Multiple sequence alignment - TraesCS6A01G382600

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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 TraesCS6A01G382600 chr6A 100.000 3774 0 0 1 3774 601948934 601952707 0.000000e+00 6970
1 TraesCS6A01G382600 chr6A 85.478 1997 174 67 831 2753 601471949 601473903 0.000000e+00 1975
2 TraesCS6A01G382600 chr6A 84.551 1560 170 48 1077 2588 601872367 601873903 0.000000e+00 1480
3 TraesCS6A01G382600 chr6A 87.112 419 40 9 681 1095 601871918 601872326 2.660000e-126 462
4 TraesCS6A01G382600 chr6B 90.878 3519 158 67 1 3416 692427058 692430516 0.000000e+00 4569
5 TraesCS6A01G382600 chr6B 90.164 1342 103 16 1286 2605 692338651 692339985 0.000000e+00 1720
6 TraesCS6A01G382600 chr6B 82.600 2069 231 67 726 2710 692258672 692260695 0.000000e+00 1707
7 TraesCS6A01G382600 chr6B 93.459 1116 41 15 1654 2757 692234337 692235432 0.000000e+00 1628
8 TraesCS6A01G382600 chr6B 83.913 920 78 38 561 1414 692233026 692233941 0.000000e+00 815
9 TraesCS6A01G382600 chr6B 96.037 429 11 4 866 1292 692337846 692338270 0.000000e+00 693
10 TraesCS6A01G382600 chr6B 95.802 262 9 2 1409 1669 692234060 692234320 4.510000e-114 422
11 TraesCS6A01G382600 chr6B 83.386 319 20 13 3 289 692335320 692335637 8.040000e-67 265
12 TraesCS6A01G382600 chr6B 93.333 180 11 1 289 468 692335977 692336155 8.040000e-67 265
13 TraesCS6A01G382600 chr6D 91.972 3114 143 38 1 3028 455249856 455252948 0.000000e+00 4266
14 TraesCS6A01G382600 chr6D 85.297 1952 183 55 726 2605 455133671 455135590 0.000000e+00 1919
15 TraesCS6A01G382600 chr6D 92.395 1144 34 20 1654 2757 455099165 455100295 0.000000e+00 1581
16 TraesCS6A01G382600 chr6D 90.692 881 42 18 831 1673 455098275 455099153 0.000000e+00 1136
17 TraesCS6A01G382600 chr6D 91.233 673 30 18 2366 3026 455295223 455295878 0.000000e+00 889
18 TraesCS6A01G382600 chr6D 79.928 558 54 26 3078 3607 455254392 455254919 1.290000e-94 357
19 TraesCS6A01G382600 chr6D 78.846 520 69 26 1 493 455131126 455131631 2.830000e-81 313
20 TraesCS6A01G382600 chr6D 84.694 294 37 5 559 848 455097973 455098262 1.720000e-73 287
21 TraesCS6A01G382600 chr7B 93.820 178 5 1 3603 3774 35101593 35101770 2.890000e-66 263
22 TraesCS6A01G382600 chr7B 92.614 176 7 1 3605 3774 302576038 302575863 8.100000e-62 248
23 TraesCS6A01G382600 chr7B 91.111 180 10 1 3601 3774 40157825 40157646 4.870000e-59 239
24 TraesCS6A01G382600 chr5A 93.182 176 6 1 3605 3774 546794063 546793888 1.740000e-63 254
25 TraesCS6A01G382600 chr2A 92.737 179 7 1 3602 3774 685744208 685744386 1.740000e-63 254
26 TraesCS6A01G382600 chr4D 91.573 178 9 1 3603 3774 499689611 499689788 1.350000e-59 241
27 TraesCS6A01G382600 chr3B 91.573 178 9 2 3603 3774 14372638 14372815 1.350000e-59 241
28 TraesCS6A01G382600 chr2D 91.667 180 5 4 3603 3774 410179212 410179035 1.350000e-59 241
29 TraesCS6A01G382600 chr1D 91.011 178 10 3 3603 3774 338271340 338271517 6.300000e-58 235


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 TraesCS6A01G382600 chr6A 601948934 601952707 3773 False 6970.000000 6970 100.000000 1 3774 1 chr6A.!!$F2 3773
1 TraesCS6A01G382600 chr6A 601471949 601473903 1954 False 1975.000000 1975 85.478000 831 2753 1 chr6A.!!$F1 1922
2 TraesCS6A01G382600 chr6A 601871918 601873903 1985 False 971.000000 1480 85.831500 681 2588 2 chr6A.!!$F3 1907
3 TraesCS6A01G382600 chr6B 692427058 692430516 3458 False 4569.000000 4569 90.878000 1 3416 1 chr6B.!!$F2 3415
4 TraesCS6A01G382600 chr6B 692258672 692260695 2023 False 1707.000000 1707 82.600000 726 2710 1 chr6B.!!$F1 1984
5 TraesCS6A01G382600 chr6B 692233026 692235432 2406 False 955.000000 1628 91.058000 561 2757 3 chr6B.!!$F3 2196
6 TraesCS6A01G382600 chr6B 692335320 692339985 4665 False 735.750000 1720 90.730000 3 2605 4 chr6B.!!$F4 2602
7 TraesCS6A01G382600 chr6D 455249856 455254919 5063 False 2311.500000 4266 85.950000 1 3607 2 chr6D.!!$F4 3606
8 TraesCS6A01G382600 chr6D 455131126 455135590 4464 False 1116.000000 1919 82.071500 1 2605 2 chr6D.!!$F3 2604
9 TraesCS6A01G382600 chr6D 455097973 455100295 2322 False 1001.333333 1581 89.260333 559 2757 3 chr6D.!!$F2 2198
10 TraesCS6A01G382600 chr6D 455295223 455295878 655 False 889.000000 889 91.233000 2366 3026 1 chr6D.!!$F1 660

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
804 4543 2.017782 TGCACCAAAGCGACAACTTTA 58.982 42.857 0.0 0.0 37.78 1.85 F
1355 5658 0.813821 GAGATCACCCTTTTGCAGCC 59.186 55.000 0.0 0.0 0.00 4.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1949 6489 0.608130 CGGTGATGTTGAGGAGGACA 59.392 55.0 0.0 0.0 0.0 4.02 R
3255 9329 0.606604 GAGTTCCCTGCCGTAGTCAA 59.393 55.0 0.0 0.0 0.0 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
26 27 7.549615 ACTAACTATTCAAGCGATAAAACCC 57.450 36.000 0.00 0.00 0.00 4.11
186 217 7.368059 AGTCAATTCGATTGGAAAGTTAAACC 58.632 34.615 7.45 0.00 40.61 3.27
194 225 2.554893 TGGAAAGTTAAACCGCATGACC 59.445 45.455 0.00 0.00 0.00 4.02
196 227 3.254903 GGAAAGTTAAACCGCATGACCTT 59.745 43.478 0.00 0.00 0.00 3.50
223 257 7.461182 TTTTTATGGATTTGACGATCAAGGT 57.539 32.000 0.00 0.00 37.70 3.50
272 308 9.047947 ACTAATCTTTTGAGGACTATGGTACTT 57.952 33.333 0.00 0.00 36.63 2.24
398 791 4.341235 CCACCTCCGTAAGATGAGTATTCA 59.659 45.833 0.00 0.00 43.02 2.57
505 1136 9.476202 AGCTGTTAAATTAATTCAGTTTTGGAC 57.524 29.630 13.80 0.73 0.00 4.02
610 3736 7.889873 TTTGGAAAATTCAGTGAACTAAGGA 57.110 32.000 7.96 0.00 0.00 3.36
743 4482 3.807622 ACACAATTCGGAGTGTACAACAG 59.192 43.478 0.00 0.00 46.32 3.16
744 4483 3.807622 CACAATTCGGAGTGTACAACAGT 59.192 43.478 0.00 0.00 31.30 3.55
804 4543 2.017782 TGCACCAAAGCGACAACTTTA 58.982 42.857 0.00 0.00 37.78 1.85
989 4797 6.659242 CCTATATAAAGCACCCCATTACCAAG 59.341 42.308 0.00 0.00 0.00 3.61
1355 5658 0.813821 GAGATCACCCTTTTGCAGCC 59.186 55.000 0.00 0.00 0.00 4.85
1435 5877 3.625853 AGCTGTAGTGACATCTAGCTCA 58.374 45.455 0.00 0.00 29.85 4.26
1907 6447 2.561733 ACATCGTCATGTACCTCGTG 57.438 50.000 0.00 0.00 41.81 4.35
1916 6456 2.048603 GTACCTCGTGTACGCCCCT 61.049 63.158 0.00 0.00 40.44 4.79
1940 6480 1.999648 AGGCCAAGATTTTCACAGCA 58.000 45.000 5.01 0.00 0.00 4.41
1949 6489 5.695851 AGATTTTCACAGCAAAGATCGTT 57.304 34.783 0.00 0.00 0.00 3.85
1965 6505 1.967779 TCGTTGTCCTCCTCAACATCA 59.032 47.619 8.98 0.00 43.40 3.07
2012 6553 2.657237 CTCTTCGCCTTCCACGGT 59.343 61.111 0.00 0.00 0.00 4.83
2154 6699 2.508663 GCGGGACCTCTTGTACGC 60.509 66.667 0.00 0.00 43.21 4.42
2364 6951 8.833493 CATACATACAATTCTCTCAAGCATGAA 58.167 33.333 0.00 0.00 34.49 2.57
2557 7154 2.027625 GTCGGCAAGACGGACAAGG 61.028 63.158 0.00 0.00 45.42 3.61
3061 7735 9.912634 TTTTACCTCATTTAGCAAAATTCTCTG 57.087 29.630 0.00 0.00 32.87 3.35
3128 9198 8.410912 AGTGAAACCTACAAAACAAATTACCTC 58.589 33.333 0.00 0.00 37.80 3.85
3129 9199 7.650504 GTGAAACCTACAAAACAAATTACCTCC 59.349 37.037 0.00 0.00 0.00 4.30
3132 9202 7.520451 ACCTACAAAACAAATTACCTCCTTC 57.480 36.000 0.00 0.00 0.00 3.46
3253 9327 2.793237 CGAACTGAACCCAAAAACGGTG 60.793 50.000 0.00 0.00 32.55 4.94
3255 9329 0.744281 CTGAACCCAAAAACGGTGCT 59.256 50.000 0.00 0.00 32.55 4.40
3271 9345 1.295423 GCTTGACTACGGCAGGGAA 59.705 57.895 0.00 0.00 0.00 3.97
3285 9359 2.417936 GGAACTCCCTCGATCGGC 59.582 66.667 16.41 0.00 0.00 5.54
3287 9361 3.486252 GAACTCCCTCGATCGGCCG 62.486 68.421 22.12 22.12 0.00 6.13
3300 9374 4.247380 GGCCGGGCTCAGATCCAG 62.247 72.222 22.87 0.00 0.00 3.86
3375 9449 1.741770 GTTGTTGCTCGATCCGGCT 60.742 57.895 0.00 0.00 0.00 5.52
3412 9486 1.302511 CACAAACACGGGAGGGGAG 60.303 63.158 0.00 0.00 37.82 4.30
3454 9552 1.961277 CTTGAGGTCCGCGCAAACT 60.961 57.895 8.75 1.64 0.00 2.66
3464 9562 2.949106 CGCAAACTGGTGAGGCAG 59.051 61.111 0.00 0.00 0.00 4.85
3561 9659 2.663196 GTCCGTGGAGTTGGAGGG 59.337 66.667 0.00 0.00 34.21 4.30
3588 9686 1.031029 AGGCGGTCGAAGGAGTAGAC 61.031 60.000 0.00 0.00 0.00 2.59
3597 9695 2.476519 CGAAGGAGTAGACGAGCTTGAC 60.477 54.545 8.31 0.65 0.00 3.18
3599 9697 1.085091 GGAGTAGACGAGCTTGACGA 58.915 55.000 8.31 0.00 34.70 4.20
3607 9705 1.469308 ACGAGCTTGACGAGGTTAGAG 59.531 52.381 8.31 0.00 35.91 2.43
3608 9706 1.795889 CGAGCTTGACGAGGTTAGAGC 60.796 57.143 0.00 0.00 35.91 4.09
3609 9707 1.202582 GAGCTTGACGAGGTTAGAGCA 59.797 52.381 0.00 0.00 35.91 4.26
3610 9708 1.827969 AGCTTGACGAGGTTAGAGCAT 59.172 47.619 0.00 0.00 30.17 3.79
3611 9709 1.929836 GCTTGACGAGGTTAGAGCATG 59.070 52.381 0.00 0.00 0.00 4.06
3612 9710 2.544685 CTTGACGAGGTTAGAGCATGG 58.455 52.381 0.00 0.00 0.00 3.66
3613 9711 1.557099 TGACGAGGTTAGAGCATGGT 58.443 50.000 0.00 0.00 0.00 3.55
3614 9712 1.899814 TGACGAGGTTAGAGCATGGTT 59.100 47.619 0.00 0.00 0.00 3.67
3615 9713 3.093814 TGACGAGGTTAGAGCATGGTTA 58.906 45.455 0.00 0.00 0.00 2.85
3616 9714 3.512329 TGACGAGGTTAGAGCATGGTTAA 59.488 43.478 0.00 0.00 0.00 2.01
3617 9715 4.161565 TGACGAGGTTAGAGCATGGTTAAT 59.838 41.667 0.00 0.00 0.00 1.40
3618 9716 4.442706 ACGAGGTTAGAGCATGGTTAATG 58.557 43.478 0.00 0.00 39.49 1.90
3619 9717 3.809832 CGAGGTTAGAGCATGGTTAATGG 59.190 47.826 0.00 0.00 36.71 3.16
3621 9719 5.452776 CGAGGTTAGAGCATGGTTAATGGTA 60.453 44.000 0.00 0.00 46.95 3.25
3622 9720 6.515512 AGGTTAGAGCATGGTTAATGGTAT 57.484 37.500 0.00 0.00 46.95 2.73
3623 9721 7.524863 CGAGGTTAGAGCATGGTTAATGGTATA 60.525 40.741 0.00 0.00 46.95 1.47
3624 9722 7.680730 AGGTTAGAGCATGGTTAATGGTATAG 58.319 38.462 0.00 0.00 46.95 1.31
3625 9723 6.371825 GGTTAGAGCATGGTTAATGGTATAGC 59.628 42.308 0.00 0.00 46.95 2.97
3626 9724 4.911390 AGAGCATGGTTAATGGTATAGCC 58.089 43.478 0.00 0.00 46.95 3.93
3658 9756 6.917217 GCTATAAGCCATTGTCCTATCATC 57.083 41.667 0.00 0.00 34.48 2.92
3659 9757 6.648192 GCTATAAGCCATTGTCCTATCATCT 58.352 40.000 0.00 0.00 34.48 2.90
3660 9758 7.786030 GCTATAAGCCATTGTCCTATCATCTA 58.214 38.462 0.00 0.00 34.48 1.98
3661 9759 8.428063 GCTATAAGCCATTGTCCTATCATCTAT 58.572 37.037 0.00 0.00 34.48 1.98
3664 9762 6.232581 AGCCATTGTCCTATCATCTATAGC 57.767 41.667 0.00 0.00 36.92 2.97
3665 9763 5.130145 AGCCATTGTCCTATCATCTATAGCC 59.870 44.000 0.00 0.00 36.92 3.93
3666 9764 5.686124 GCCATTGTCCTATCATCTATAGCCC 60.686 48.000 0.00 0.00 36.92 5.19
3667 9765 5.426509 CCATTGTCCTATCATCTATAGCCCA 59.573 44.000 0.00 0.00 36.92 5.36
3668 9766 6.100859 CCATTGTCCTATCATCTATAGCCCAT 59.899 42.308 0.00 0.00 36.92 4.00
3669 9767 6.798427 TTGTCCTATCATCTATAGCCCATC 57.202 41.667 0.00 0.00 36.92 3.51
3670 9768 6.097439 TGTCCTATCATCTATAGCCCATCT 57.903 41.667 0.00 0.00 36.92 2.90
3671 9769 6.506661 TGTCCTATCATCTATAGCCCATCTT 58.493 40.000 0.00 0.00 36.92 2.40
3672 9770 7.652554 TGTCCTATCATCTATAGCCCATCTTA 58.347 38.462 0.00 0.00 36.92 2.10
3673 9771 8.292480 TGTCCTATCATCTATAGCCCATCTTAT 58.708 37.037 0.00 0.00 36.92 1.73
3674 9772 9.815306 GTCCTATCATCTATAGCCCATCTTATA 57.185 37.037 0.00 0.00 36.92 0.98
3676 9774 8.748412 CCTATCATCTATAGCCCATCTTATAGC 58.252 40.741 0.00 0.00 36.92 2.97
3677 9775 6.985653 TCATCTATAGCCCATCTTATAGCC 57.014 41.667 0.00 0.00 0.00 3.93
3678 9776 6.443832 TCATCTATAGCCCATCTTATAGCCA 58.556 40.000 0.00 0.00 0.00 4.75
3679 9777 6.902974 TCATCTATAGCCCATCTTATAGCCAA 59.097 38.462 0.00 0.00 0.00 4.52
3680 9778 7.570232 TCATCTATAGCCCATCTTATAGCCAAT 59.430 37.037 0.00 0.00 0.00 3.16
3681 9779 8.874156 CATCTATAGCCCATCTTATAGCCAATA 58.126 37.037 0.00 0.00 0.00 1.90
3682 9780 9.626840 ATCTATAGCCCATCTTATAGCCAATAT 57.373 33.333 0.00 0.00 0.00 1.28
3683 9781 8.874156 TCTATAGCCCATCTTATAGCCAATATG 58.126 37.037 0.00 0.00 0.00 1.78
3684 9782 5.786121 AGCCCATCTTATAGCCAATATGT 57.214 39.130 0.00 0.00 0.00 2.29
3685 9783 6.891306 AGCCCATCTTATAGCCAATATGTA 57.109 37.500 0.00 0.00 0.00 2.29
3686 9784 6.653989 AGCCCATCTTATAGCCAATATGTAC 58.346 40.000 0.00 0.00 0.00 2.90
3687 9785 6.215431 AGCCCATCTTATAGCCAATATGTACA 59.785 38.462 0.00 0.00 0.00 2.90
3688 9786 6.884295 GCCCATCTTATAGCCAATATGTACAA 59.116 38.462 0.00 0.00 0.00 2.41
3689 9787 7.557719 GCCCATCTTATAGCCAATATGTACAAT 59.442 37.037 0.00 0.00 0.00 2.71
3734 9832 9.762381 TTTTTATTATATGACCCACCTTTCACT 57.238 29.630 0.00 0.00 0.00 3.41
3735 9833 8.974060 TTTATTATATGACCCACCTTTCACTC 57.026 34.615 0.00 0.00 0.00 3.51
3736 9834 6.831664 ATTATATGACCCACCTTTCACTCT 57.168 37.500 0.00 0.00 0.00 3.24
3737 9835 4.762289 ATATGACCCACCTTTCACTCTC 57.238 45.455 0.00 0.00 0.00 3.20
3738 9836 1.801242 TGACCCACCTTTCACTCTCA 58.199 50.000 0.00 0.00 0.00 3.27
3739 9837 1.416401 TGACCCACCTTTCACTCTCAC 59.584 52.381 0.00 0.00 0.00 3.51
3740 9838 1.416401 GACCCACCTTTCACTCTCACA 59.584 52.381 0.00 0.00 0.00 3.58
3741 9839 1.843851 ACCCACCTTTCACTCTCACAA 59.156 47.619 0.00 0.00 0.00 3.33
3742 9840 2.241176 ACCCACCTTTCACTCTCACAAA 59.759 45.455 0.00 0.00 0.00 2.83
3743 9841 2.880890 CCCACCTTTCACTCTCACAAAG 59.119 50.000 0.00 0.00 0.00 2.77
3744 9842 3.545703 CCACCTTTCACTCTCACAAAGT 58.454 45.455 0.00 0.00 0.00 2.66
3745 9843 3.313526 CCACCTTTCACTCTCACAAAGTG 59.686 47.826 0.00 0.00 44.43 3.16
3746 9844 2.945668 ACCTTTCACTCTCACAAAGTGC 59.054 45.455 0.00 0.00 43.09 4.40
3747 9845 2.291741 CCTTTCACTCTCACAAAGTGCC 59.708 50.000 0.00 0.00 43.09 5.01
3748 9846 3.209410 CTTTCACTCTCACAAAGTGCCT 58.791 45.455 0.00 0.00 43.09 4.75
3749 9847 4.380531 CTTTCACTCTCACAAAGTGCCTA 58.619 43.478 0.00 0.00 43.09 3.93
3750 9848 3.667497 TCACTCTCACAAAGTGCCTAG 57.333 47.619 0.00 0.00 43.09 3.02
3751 9849 2.300152 TCACTCTCACAAAGTGCCTAGG 59.700 50.000 3.67 3.67 43.09 3.02
3752 9850 2.300152 CACTCTCACAAAGTGCCTAGGA 59.700 50.000 14.75 0.00 37.88 2.94
3753 9851 2.564947 ACTCTCACAAAGTGCCTAGGAG 59.435 50.000 14.75 0.00 32.98 3.69
3754 9852 1.276421 TCTCACAAAGTGCCTAGGAGC 59.724 52.381 14.75 3.68 32.98 4.70
3755 9853 1.002430 CTCACAAAGTGCCTAGGAGCA 59.998 52.381 14.75 0.22 41.46 4.26
3770 9868 3.191539 GCACGTGCTAGAGCTGGC 61.192 66.667 32.55 1.87 42.66 4.85
3771 9869 2.575993 CACGTGCTAGAGCTGGCT 59.424 61.111 0.82 0.00 42.66 4.75
3772 9870 1.518133 CACGTGCTAGAGCTGGCTC 60.518 63.158 14.02 14.02 42.66 4.70
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
10 11 4.339814 AGTTTGTGGGTTTTATCGCTTGAA 59.660 37.500 0.00 0.00 0.00 2.69
26 27 9.903682 AATAAGATGTTTGAGATCAAGTTTGTG 57.096 29.630 0.00 0.00 37.15 3.33
63 74 3.491267 GTCTTAGACCGTGATAGCATTGC 59.509 47.826 0.00 0.00 0.00 3.56
74 85 1.101331 GTCGGGATGTCTTAGACCGT 58.899 55.000 10.10 0.00 44.54 4.83
223 257 7.118723 AGTTCCTAGAAATGATGCAACCAATA 58.881 34.615 0.00 0.00 0.00 1.90
418 811 9.236691 TCGAACGTACCAACATAATTATACTTC 57.763 33.333 0.00 0.00 0.00 3.01
567 3690 7.831691 TCCAAATGAAATGTCTTACAGGAAA 57.168 32.000 0.00 0.00 0.00 3.13
599 3722 5.420739 AGGACTCTTCAGATCCTTAGTTCAC 59.579 44.000 0.00 0.00 40.03 3.18
610 3736 3.768757 CCAACTGAGAGGACTCTTCAGAT 59.231 47.826 23.29 15.10 42.99 2.90
743 4482 0.886563 AATGCCTCTGCTGCTGAAAC 59.113 50.000 10.47 6.17 38.71 2.78
744 4483 2.495155 TAATGCCTCTGCTGCTGAAA 57.505 45.000 10.47 0.48 38.71 2.69
989 4797 6.149474 TGAAACTCTTAGCCTGAATTGTAAGC 59.851 38.462 0.00 0.00 0.00 3.09
1418 5860 3.490078 GGCACTGAGCTAGATGTCACTAC 60.490 52.174 0.00 0.00 44.79 2.73
1435 5877 0.836606 CTTTTGGGGTTTTGGGCACT 59.163 50.000 0.00 0.00 0.00 4.40
1907 6447 2.820261 GCCTTCCTAGGGGCGTAC 59.180 66.667 12.69 0.00 42.25 3.67
1916 6456 4.335416 CTGTGAAAATCTTGGCCTTCCTA 58.665 43.478 3.32 0.00 0.00 2.94
1940 6480 3.071023 TGTTGAGGAGGACAACGATCTTT 59.929 43.478 0.00 0.00 46.96 2.52
1949 6489 0.608130 CGGTGATGTTGAGGAGGACA 59.392 55.000 0.00 0.00 0.00 4.02
2364 6951 8.788806 TGGAAACATAATTTTAATCGTCAGTGT 58.211 29.630 0.00 0.00 33.40 3.55
2720 7349 1.930567 TATTAACGGTTGCTCGGCTC 58.069 50.000 3.07 0.00 0.00 4.70
3104 9174 7.562088 AGGAGGTAATTTGTTTTGTAGGTTTCA 59.438 33.333 0.00 0.00 0.00 2.69
3138 9208 8.045507 TCTACAATCAGCAGAGAATGAGAAAAT 58.954 33.333 0.00 0.00 0.00 1.82
3139 9209 7.389232 TCTACAATCAGCAGAGAATGAGAAAA 58.611 34.615 0.00 0.00 0.00 2.29
3143 9213 5.177881 GCATCTACAATCAGCAGAGAATGAG 59.822 44.000 0.00 0.00 0.00 2.90
3144 9214 5.055144 GCATCTACAATCAGCAGAGAATGA 58.945 41.667 0.00 0.00 0.00 2.57
3145 9215 4.213694 GGCATCTACAATCAGCAGAGAATG 59.786 45.833 0.00 0.00 0.00 2.67
3236 9310 0.744281 AGCACCGTTTTTGGGTTCAG 59.256 50.000 0.00 0.00 34.97 3.02
3253 9327 1.019805 GTTCCCTGCCGTAGTCAAGC 61.020 60.000 0.00 0.00 0.00 4.01
3255 9329 0.606604 GAGTTCCCTGCCGTAGTCAA 59.393 55.000 0.00 0.00 0.00 3.18
3280 9354 3.620785 GATCTGAGCCCGGCCGAT 61.621 66.667 30.73 12.65 0.00 4.18
3289 9363 1.877258 GCATAGTGGCTGGATCTGAGC 60.877 57.143 8.33 8.33 35.57 4.26
3300 9374 2.418083 GGTTGCCTGGCATAGTGGC 61.418 63.158 24.03 8.45 46.26 5.01
3325 9399 1.069358 CGAGGAGGGAATAGAACAGGC 59.931 57.143 0.00 0.00 0.00 4.85
3375 9449 2.203788 AAGAGGAGCACCGGGTCA 60.204 61.111 6.32 0.00 43.32 4.02
3412 9486 1.745087 TCAATTGATTTGAGCTCCGCC 59.255 47.619 12.15 0.00 39.44 6.13
3508 9606 4.273318 GCTACTCCTCCATCCATGTTTTT 58.727 43.478 0.00 0.00 0.00 1.94
3514 9612 0.833834 CCCGCTACTCCTCCATCCAT 60.834 60.000 0.00 0.00 0.00 3.41
3527 9625 4.124351 CGTCGAGGTTGCCCGCTA 62.124 66.667 0.00 0.00 35.12 4.26
3542 9640 2.571216 CCTCCAACTCCACGGACGT 61.571 63.158 0.00 0.00 0.00 4.34
3545 9643 3.319198 GCCCTCCAACTCCACGGA 61.319 66.667 0.00 0.00 0.00 4.69
3566 9664 1.030488 TACTCCTTCGACCGCCTCAG 61.030 60.000 0.00 0.00 0.00 3.35
3576 9674 1.738350 TCAAGCTCGTCTACTCCTTCG 59.262 52.381 0.00 0.00 0.00 3.79
3588 9686 1.795889 GCTCTAACCTCGTCAAGCTCG 60.796 57.143 0.00 0.00 0.00 5.03
3597 9695 3.809832 CCATTAACCATGCTCTAACCTCG 59.190 47.826 0.00 0.00 0.00 4.63
3599 9697 4.862641 ACCATTAACCATGCTCTAACCT 57.137 40.909 0.00 0.00 0.00 3.50
3635 9733 6.648192 AGATGATAGGACAATGGCTTATAGC 58.352 40.000 0.00 0.00 41.46 2.97
3638 9736 8.428063 GCTATAGATGATAGGACAATGGCTTAT 58.572 37.037 3.21 0.00 38.43 1.73
3639 9737 7.147655 GGCTATAGATGATAGGACAATGGCTTA 60.148 40.741 3.21 0.00 38.43 3.09
3640 9738 6.352565 GGCTATAGATGATAGGACAATGGCTT 60.353 42.308 3.21 0.00 38.43 4.35
3641 9739 5.130145 GGCTATAGATGATAGGACAATGGCT 59.870 44.000 3.21 0.00 38.43 4.75
3642 9740 5.363939 GGCTATAGATGATAGGACAATGGC 58.636 45.833 3.21 0.00 38.43 4.40
3643 9741 5.426509 TGGGCTATAGATGATAGGACAATGG 59.573 44.000 3.21 0.00 38.43 3.16
3644 9742 6.550938 TGGGCTATAGATGATAGGACAATG 57.449 41.667 3.21 0.00 38.43 2.82
3645 9743 7.138250 AGATGGGCTATAGATGATAGGACAAT 58.862 38.462 3.21 0.00 38.43 2.71
3646 9744 6.506661 AGATGGGCTATAGATGATAGGACAA 58.493 40.000 3.21 0.00 38.43 3.18
3647 9745 6.097439 AGATGGGCTATAGATGATAGGACA 57.903 41.667 3.21 0.00 38.43 4.02
3648 9746 8.719645 ATAAGATGGGCTATAGATGATAGGAC 57.280 38.462 3.21 0.00 38.43 3.85
3650 9748 8.748412 GCTATAAGATGGGCTATAGATGATAGG 58.252 40.741 3.21 0.00 38.43 2.57
3651 9749 8.748412 GGCTATAAGATGGGCTATAGATGATAG 58.252 40.741 3.21 0.46 40.65 2.08
3652 9750 8.234525 TGGCTATAAGATGGGCTATAGATGATA 58.765 37.037 3.21 0.00 37.22 2.15
3653 9751 7.078396 TGGCTATAAGATGGGCTATAGATGAT 58.922 38.462 3.21 0.00 37.22 2.45
3654 9752 6.443832 TGGCTATAAGATGGGCTATAGATGA 58.556 40.000 3.21 0.00 37.22 2.92
3655 9753 6.737720 TGGCTATAAGATGGGCTATAGATG 57.262 41.667 3.21 0.00 37.22 2.90
3656 9754 7.944414 ATTGGCTATAAGATGGGCTATAGAT 57.056 36.000 3.21 0.00 37.22 1.98
3657 9755 8.874156 CATATTGGCTATAAGATGGGCTATAGA 58.126 37.037 3.21 0.00 37.41 1.98
3658 9756 8.654997 ACATATTGGCTATAAGATGGGCTATAG 58.345 37.037 0.00 0.00 37.41 1.31
3659 9757 8.567198 ACATATTGGCTATAAGATGGGCTATA 57.433 34.615 0.00 3.91 38.02 1.31
3660 9758 7.457380 ACATATTGGCTATAAGATGGGCTAT 57.543 36.000 0.00 0.00 34.46 2.97
3661 9759 6.891306 ACATATTGGCTATAAGATGGGCTA 57.109 37.500 0.00 0.00 34.46 3.93
3662 9760 5.786121 ACATATTGGCTATAAGATGGGCT 57.214 39.130 0.00 0.00 34.46 5.19
3663 9761 6.414732 TGTACATATTGGCTATAAGATGGGC 58.585 40.000 0.00 0.00 34.46 5.36
3708 9806 9.762381 AGTGAAAGGTGGGTCATATAATAAAAA 57.238 29.630 0.00 0.00 0.00 1.94
3709 9807 9.403583 GAGTGAAAGGTGGGTCATATAATAAAA 57.596 33.333 0.00 0.00 0.00 1.52
3710 9808 8.778059 AGAGTGAAAGGTGGGTCATATAATAAA 58.222 33.333 0.00 0.00 0.00 1.40
3711 9809 8.331931 AGAGTGAAAGGTGGGTCATATAATAA 57.668 34.615 0.00 0.00 0.00 1.40
3712 9810 7.567250 TGAGAGTGAAAGGTGGGTCATATAATA 59.433 37.037 0.00 0.00 0.00 0.98
3713 9811 6.386927 TGAGAGTGAAAGGTGGGTCATATAAT 59.613 38.462 0.00 0.00 0.00 1.28
3714 9812 5.724370 TGAGAGTGAAAGGTGGGTCATATAA 59.276 40.000 0.00 0.00 0.00 0.98
3715 9813 5.128827 GTGAGAGTGAAAGGTGGGTCATATA 59.871 44.000 0.00 0.00 0.00 0.86
3716 9814 4.080863 GTGAGAGTGAAAGGTGGGTCATAT 60.081 45.833 0.00 0.00 0.00 1.78
3717 9815 3.260884 GTGAGAGTGAAAGGTGGGTCATA 59.739 47.826 0.00 0.00 0.00 2.15
3718 9816 2.039084 GTGAGAGTGAAAGGTGGGTCAT 59.961 50.000 0.00 0.00 0.00 3.06
3719 9817 1.416401 GTGAGAGTGAAAGGTGGGTCA 59.584 52.381 0.00 0.00 0.00 4.02
3720 9818 1.416401 TGTGAGAGTGAAAGGTGGGTC 59.584 52.381 0.00 0.00 0.00 4.46
3721 9819 1.507140 TGTGAGAGTGAAAGGTGGGT 58.493 50.000 0.00 0.00 0.00 4.51
3722 9820 2.638480 TTGTGAGAGTGAAAGGTGGG 57.362 50.000 0.00 0.00 0.00 4.61
3723 9821 3.313526 CACTTTGTGAGAGTGAAAGGTGG 59.686 47.826 0.00 0.00 45.72 4.61
3724 9822 3.242870 GCACTTTGTGAGAGTGAAAGGTG 60.243 47.826 8.33 0.00 45.72 4.00
3725 9823 2.945668 GCACTTTGTGAGAGTGAAAGGT 59.054 45.455 8.33 0.00 45.72 3.50
3726 9824 2.291741 GGCACTTTGTGAGAGTGAAAGG 59.708 50.000 8.33 0.00 45.72 3.11
3727 9825 3.209410 AGGCACTTTGTGAGAGTGAAAG 58.791 45.455 8.33 0.00 45.72 2.62
3728 9826 3.281727 AGGCACTTTGTGAGAGTGAAA 57.718 42.857 8.33 0.00 45.72 2.69
3729 9827 3.244215 CCTAGGCACTTTGTGAGAGTGAA 60.244 47.826 8.33 0.00 45.72 3.18
3730 9828 2.300152 CCTAGGCACTTTGTGAGAGTGA 59.700 50.000 8.33 0.00 45.72 3.41
3731 9829 2.300152 TCCTAGGCACTTTGTGAGAGTG 59.700 50.000 2.96 0.10 45.64 3.51
3732 9830 2.564947 CTCCTAGGCACTTTGTGAGAGT 59.435 50.000 2.96 0.00 41.75 3.24
3733 9831 2.676463 GCTCCTAGGCACTTTGTGAGAG 60.676 54.545 2.96 0.00 41.75 3.20
3734 9832 1.276421 GCTCCTAGGCACTTTGTGAGA 59.724 52.381 2.96 0.00 41.75 3.27
3735 9833 1.002430 TGCTCCTAGGCACTTTGTGAG 59.998 52.381 2.96 0.00 41.75 3.51
3736 9834 1.055849 TGCTCCTAGGCACTTTGTGA 58.944 50.000 2.96 0.00 41.75 3.58
3737 9835 3.631453 TGCTCCTAGGCACTTTGTG 57.369 52.632 2.96 0.00 41.75 3.33
3753 9851 3.191539 GCCAGCTCTAGCACGTGC 61.192 66.667 32.79 32.79 45.16 5.34
3754 9852 1.518133 GAGCCAGCTCTAGCACGTG 60.518 63.158 12.28 12.28 45.16 4.49
3755 9853 2.888863 GAGCCAGCTCTAGCACGT 59.111 61.111 12.42 0.00 45.16 4.49


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

AutoCloner maintained by Alex Coulton.