Multiple sequence alignment - TraesCS6D01G211800

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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 TraesCS6D01G211800 chr6D 100.000 3476 0 0 1 3476 299054696 299058171 0.000000e+00 6420
1 TraesCS6D01G211800 chr6A 96.862 2549 70 5 748 3291 420410899 420408356 0.000000e+00 4255
2 TraesCS6D01G211800 chr6A 93.778 450 24 3 177 624 420411346 420410899 0.000000e+00 673
3 TraesCS6D01G211800 chr6A 93.750 128 5 2 59 185 420411499 420411374 4.580000e-44 189
4 TraesCS6D01G211800 chr6B 96.913 2073 53 4 897 2966 462134096 462136160 0.000000e+00 3463
5 TraesCS6D01G211800 chr6B 94.530 457 19 4 2963 3414 462138089 462138544 0.000000e+00 701
6 TraesCS6D01G211800 chr6B 84.380 685 48 30 4 659 462133114 462133768 4.930000e-173 617
7 TraesCS6D01G211800 chr6B 82.993 294 25 9 646 916 462133790 462134081 3.470000e-60 243


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 TraesCS6D01G211800 chr6D 299054696 299058171 3475 False 6420.000000 6420 100.000000 1 3476 1 chr6D.!!$F1 3475
1 TraesCS6D01G211800 chr6A 420408356 420411499 3143 True 1705.666667 4255 94.796667 59 3291 3 chr6A.!!$R1 3232
2 TraesCS6D01G211800 chr6B 462133114 462138544 5430 False 1256.000000 3463 89.704000 4 3414 4 chr6B.!!$F1 3410

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
439 486 0.036388 TTCCTGCATCCCGTTCTCAC 60.036 55.0 0.00 0.0 0.00 3.51 F
731 839 0.038310 GGTCCAGTTGGGGAGGAAAG 59.962 60.0 0.00 0.0 37.71 2.62 F
1626 1786 0.527817 CGTGGAGCTCGATGGTTACC 60.528 60.0 9.93 0.0 0.00 2.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1752 1912 0.464373 CCCACATGCCGTGCTCTATT 60.464 55.000 0.00 0.0 44.91 1.73 R
2034 2194 0.737715 GACCTGAGTGGCTACAAGCG 60.738 60.000 2.02 0.0 43.62 4.68 R
3424 5526 1.070445 GAGCCTCGTCCATCCCATG 59.930 63.158 0.00 0.0 0.00 3.66 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
23 24 6.903883 GAGTGTGAGTTTTTGTAGAGTGAA 57.096 37.500 0.00 0.00 0.00 3.18
24 25 7.484035 GAGTGTGAGTTTTTGTAGAGTGAAT 57.516 36.000 0.00 0.00 0.00 2.57
31 34 7.773224 TGAGTTTTTGTAGAGTGAATCTGGAAA 59.227 33.333 0.00 0.00 39.20 3.13
33 36 8.966868 AGTTTTTGTAGAGTGAATCTGGAAAAA 58.033 29.630 8.56 8.56 39.20 1.94
39 42 8.593679 TGTAGAGTGAATCTGGAAAAACATCTA 58.406 33.333 0.00 0.00 39.20 1.98
51 54 6.070767 TGGAAAAACATCTAGGACAGGAGTAG 60.071 42.308 0.00 0.00 0.00 2.57
52 55 6.070710 GGAAAAACATCTAGGACAGGAGTAGT 60.071 42.308 0.00 0.00 0.00 2.73
53 56 7.123847 GGAAAAACATCTAGGACAGGAGTAGTA 59.876 40.741 0.00 0.00 0.00 1.82
54 57 7.648039 AAAACATCTAGGACAGGAGTAGTAG 57.352 40.000 0.00 0.00 0.00 2.57
55 58 6.578313 AACATCTAGGACAGGAGTAGTAGA 57.422 41.667 0.00 0.00 30.73 2.59
56 59 6.773583 ACATCTAGGACAGGAGTAGTAGAT 57.226 41.667 0.00 0.00 35.07 1.98
57 60 7.156694 ACATCTAGGACAGGAGTAGTAGATT 57.843 40.000 0.00 0.00 33.62 2.40
123 126 2.712057 AGCGTTTCCTCTTGCATTTG 57.288 45.000 0.00 0.00 0.00 2.32
128 131 4.320202 GCGTTTCCTCTTGCATTTGTTCTA 60.320 41.667 0.00 0.00 0.00 2.10
171 209 3.998913 TCTCATCCACCATAAGCACAA 57.001 42.857 0.00 0.00 0.00 3.33
173 211 4.858850 TCTCATCCACCATAAGCACAAAT 58.141 39.130 0.00 0.00 0.00 2.32
175 213 5.125900 TCTCATCCACCATAAGCACAAATTG 59.874 40.000 0.00 0.00 0.00 2.32
192 230 5.477984 ACAAATTGTGATAACTCAGCCACAT 59.522 36.000 0.00 0.00 39.01 3.21
195 233 3.599343 TGTGATAACTCAGCCACATGTC 58.401 45.455 0.00 0.00 34.96 3.06
202 240 0.752658 TCAGCCACATGTCCTATCCG 59.247 55.000 0.00 0.00 0.00 4.18
432 479 0.467384 ACTCATCTTCCTGCATCCCG 59.533 55.000 0.00 0.00 0.00 5.14
439 486 0.036388 TTCCTGCATCCCGTTCTCAC 60.036 55.000 0.00 0.00 0.00 3.51
449 496 2.637872 TCCCGTTCTCACCAGAAGAAAT 59.362 45.455 0.00 0.00 39.45 2.17
450 497 3.072476 TCCCGTTCTCACCAGAAGAAATT 59.928 43.478 0.00 0.00 39.45 1.82
561 616 2.845363 TGGGGGAAAGAGTCGTTTAC 57.155 50.000 0.00 0.00 0.00 2.01
562 617 2.332117 TGGGGGAAAGAGTCGTTTACT 58.668 47.619 0.00 0.00 42.80 2.24
563 618 2.707257 TGGGGGAAAGAGTCGTTTACTT 59.293 45.455 0.00 0.00 39.07 2.24
564 619 3.072211 GGGGGAAAGAGTCGTTTACTTG 58.928 50.000 0.00 0.00 39.07 3.16
624 681 6.481954 TTCTTCCTCGTTTTCTGCTTATTC 57.518 37.500 0.00 0.00 0.00 1.75
669 772 7.151308 TGATCGCATATTTTTGTGAAAACCTT 58.849 30.769 0.00 0.00 39.39 3.50
678 781 2.297701 TGTGAAAACCTTGTCAGGAGC 58.702 47.619 0.00 0.00 44.19 4.70
680 783 1.134220 TGAAAACCTTGTCAGGAGCGT 60.134 47.619 0.00 0.00 44.19 5.07
683 786 0.608640 AACCTTGTCAGGAGCGTAGG 59.391 55.000 0.00 0.00 44.19 3.18
692 795 1.295423 GGAGCGTAGGTTCCTGCAA 59.705 57.895 10.72 0.00 40.18 4.08
695 798 1.398390 GAGCGTAGGTTCCTGCAATTG 59.602 52.381 0.00 0.00 39.88 2.32
696 799 0.451783 GCGTAGGTTCCTGCAATTGG 59.548 55.000 7.72 0.00 0.00 3.16
700 806 3.181497 CGTAGGTTCCTGCAATTGGATTG 60.181 47.826 7.72 0.00 43.06 2.67
721 829 4.645535 TGAGAAGAGAATTGGTCCAGTTG 58.354 43.478 4.02 0.00 0.00 3.16
723 831 2.887151 AGAGAATTGGTCCAGTTGGG 57.113 50.000 4.02 0.00 35.41 4.12
731 839 0.038310 GGTCCAGTTGGGGAGGAAAG 59.962 60.000 0.00 0.00 37.71 2.62
740 848 4.111053 GGAGGAAAGTCGGGCCCC 62.111 72.222 18.66 2.17 0.00 5.80
987 1147 1.946475 GCCGGTCCTACCTGTCAGTC 61.946 65.000 1.90 0.00 35.66 3.51
989 1149 0.611062 CGGTCCTACCTGTCAGTCCA 60.611 60.000 0.00 0.00 35.66 4.02
1104 1264 2.914289 GCCCTCATCACCTCTGGG 59.086 66.667 0.00 0.00 40.74 4.45
1124 1284 1.159664 ACCTCTCCTCCTGCACCTT 59.840 57.895 0.00 0.00 0.00 3.50
1362 1522 3.404773 GCCTACTTCAGGGCCACT 58.595 61.111 6.18 0.00 45.66 4.00
1521 1681 1.905637 GGAACGTGGTTTCCTGGAAT 58.094 50.000 10.45 0.00 41.80 3.01
1522 1682 3.062122 GGAACGTGGTTTCCTGGAATA 57.938 47.619 10.45 0.00 41.80 1.75
1583 1743 0.874607 GCGCGGAAGGTGTTCGATAT 60.875 55.000 8.83 0.00 32.92 1.63
1602 1762 2.283143 TAATGCCCAGCCGGAATGCT 62.283 55.000 5.05 0.00 44.00 3.79
1626 1786 0.527817 CGTGGAGCTCGATGGTTACC 60.528 60.000 9.93 0.00 0.00 2.85
1681 1841 3.855255 TGAGGGTGTTCAGTGAAATGA 57.145 42.857 7.25 0.00 0.00 2.57
1686 1846 3.334691 GGTGTTCAGTGAAATGATCGGA 58.665 45.455 7.25 0.00 0.00 4.55
1689 1849 4.213270 GTGTTCAGTGAAATGATCGGAACA 59.787 41.667 7.25 0.00 40.64 3.18
2004 2164 1.194781 AGATGGCTGGTGTTCGACCT 61.195 55.000 0.00 0.00 46.32 3.85
2034 2194 2.361104 TTCATCGGGTTGCTGGGC 60.361 61.111 0.00 0.00 0.00 5.36
2379 2539 0.106569 GATGGGATGACATGGCCACA 60.107 55.000 8.16 0.93 0.00 4.17
2653 2813 2.296752 TGCACACTGAAATCAACATGGG 59.703 45.455 0.00 0.00 0.00 4.00
2685 2845 4.562143 GCAAAATCCTGTCAAGAAGCCAAT 60.562 41.667 0.00 0.00 0.00 3.16
2745 2908 6.541641 AGAAGCTCAGAAAATATGCACCTAAG 59.458 38.462 0.00 0.00 0.00 2.18
2746 2909 5.128919 AGCTCAGAAAATATGCACCTAAGG 58.871 41.667 0.00 0.00 0.00 2.69
2747 2910 5.104360 AGCTCAGAAAATATGCACCTAAGGA 60.104 40.000 0.00 0.00 0.00 3.36
2770 2933 6.370442 GGACTACGGCATGCATATTTGTAATA 59.630 38.462 21.36 0.00 0.00 0.98
2771 2934 7.364522 ACTACGGCATGCATATTTGTAATAG 57.635 36.000 21.36 7.49 0.00 1.73
2776 2939 9.008965 ACGGCATGCATATTTGTAATAGAATTA 57.991 29.630 21.36 0.00 0.00 1.40
2909 3074 2.092211 GCAAACCACTCGAGTATTGTCG 59.908 50.000 25.83 16.63 41.51 4.35
3000 5097 6.767902 ACAGAATTGAAGTTCAGTTCAGCTTA 59.232 34.615 31.03 7.13 43.07 3.09
3101 5198 6.600427 TGGGTAAATTTTCCGAAGTATTCCTC 59.400 38.462 7.66 0.00 43.81 3.71
3108 5205 4.467198 TCCGAAGTATTCCTCAGGAAAC 57.533 45.455 11.13 10.14 45.41 2.78
3187 5288 1.159285 ACGTGTCCATGACATTGCAG 58.841 50.000 0.00 0.00 44.63 4.41
3244 5345 1.276138 TGCGAATCAAAGAGAGGCTGA 59.724 47.619 0.00 0.00 0.00 4.26
3277 5378 5.325239 AGCTATGCTTACTTTGGTTTTCCT 58.675 37.500 0.00 0.00 36.76 3.36
3323 5424 4.535526 AACTGTTTGTTTGCCTCTGTTT 57.464 36.364 0.00 0.00 34.84 2.83
3340 5441 4.101119 TCTGTTTCGGGAGGGAGATATTTC 59.899 45.833 0.00 0.00 0.00 2.17
3414 5516 4.158394 CAGACAAGGTTCCAACATAATGGG 59.842 45.833 0.00 0.00 41.05 4.00
3415 5517 4.086457 GACAAGGTTCCAACATAATGGGT 58.914 43.478 0.00 0.00 41.05 4.51
3416 5518 3.831911 ACAAGGTTCCAACATAATGGGTG 59.168 43.478 0.00 0.00 41.05 4.61
3417 5519 2.456577 AGGTTCCAACATAATGGGTGC 58.543 47.619 0.00 0.00 41.05 5.01
3418 5520 2.175202 GGTTCCAACATAATGGGTGCA 58.825 47.619 0.00 0.00 41.05 4.57
3419 5521 2.765699 GGTTCCAACATAATGGGTGCAT 59.234 45.455 0.00 0.00 41.05 3.96
3420 5522 3.181476 GGTTCCAACATAATGGGTGCATC 60.181 47.826 0.00 0.00 41.05 3.91
3421 5523 3.378861 TCCAACATAATGGGTGCATCA 57.621 42.857 0.00 0.00 41.05 3.07
3422 5524 3.913509 TCCAACATAATGGGTGCATCAT 58.086 40.909 0.00 0.00 41.05 2.45
3423 5525 3.890756 TCCAACATAATGGGTGCATCATC 59.109 43.478 0.00 0.00 41.05 2.92
3424 5526 3.006110 CCAACATAATGGGTGCATCATCC 59.994 47.826 0.00 0.00 36.79 3.51
3429 5531 1.230783 TGGGTGCATCATCCATGGG 59.769 57.895 13.02 0.00 40.05 4.00
3430 5532 1.287773 TGGGTGCATCATCCATGGGA 61.288 55.000 13.02 1.95 40.05 4.37
3431 5533 0.113776 GGGTGCATCATCCATGGGAT 59.886 55.000 13.02 4.66 44.21 3.85
3441 5543 3.234349 CATGGGATGGACGAGGCT 58.766 61.111 0.00 0.00 0.00 4.58
3442 5544 1.070445 CATGGGATGGACGAGGCTC 59.930 63.158 3.87 3.87 0.00 4.70
3443 5545 1.074926 ATGGGATGGACGAGGCTCT 60.075 57.895 13.50 0.00 0.00 4.09
3444 5546 1.406065 ATGGGATGGACGAGGCTCTG 61.406 60.000 13.50 8.77 0.00 3.35
3445 5547 2.060980 GGGATGGACGAGGCTCTGT 61.061 63.158 13.50 12.03 0.00 3.41
3446 5548 1.439644 GGATGGACGAGGCTCTGTC 59.560 63.158 22.64 22.64 0.00 3.51
3456 5558 1.127343 AGGCTCTGTCCTCTAATGGC 58.873 55.000 0.00 0.00 0.00 4.40
3457 5559 1.127343 GGCTCTGTCCTCTAATGGCT 58.873 55.000 0.00 0.00 0.00 4.75
3458 5560 1.202627 GGCTCTGTCCTCTAATGGCTG 60.203 57.143 0.00 0.00 0.00 4.85
3459 5561 1.202627 GCTCTGTCCTCTAATGGCTGG 60.203 57.143 0.00 0.00 0.00 4.85
3460 5562 2.392662 CTCTGTCCTCTAATGGCTGGA 58.607 52.381 0.00 0.00 0.00 3.86
3461 5563 2.364970 CTCTGTCCTCTAATGGCTGGAG 59.635 54.545 0.00 0.00 0.00 3.86
3462 5564 2.114616 CTGTCCTCTAATGGCTGGAGT 58.885 52.381 0.00 0.00 0.00 3.85
3463 5565 2.503356 CTGTCCTCTAATGGCTGGAGTT 59.497 50.000 0.00 0.00 0.00 3.01
3464 5566 2.912956 TGTCCTCTAATGGCTGGAGTTT 59.087 45.455 0.00 0.00 0.00 2.66
3465 5567 3.330701 TGTCCTCTAATGGCTGGAGTTTT 59.669 43.478 0.00 0.00 0.00 2.43
3466 5568 4.534500 TGTCCTCTAATGGCTGGAGTTTTA 59.466 41.667 0.00 0.00 0.00 1.52
3467 5569 5.191722 TGTCCTCTAATGGCTGGAGTTTTAT 59.808 40.000 0.00 0.00 0.00 1.40
3468 5570 5.529060 GTCCTCTAATGGCTGGAGTTTTATG 59.471 44.000 0.00 0.00 0.00 1.90
3469 5571 5.191722 TCCTCTAATGGCTGGAGTTTTATGT 59.808 40.000 0.00 0.00 0.00 2.29
3470 5572 5.297776 CCTCTAATGGCTGGAGTTTTATGTG 59.702 44.000 0.00 0.00 0.00 3.21
3471 5573 5.192927 TCTAATGGCTGGAGTTTTATGTGG 58.807 41.667 0.00 0.00 0.00 4.17
3472 5574 3.737559 ATGGCTGGAGTTTTATGTGGA 57.262 42.857 0.00 0.00 0.00 4.02
3473 5575 3.737559 TGGCTGGAGTTTTATGTGGAT 57.262 42.857 0.00 0.00 0.00 3.41
3474 5576 4.046286 TGGCTGGAGTTTTATGTGGATT 57.954 40.909 0.00 0.00 0.00 3.01
3475 5577 5.186256 TGGCTGGAGTTTTATGTGGATTA 57.814 39.130 0.00 0.00 0.00 1.75
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 6.903883 TTCACTCTACAAAAACTCACACTC 57.096 37.500 0.00 0.00 0.00 3.51
1 2 7.225538 CAGATTCACTCTACAAAAACTCACACT 59.774 37.037 0.00 0.00 31.13 3.55
2 3 7.348201 CAGATTCACTCTACAAAAACTCACAC 58.652 38.462 0.00 0.00 31.13 3.82
3 4 6.483307 CCAGATTCACTCTACAAAAACTCACA 59.517 38.462 0.00 0.00 31.13 3.58
4 5 6.706270 TCCAGATTCACTCTACAAAAACTCAC 59.294 38.462 0.00 0.00 31.13 3.51
5 6 6.826668 TCCAGATTCACTCTACAAAAACTCA 58.173 36.000 0.00 0.00 31.13 3.41
6 7 7.730364 TTCCAGATTCACTCTACAAAAACTC 57.270 36.000 0.00 0.00 31.13 3.01
7 8 8.519799 TTTTCCAGATTCACTCTACAAAAACT 57.480 30.769 0.00 0.00 31.13 2.66
8 9 9.020813 GTTTTTCCAGATTCACTCTACAAAAAC 57.979 33.333 12.85 12.85 41.53 2.43
9 10 8.744652 TGTTTTTCCAGATTCACTCTACAAAAA 58.255 29.630 0.00 0.00 34.43 1.94
21 22 6.317391 CCTGTCCTAGATGTTTTTCCAGATTC 59.683 42.308 0.00 0.00 0.00 2.52
23 24 5.488919 TCCTGTCCTAGATGTTTTTCCAGAT 59.511 40.000 0.00 0.00 0.00 2.90
24 25 4.844085 TCCTGTCCTAGATGTTTTTCCAGA 59.156 41.667 0.00 0.00 0.00 3.86
31 34 6.971340 TCTACTACTCCTGTCCTAGATGTTT 58.029 40.000 0.00 0.00 0.00 2.83
33 36 6.773583 ATCTACTACTCCTGTCCTAGATGT 57.226 41.667 0.00 0.00 30.26 3.06
39 42 6.578313 TCTACAATCTACTACTCCTGTCCT 57.422 41.667 0.00 0.00 0.00 3.85
51 54 7.753309 TCCTTGAGCTCTATCTACAATCTAC 57.247 40.000 16.19 0.00 0.00 2.59
52 55 8.768501 TTTCCTTGAGCTCTATCTACAATCTA 57.231 34.615 16.19 0.00 0.00 1.98
53 56 7.667575 TTTCCTTGAGCTCTATCTACAATCT 57.332 36.000 16.19 0.00 0.00 2.40
54 57 7.042119 GCTTTTCCTTGAGCTCTATCTACAATC 60.042 40.741 16.19 0.00 36.01 2.67
55 58 6.765512 GCTTTTCCTTGAGCTCTATCTACAAT 59.234 38.462 16.19 0.00 36.01 2.71
56 59 6.109359 GCTTTTCCTTGAGCTCTATCTACAA 58.891 40.000 16.19 0.00 36.01 2.41
57 60 5.395768 GGCTTTTCCTTGAGCTCTATCTACA 60.396 44.000 16.19 0.00 38.89 2.74
171 209 5.012239 ACATGTGGCTGAGTTATCACAATT 58.988 37.500 0.00 0.00 42.35 2.32
173 211 4.002982 GACATGTGGCTGAGTTATCACAA 58.997 43.478 1.15 0.00 42.35 3.33
175 213 2.939103 GGACATGTGGCTGAGTTATCAC 59.061 50.000 1.15 0.00 0.00 3.06
185 223 0.398522 TCCGGATAGGACATGTGGCT 60.399 55.000 1.15 0.00 45.98 4.75
432 479 8.188139 TGTACAAAAATTTCTTCTGGTGAGAAC 58.812 33.333 0.00 0.00 34.36 3.01
522 573 3.494232 CAAGAACAAAACCGTTTCGTGT 58.506 40.909 0.00 0.00 0.00 4.49
561 616 5.032863 CCATCGCAGAAAAGAATAAGCAAG 58.967 41.667 0.00 0.00 43.58 4.01
562 617 4.142403 CCCATCGCAGAAAAGAATAAGCAA 60.142 41.667 0.00 0.00 43.58 3.91
563 618 3.378112 CCCATCGCAGAAAAGAATAAGCA 59.622 43.478 0.00 0.00 43.58 3.91
564 619 3.627577 TCCCATCGCAGAAAAGAATAAGC 59.372 43.478 0.00 0.00 43.58 3.09
624 681 2.401583 TCCGATCCAAATCACCACAG 57.598 50.000 0.00 0.00 31.76 3.66
654 721 5.719173 CTCCTGACAAGGTTTTCACAAAAA 58.281 37.500 0.00 0.00 44.82 1.94
669 772 0.251653 AGGAACCTACGCTCCTGACA 60.252 55.000 0.00 0.00 40.70 3.58
678 781 2.107950 TCCAATTGCAGGAACCTACG 57.892 50.000 0.00 0.00 30.71 3.51
680 783 4.018506 TCTCAATCCAATTGCAGGAACCTA 60.019 41.667 0.00 0.00 38.93 3.08
683 786 4.460382 TCTTCTCAATCCAATTGCAGGAAC 59.540 41.667 0.00 0.00 38.93 3.62
692 795 5.890419 GGACCAATTCTCTTCTCAATCCAAT 59.110 40.000 0.00 0.00 0.00 3.16
695 798 4.848357 TGGACCAATTCTCTTCTCAATCC 58.152 43.478 0.00 0.00 0.00 3.01
696 799 5.495640 ACTGGACCAATTCTCTTCTCAATC 58.504 41.667 0.00 0.00 0.00 2.67
700 806 4.006319 CCAACTGGACCAATTCTCTTCTC 58.994 47.826 0.00 0.00 37.39 2.87
721 829 4.111053 GGCCCGACTTTCCTCCCC 62.111 72.222 0.00 0.00 0.00 4.81
723 831 4.111053 GGGGCCCGACTTTCCTCC 62.111 72.222 17.79 0.00 0.00 4.30
740 848 1.684450 ACCGGGTTTTGTAAGGCTTTG 59.316 47.619 4.45 0.00 0.00 2.77
754 862 1.335132 AATCTGCATCGGTACCGGGT 61.335 55.000 32.80 19.60 40.25 5.28
987 1147 2.124403 GCCATGGGAGAGCACTGG 60.124 66.667 15.13 0.00 0.00 4.00
989 1149 2.293318 TTCGCCATGGGAGAGCACT 61.293 57.895 15.13 0.00 32.27 4.40
1104 1264 2.267324 GTGCAGGAGGAGAGGTGC 59.733 66.667 0.00 0.00 36.42 5.01
1124 1284 1.318158 GCGGAGGAGGGAGTTAACGA 61.318 60.000 0.00 0.00 0.00 3.85
1428 1588 3.344137 ATGCCCGGTGACCATGGTC 62.344 63.158 33.97 33.97 44.77 4.02
1583 1743 1.827789 GCATTCCGGCTGGGCATTA 60.828 57.895 12.87 0.00 35.24 1.90
1602 1762 2.755876 ATCGAGCTCCACGAGGCA 60.756 61.111 8.47 0.00 42.81 4.75
1626 1786 3.958147 ATTGGACTGCACGAGCCCG 62.958 63.158 1.39 0.00 41.13 6.13
1681 1841 1.374252 GCACGACACCTGTTCCGAT 60.374 57.895 0.00 0.00 0.00 4.18
1752 1912 0.464373 CCCACATGCCGTGCTCTATT 60.464 55.000 0.00 0.00 44.91 1.73
1821 1981 2.975410 ACATGTCAACAATCGCTGTG 57.025 45.000 0.00 0.00 38.67 3.66
2004 2164 6.653320 GCAACCCGATGAAGGTTATATCATTA 59.347 38.462 0.00 0.00 45.96 1.90
2034 2194 0.737715 GACCTGAGTGGCTACAAGCG 60.738 60.000 2.02 0.00 43.62 4.68
2379 2539 1.078848 CTTAAGGAGCCTGCGCACT 60.079 57.895 5.66 2.00 37.52 4.40
2625 2785 5.221204 TGTTGATTTCAGTGTGCAGCATAAA 60.221 36.000 0.00 0.00 0.00 1.40
2745 2908 2.878406 ACAAATATGCATGCCGTAGTCC 59.122 45.455 16.68 0.00 0.00 3.85
2746 2909 5.666969 TTACAAATATGCATGCCGTAGTC 57.333 39.130 16.68 0.00 0.00 2.59
2747 2910 7.158697 TCTATTACAAATATGCATGCCGTAGT 58.841 34.615 16.68 8.86 0.00 2.73
2770 2933 3.244700 CCGCCTCTTCCCATCATAATTCT 60.245 47.826 0.00 0.00 0.00 2.40
2771 2934 3.077359 CCGCCTCTTCCCATCATAATTC 58.923 50.000 0.00 0.00 0.00 2.17
2776 2939 1.384502 TCCCGCCTCTTCCCATCAT 60.385 57.895 0.00 0.00 0.00 2.45
2867 3032 6.796705 TGCATACATCTGATTCAAGCATAG 57.203 37.500 0.00 0.00 0.00 2.23
3000 5097 2.158755 CCTAATGAATCAACGAGGCCCT 60.159 50.000 0.00 0.00 0.00 5.19
3108 5205 6.490040 TCCAAGAGGTTTGAGTAAATGGAAAG 59.510 38.462 0.00 0.00 30.78 2.62
3117 5214 6.837312 TGAATCTTTCCAAGAGGTTTGAGTA 58.163 36.000 0.00 0.00 41.61 2.59
3153 5250 1.198178 ACACGTTTGTTTCGTTGCACT 59.802 42.857 0.00 0.00 39.55 4.40
3187 5288 6.151144 ACACATAAATAGGGAAGTTGCAAGAC 59.849 38.462 0.00 0.00 0.00 3.01
3244 5345 5.867903 AGTAAGCATAGCTTCTCTCATGT 57.132 39.130 7.62 0.00 46.77 3.21
3424 5526 1.070445 GAGCCTCGTCCATCCCATG 59.930 63.158 0.00 0.00 0.00 3.66
3425 5527 1.074926 AGAGCCTCGTCCATCCCAT 60.075 57.895 0.00 0.00 0.00 4.00
3426 5528 2.060383 CAGAGCCTCGTCCATCCCA 61.060 63.158 0.00 0.00 0.00 4.37
3427 5529 2.022240 GACAGAGCCTCGTCCATCCC 62.022 65.000 5.69 0.00 0.00 3.85
3428 5530 1.439644 GACAGAGCCTCGTCCATCC 59.560 63.158 5.69 0.00 0.00 3.51
3437 5539 1.127343 GCCATTAGAGGACAGAGCCT 58.873 55.000 0.00 0.00 42.17 4.58
3438 5540 1.127343 AGCCATTAGAGGACAGAGCC 58.873 55.000 0.00 0.00 0.00 4.70
3439 5541 1.202627 CCAGCCATTAGAGGACAGAGC 60.203 57.143 0.00 0.00 0.00 4.09
3440 5542 2.364970 CTCCAGCCATTAGAGGACAGAG 59.635 54.545 0.00 0.00 0.00 3.35
3441 5543 2.292521 ACTCCAGCCATTAGAGGACAGA 60.293 50.000 0.00 0.00 31.70 3.41
3442 5544 2.114616 ACTCCAGCCATTAGAGGACAG 58.885 52.381 0.00 0.00 31.70 3.51
3443 5545 2.254152 ACTCCAGCCATTAGAGGACA 57.746 50.000 0.00 0.00 31.70 4.02
3444 5546 3.636153 AAACTCCAGCCATTAGAGGAC 57.364 47.619 0.00 0.00 31.70 3.85
3445 5547 5.191722 ACATAAAACTCCAGCCATTAGAGGA 59.808 40.000 0.00 0.00 31.70 3.71
3446 5548 5.297776 CACATAAAACTCCAGCCATTAGAGG 59.702 44.000 0.00 0.00 31.70 3.69
3447 5549 5.297776 CCACATAAAACTCCAGCCATTAGAG 59.702 44.000 0.00 0.00 0.00 2.43
3448 5550 5.045213 TCCACATAAAACTCCAGCCATTAGA 60.045 40.000 0.00 0.00 0.00 2.10
3449 5551 5.192927 TCCACATAAAACTCCAGCCATTAG 58.807 41.667 0.00 0.00 0.00 1.73
3450 5552 5.186256 TCCACATAAAACTCCAGCCATTA 57.814 39.130 0.00 0.00 0.00 1.90
3451 5553 4.046286 TCCACATAAAACTCCAGCCATT 57.954 40.909 0.00 0.00 0.00 3.16
3452 5554 3.737559 TCCACATAAAACTCCAGCCAT 57.262 42.857 0.00 0.00 0.00 4.40
3453 5555 3.737559 ATCCACATAAAACTCCAGCCA 57.262 42.857 0.00 0.00 0.00 4.75


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

AutoCloner maintained by Alex Coulton.