCCAATGAAATATTCTTCTTCTGCTGG 59.932 37.037 0.00 0.00 0.00 4.85
2838 2961 4.956085 TGTTATGACCATCACTTATCGGG 58.044 43.478 0.00 0.00 0.00 5.14
2946 3069 4.247380 GGCCATCCTGCTCTCCCG 62.247 72.222 0.00 0.00 0.00 5.14
3114 3237 1.305219 TTCCGCTTGCCATACTGTGC 61.305 55.000 0.00 0.00 0.00 4.57
3123 3246 1.398390 CTGTCATAACTTCCGCTTGCC 59.602 52.381 0.00 0.00 0.00 4.52
3144 3267 6.320494 TCAAACGTAAAAATGCCATAGTGT 57.680 33.333 0.00 0.00 0.00 3.55
3174 3297 2.200373 AGTTGACATGGTACTTGGCC 57.800 50.000 0.00 0.00 0.00 5.36
3204 3327 1.301716 GTTCTTGAGCGCCACAGGA 60.302 57.895 2.29 8.43 0.00 3.86
3222 3345 1.227380 GTAGCCCACATCCAGAGCG 60.227 63.158 0.00 0.00 0.00 5.03
3236 3359 2.614057 CACCATTTCGATGGAAGGTAGC 59.386 50.000 12.02 0.00 44.39 3.58
3368 3491 0.478072 TGACACATTTCCAGGCCAGT 59.522 50.000 5.01 0.00 0.00 4.00
3534 3657 2.738139 GCGGCAAATGTTGGGTGC 60.738 61.111 0.00 0.00 37.55 5.01
3551 3674 2.093658 ACCCAAACTAGTATCCACAGCG 60.094 50.000 0.00 0.00 0.00 5.18
3569 3692 6.149633 CAGTCTAAACTGTAAATGCAAACCC 58.850 40.000 0.00 0.00 46.52 4.11
3590 3713 1.561076 TCATTGGGCAGCTACATCAGT 59.439 47.619 0.00 0.00 0.00 3.41
3634 3784 6.336566 ACATGAGACACATAGACACATCTTC 58.663 40.000 0.00 0.00 37.46 2.87
3671 3821 2.092968 ACAGTGCACCAAGACTTCTGAA 60.093 45.455 14.63 0.00 0.00 3.02
3675 3825 1.953559 TGACAGTGCACCAAGACTTC 58.046 50.000 14.63 0.27 0.00 3.01
3685 3835 7.620880 AGATATTAGGTAGTTTTGACAGTGCA 58.379 34.615 0.00 0.00 0.00 4.57
3701 3851 6.618287 TTGCACAATTTCGGAGATATTAGG 57.382 37.500 0.00 0.00 36.09 2.69
3705 3857 6.201517 CGAATTTGCACAATTTCGGAGATAT 58.798 36.000 22.92 0.00 44.06 1.63
3733 3893 2.555757 GTGGAGTCCTGTACAACGTACT 59.444 50.000 11.33 0.00 0.00 2.73
3734 3894 2.666619 CGTGGAGTCCTGTACAACGTAC 60.667 54.545 11.33 0.00 31.15 3.67
3744 3904 1.409427 GGAAGGTATCGTGGAGTCCTG 59.591 57.143 11.33 3.04 0.00 3.86
3754 3914 5.008415 AGTTGATAGTACGTGGAAGGTATCG 59.992 44.000 0.00 0.00 39.60 2.92
3772 4315 4.881850 GTGATCCCAAAATCCGTAGTTGAT 59.118 41.667 0.00 0.00 0.00 2.57
3773 4316 4.258543 GTGATCCCAAAATCCGTAGTTGA 58.741 43.478 0.00 0.00 0.00 3.18
3774 4317 3.063452 CGTGATCCCAAAATCCGTAGTTG 59.937 47.826 0.00 0.00 0.00 3.16
3775 4318 3.267483 CGTGATCCCAAAATCCGTAGTT 58.733 45.455 0.00 0.00 0.00 2.24
3776 4319 2.901249 CGTGATCCCAAAATCCGTAGT 58.099 47.619 0.00 0.00 0.00 2.73
3777 4320 1.597663 GCGTGATCCCAAAATCCGTAG 59.402 52.381 0.00 0.00 0.00 3.51
3778 4321 1.658994 GCGTGATCCCAAAATCCGTA 58.341 50.000 0.00 0.00 0.00 4.02
3779 4322 1.029947 GGCGTGATCCCAAAATCCGT 61.030 55.000 0.00 0.00 0.00 4.69
3780 4323 1.724582 GGGCGTGATCCCAAAATCCG 61.725 60.000 0.00 0.00 45.82 4.18
3781 4324 2.115510 GGGCGTGATCCCAAAATCC 58.884 57.895 0.00 0.00 45.82 3.01
3807 4699 9.569167 TTCGTATGTTACTCTATCAACAGAAAG 57.431 33.333 0.00 0.00 38.01 2.62
3815 4707 8.380867 TCCTATCCTTCGTATGTTACTCTATCA 58.619 37.037 0.00 0.00 0.00 2.15
3827 4719 2.258109 GCCCCTTCCTATCCTTCGTAT 58.742 52.381 0.00 0.00 0.00 3.06
3837 4729 2.400269 AAACGCGTTGCCCCTTCCTA 62.400 55.000 27.34 0.00 0.00 2.94
3868 4766 3.365969 GGCGAAGTCCAAACGAATCAAAT 60.366 43.478 0.00 0.00 0.00 2.32
3936 6289 0.736053 GAGTGAGGAGGCTGACGTAG 59.264 60.000 0.00 0.00 0.00 3.51
3974 6327 4.384940 GAAGAAGCCATGATCTTAGGTCC 58.615 47.826 0.00 0.00 36.08 4.46
3997 6350 2.124693 CGTGGAGAGGAGAGAGCCC 61.125 68.421 0.00 0.00 0.00 5.19
4010 6363 4.007644 CAGCACCAGGAGCGTGGA 62.008 66.667 15.43 0.00 40.44 4.02
4326 6688 2.164673 CGTTGTTGTCGTCGTCGC 59.835 61.111 0.00 0.00 36.96 5.19
4344 6712 4.241555 GATGATGCCCCTCGCCGT 62.242 66.667 0.00 0.00 36.24 5.68
4452 6838 2.985847 GCGCACCAAGCCCTTTCT 60.986 61.111 0.30 0.00 41.38 2.52
4480 6866 4.920340 CACACACTGACTCAGCTTAGTTAG 59.080 45.833 16.08 16.08 38.65 2.34


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

AutoCloner maintained by Alex Coulton.