Multiple sequence alignment - TraesCS3D01G231800

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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 TraesCS3D01G231800 chr3D 100.000 6160 0 0 1 6160 317559782 317553623 0.000000e+00 11376
1 TraesCS3D01G231800 chr3D 88.525 183 19 2 1068 1249 317558553 317558372 2.890000e-53 220
2 TraesCS3D01G231800 chr3D 88.525 183 19 2 1230 1411 317558715 317558534 2.890000e-53 220
3 TraesCS3D01G231800 chr3D 92.381 105 8 0 313 417 317559365 317559261 3.850000e-32 150
4 TraesCS3D01G231800 chr3D 92.381 105 8 0 418 522 317559470 317559366 3.850000e-32 150
5 TraesCS3D01G231800 chr3D 86.260 131 10 6 1 129 21923177 21923053 1.080000e-27 135
6 TraesCS3D01G231800 chr3D 86.508 126 13 4 1 126 45623960 45624081 1.080000e-27 135
7 TraesCS3D01G231800 chr3B 95.665 5975 169 32 126 6052 401404494 401410426 0.000000e+00 9516
8 TraesCS3D01G231800 chr3B 88.043 184 20 2 1230 1412 401405409 401405591 3.740000e-52 217
9 TraesCS3D01G231800 chr3B 98.095 105 1 1 6056 6160 401410554 401410657 1.360000e-41 182
10 TraesCS3D01G231800 chr3B 90.566 106 9 1 418 522 401404681 401404786 8.330000e-29 139
11 TraesCS3D01G231800 chr3A 96.401 5474 128 23 126 5566 447269218 447274655 0.000000e+00 8953
12 TraesCS3D01G231800 chr3A 97.359 2802 47 10 2772 5566 408942751 408945532 0.000000e+00 4739
13 TraesCS3D01G231800 chr3A 94.440 2680 89 15 126 2783 408940079 408942720 0.000000e+00 4069
14 TraesCS3D01G231800 chr3A 96.726 336 8 1 5566 5898 408945815 408946150 1.940000e-154 556
15 TraesCS3D01G231800 chr3A 95.299 234 10 1 5895 6128 408946472 408946704 2.710000e-98 370
16 TraesCS3D01G231800 chr3A 87.745 204 22 3 1048 1249 408941149 408941351 1.030000e-57 235
17 TraesCS3D01G231800 chr3A 87.745 204 22 3 1048 1249 447270304 447270506 1.030000e-57 235
18 TraesCS3D01G231800 chr3A 88.587 184 19 2 1230 1412 447270154 447270336 8.040000e-54 222
19 TraesCS3D01G231800 chr3A 85.204 196 19 6 1218 1412 408940995 408941181 6.300000e-45 193
20 TraesCS3D01G231800 chr3A 93.000 100 7 0 418 517 408940266 408940365 4.980000e-31 147
21 TraesCS3D01G231800 chr3A 88.235 119 10 4 8 126 659427560 659427674 8.330000e-29 139
22 TraesCS3D01G231800 chr6A 84.063 1324 145 27 4444 5736 1463712 1462424 0.000000e+00 1216
23 TraesCS3D01G231800 chr6A 81.563 1497 187 37 2857 4344 1465130 1463714 0.000000e+00 1153
24 TraesCS3D01G231800 chr6A 87.395 119 12 3 8 126 551365637 551365522 3.870000e-27 134
25 TraesCS3D01G231800 chr6A 83.099 142 23 1 4279 4420 452630057 452630197 1.800000e-25 128
26 TraesCS3D01G231800 chr6D 87.778 450 55 0 3670 4119 465354323 465353874 1.520000e-145 527
27 TraesCS3D01G231800 chr6D 86.667 450 58 1 3670 4119 465352800 465352353 1.190000e-136 497
28 TraesCS3D01G231800 chr4B 84.698 464 56 7 4063 4525 669916317 669915868 3.390000e-122 449
29 TraesCS3D01G231800 chr4B 82.960 446 62 7 4081 4525 669914427 669913995 2.080000e-104 390
30 TraesCS3D01G231800 chr4B 83.803 426 52 9 3879 4303 669912450 669912041 7.490000e-104 388
31 TraesCS3D01G231800 chr4B 83.693 417 52 6 3885 4300 669910747 669911148 4.510000e-101 379
32 TraesCS3D01G231800 chr4B 82.274 299 39 7 3971 4268 669912041 669911756 4.770000e-61 246
33 TraesCS3D01G231800 chr4A 88.034 117 10 4 8 124 75266890 75266778 1.080000e-27 135
34 TraesCS3D01G231800 chr7B 87.395 119 11 4 8 126 856840 856954 3.870000e-27 134
35 TraesCS3D01G231800 chr5D 84.507 142 14 8 1 139 394244721 394244857 3.870000e-27 134
36 TraesCS3D01G231800 chr2B 85.827 127 17 1 4720 4845 114043405 114043531 3.870000e-27 134
37 TraesCS3D01G231800 chr2A 85.714 126 13 5 8 133 632610477 632610597 1.800000e-25 128
38 TraesCS3D01G231800 chr2A 84.615 130 16 4 1 130 87811044 87811169 6.480000e-25 126


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 TraesCS3D01G231800 chr3D 317553623 317559782 6159 True 2423.200000 11376 92.362400 1 6160 5 chr3D.!!$R2 6159
1 TraesCS3D01G231800 chr3B 401404494 401410426 5932 False 9516.000000 9516 95.665000 126 6052 1 chr3B.!!$F1 5926
2 TraesCS3D01G231800 chr3A 447269218 447274655 5437 False 8953.000000 8953 96.401000 126 5566 1 chr3A.!!$F1 5440
3 TraesCS3D01G231800 chr3A 408940079 408946704 6625 False 1472.714286 4739 92.824714 126 6128 7 chr3A.!!$F3 6002
4 TraesCS3D01G231800 chr6A 1462424 1465130 2706 True 1184.500000 1216 82.813000 2857 5736 2 chr6A.!!$R2 2879
5 TraesCS3D01G231800 chr6D 465352353 465354323 1970 True 512.000000 527 87.222500 3670 4119 2 chr6D.!!$R1 449
6 TraesCS3D01G231800 chr4B 669911756 669916317 4561 True 368.250000 449 83.433750 3879 4525 4 chr4B.!!$R1 646

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
639 649 0.179094 CATTGGCATCGGCATTGCTT 60.179 50.000 8.82 0.00 43.71 3.91 F
641 651 0.390078 TTGGCATCGGCATTGCTTTG 60.390 50.000 8.82 5.28 43.71 2.77 F
1510 1541 0.891373 CTTGTCAAGCGAGGAGGAGA 59.109 55.000 0.00 0.00 0.00 3.71 F
1587 1618 1.162698 ACGGAATTGAGACGAGTCGA 58.837 50.000 21.50 0.00 34.09 4.20 F
2253 2299 1.363744 CCCACAGCGATGAAGACTTC 58.636 55.000 8.12 8.34 0.00 3.01 F
2581 2627 1.403514 CCACTCTTCAGAACGCCTCTC 60.404 57.143 0.00 0.00 29.07 3.20 F
4184 4383 0.846693 AAGGAGTTGCTTCCACCAGT 59.153 50.000 5.49 0.00 39.84 4.00 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2158 2204 0.320374 TCATCGGCGTTTTGTCCTCT 59.680 50.000 6.85 0.00 0.00 3.69 R
2362 2408 1.780309 TCCTTCTTTCTTTGCCCTCCA 59.220 47.619 0.00 0.00 0.00 3.86 R
3001 3096 1.117994 TTCATGCTCATCGCTCTCCT 58.882 50.000 0.00 0.00 40.11 3.69 R
3378 3482 1.134848 GCCAGTTTTGTCACTTGCCAA 60.135 47.619 0.00 0.00 30.76 4.52 R
4184 4383 0.742281 GAGGCGCTGCTCTTGATTGA 60.742 55.000 7.64 0.00 0.00 2.57 R
4203 4402 0.835941 CCTTCATCCTCCTCCACCTG 59.164 60.000 0.00 0.00 0.00 4.00 R
5834 9473 2.363788 TCAAATCTGAAGACGGACCG 57.636 50.000 13.61 13.61 33.97 4.79 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
22 23 3.755628 GCGGTGGGCGAGTAGTGA 61.756 66.667 0.00 0.00 0.00 3.41
23 24 2.490217 CGGTGGGCGAGTAGTGAG 59.510 66.667 0.00 0.00 0.00 3.51
24 25 2.893398 GGTGGGCGAGTAGTGAGG 59.107 66.667 0.00 0.00 0.00 3.86
25 26 1.681327 GGTGGGCGAGTAGTGAGGA 60.681 63.158 0.00 0.00 0.00 3.71
26 27 1.668101 GGTGGGCGAGTAGTGAGGAG 61.668 65.000 0.00 0.00 0.00 3.69
27 28 0.966370 GTGGGCGAGTAGTGAGGAGT 60.966 60.000 0.00 0.00 0.00 3.85
28 29 0.622136 TGGGCGAGTAGTGAGGAGTA 59.378 55.000 0.00 0.00 0.00 2.59
29 30 1.005097 TGGGCGAGTAGTGAGGAGTAA 59.995 52.381 0.00 0.00 0.00 2.24
30 31 1.404748 GGGCGAGTAGTGAGGAGTAAC 59.595 57.143 0.00 0.00 0.00 2.50
31 32 1.063764 GGCGAGTAGTGAGGAGTAACG 59.936 57.143 0.00 0.00 0.00 3.18
32 33 1.736681 GCGAGTAGTGAGGAGTAACGT 59.263 52.381 0.00 0.00 0.00 3.99
33 34 2.161211 GCGAGTAGTGAGGAGTAACGTT 59.839 50.000 5.88 5.88 0.00 3.99
34 35 3.744987 CGAGTAGTGAGGAGTAACGTTG 58.255 50.000 11.99 0.00 0.00 4.10
35 36 3.188048 CGAGTAGTGAGGAGTAACGTTGT 59.812 47.826 11.99 0.00 0.00 3.32
36 37 4.389992 CGAGTAGTGAGGAGTAACGTTGTA 59.610 45.833 11.99 0.00 0.00 2.41
37 38 5.106948 CGAGTAGTGAGGAGTAACGTTGTAA 60.107 44.000 11.99 0.00 0.00 2.41
38 39 6.006759 AGTAGTGAGGAGTAACGTTGTAAC 57.993 41.667 11.99 0.61 0.00 2.50
54 55 6.817270 GTTGTAACGAGACTCTTGTAAACA 57.183 37.500 0.03 5.20 0.00 2.83
55 56 7.404139 GTTGTAACGAGACTCTTGTAAACAT 57.596 36.000 12.30 0.00 29.79 2.71
56 57 7.281484 GTTGTAACGAGACTCTTGTAAACATG 58.719 38.462 12.30 0.00 29.79 3.21
57 58 5.924254 TGTAACGAGACTCTTGTAAACATGG 59.076 40.000 0.03 0.00 0.00 3.66
58 59 3.926616 ACGAGACTCTTGTAAACATGGG 58.073 45.455 0.03 0.00 0.00 4.00
59 60 3.576982 ACGAGACTCTTGTAAACATGGGA 59.423 43.478 0.03 0.00 0.00 4.37
60 61 4.177026 CGAGACTCTTGTAAACATGGGAG 58.823 47.826 0.03 5.21 0.00 4.30
61 62 4.508662 GAGACTCTTGTAAACATGGGAGG 58.491 47.826 0.00 0.00 0.00 4.30
62 63 3.264450 AGACTCTTGTAAACATGGGAGGG 59.736 47.826 0.00 0.00 0.00 4.30
63 64 2.308866 ACTCTTGTAAACATGGGAGGGG 59.691 50.000 0.00 0.00 0.00 4.79
64 65 1.638589 TCTTGTAAACATGGGAGGGGG 59.361 52.381 0.00 0.00 0.00 5.40
86 87 3.036075 GCATGCTTTTGCCTTTCTTCT 57.964 42.857 11.37 0.00 46.87 2.85
87 88 3.396560 GCATGCTTTTGCCTTTCTTCTT 58.603 40.909 11.37 0.00 46.87 2.52
88 89 3.811497 GCATGCTTTTGCCTTTCTTCTTT 59.189 39.130 11.37 0.00 46.87 2.52
89 90 4.990426 GCATGCTTTTGCCTTTCTTCTTTA 59.010 37.500 11.37 0.00 46.87 1.85
90 91 5.466393 GCATGCTTTTGCCTTTCTTCTTTAA 59.534 36.000 11.37 0.00 46.87 1.52
91 92 6.148315 GCATGCTTTTGCCTTTCTTCTTTAAT 59.852 34.615 11.37 0.00 46.87 1.40
92 93 7.331687 GCATGCTTTTGCCTTTCTTCTTTAATA 59.668 33.333 11.37 0.00 46.87 0.98
93 94 9.374838 CATGCTTTTGCCTTTCTTCTTTAATAT 57.625 29.630 0.00 0.00 46.87 1.28
122 123 2.892374 CACACTCGTGCATATTGGAGA 58.108 47.619 0.00 0.00 36.06 3.71
123 124 3.261580 CACACTCGTGCATATTGGAGAA 58.738 45.455 0.00 0.00 36.06 2.87
124 125 3.684305 CACACTCGTGCATATTGGAGAAA 59.316 43.478 0.00 0.00 36.06 2.52
130 131 6.597672 ACTCGTGCATATTGGAGAAAACAATA 59.402 34.615 0.00 0.00 42.86 1.90
298 299 7.357303 ACTCGTTGTTATTTCACATAAACCAC 58.643 34.615 0.00 0.00 0.00 4.16
310 311 6.220930 TCACATAAACCACAAGAGTAGTCAC 58.779 40.000 0.00 0.00 0.00 3.67
318 319 5.171476 CCACAAGAGTAGTCACGATTCATT 58.829 41.667 0.00 0.00 0.00 2.57
361 362 8.704668 TCTGCTATGAGTAATAATGAAGGAACA 58.295 33.333 0.00 0.00 0.00 3.18
362 363 9.499479 CTGCTATGAGTAATAATGAAGGAACAT 57.501 33.333 0.00 0.00 0.00 2.71
481 483 8.924511 ATGGAGGAACATTATGTCGATAAATT 57.075 30.769 0.00 0.00 0.00 1.82
507 509 6.619801 AAATTAATGGAGGAGCGTTATGTC 57.380 37.500 0.00 0.00 0.00 3.06
551 555 6.260050 GGAGCAACTTCCATAATCGTGATTTA 59.740 38.462 0.00 0.00 37.20 1.40
552 556 7.041098 GGAGCAACTTCCATAATCGTGATTTAT 60.041 37.037 0.00 0.00 37.20 1.40
553 557 8.902540 AGCAACTTCCATAATCGTGATTTATA 57.097 30.769 0.00 0.00 32.50 0.98
554 558 9.507329 AGCAACTTCCATAATCGTGATTTATAT 57.493 29.630 0.00 0.00 32.50 0.86
555 559 9.760660 GCAACTTCCATAATCGTGATTTATATC 57.239 33.333 0.00 0.00 32.50 1.63
585 589 4.951094 TGTGTGTAAAGTAAAAGCAAGGGT 59.049 37.500 0.00 0.00 0.00 4.34
630 640 4.021650 GCATTGGCATTGGCATCG 57.978 55.556 14.21 9.12 43.71 3.84
631 641 1.593209 GCATTGGCATTGGCATCGG 60.593 57.895 14.21 7.69 43.71 4.18
632 642 1.593209 CATTGGCATTGGCATCGGC 60.593 57.895 14.21 3.61 43.71 5.54
633 643 2.059190 ATTGGCATTGGCATCGGCA 61.059 52.632 14.21 8.56 43.71 5.69
634 644 1.404479 ATTGGCATTGGCATCGGCAT 61.404 50.000 14.21 1.07 43.71 4.40
635 645 1.615165 TTGGCATTGGCATCGGCATT 61.615 50.000 14.21 0.00 43.71 3.56
636 646 1.593209 GGCATTGGCATCGGCATTG 60.593 57.895 5.17 7.76 43.71 2.82
637 647 4.021650 CATTGGCATCGGCATTGC 57.978 55.556 0.00 0.00 43.71 3.56
638 648 1.440060 CATTGGCATCGGCATTGCT 59.560 52.632 8.82 0.00 43.71 3.91
639 649 0.179094 CATTGGCATCGGCATTGCTT 60.179 50.000 8.82 0.00 43.71 3.91
640 650 0.538118 ATTGGCATCGGCATTGCTTT 59.462 45.000 8.82 0.00 43.71 3.51
641 651 0.390078 TTGGCATCGGCATTGCTTTG 60.390 50.000 8.82 5.28 43.71 2.77
642 652 2.169146 GGCATCGGCATTGCTTTGC 61.169 57.895 17.02 17.02 43.71 3.68
687 697 2.099756 GGTGTTCCATTATTGCTGGAGC 59.900 50.000 0.00 0.00 43.46 4.70
902 923 1.516169 CGCGCCCAATTTTAGCCAC 60.516 57.895 0.00 0.00 0.00 5.01
916 937 4.704833 CCACCCAGCAGACCCACG 62.705 72.222 0.00 0.00 0.00 4.94
1510 1541 0.891373 CTTGTCAAGCGAGGAGGAGA 59.109 55.000 0.00 0.00 0.00 3.71
1520 1551 2.770475 GGAGGAGAAGGAGGCCCC 60.770 72.222 0.00 0.00 0.00 5.80
1521 1552 3.157949 GAGGAGAAGGAGGCCCCG 61.158 72.222 0.00 0.00 40.87 5.73
1587 1618 1.162698 ACGGAATTGAGACGAGTCGA 58.837 50.000 21.50 0.00 34.09 4.20
1621 1652 3.492311 GACGATGGCGAGGAGGAGC 62.492 68.421 0.00 0.00 41.64 4.70
1752 1783 1.756538 GAGCAGGAAGAAGAGGAGGAG 59.243 57.143 0.00 0.00 0.00 3.69
1877 1923 4.610714 GGGCGGCGAGATCTTCCC 62.611 72.222 12.98 5.79 0.00 3.97
2067 2113 1.739049 GGATGCAGAGGAGGACGAG 59.261 63.158 0.00 0.00 0.00 4.18
2193 2239 3.004210 CCGATGATGACTCTGACGAAGAT 59.996 47.826 0.00 0.00 33.29 2.40
2253 2299 1.363744 CCCACAGCGATGAAGACTTC 58.636 55.000 8.12 8.34 0.00 3.01
2318 2364 2.158856 AGCGCATGGAAGAAGATGATGA 60.159 45.455 11.47 0.00 0.00 2.92
2478 2524 2.288457 TGTCACCTTCAAGAAGAGCTCG 60.288 50.000 8.37 0.00 40.79 5.03
2581 2627 1.403514 CCACTCTTCAGAACGCCTCTC 60.404 57.143 0.00 0.00 29.07 3.20
2582 2628 1.543802 CACTCTTCAGAACGCCTCTCT 59.456 52.381 0.00 0.00 29.07 3.10
2796 2884 9.668497 GTAACTAAATAATCTGTTCCTCCTGTT 57.332 33.333 0.00 0.00 0.00 3.16
2802 2890 9.533831 AAATAATCTGTTCCTCCTGTTAATTGT 57.466 29.630 0.00 0.00 0.00 2.71
2803 2891 8.738645 ATAATCTGTTCCTCCTGTTAATTGTC 57.261 34.615 0.00 0.00 0.00 3.18
2804 2892 4.906618 TCTGTTCCTCCTGTTAATTGTCC 58.093 43.478 0.00 0.00 0.00 4.02
2805 2893 4.349636 TCTGTTCCTCCTGTTAATTGTCCA 59.650 41.667 0.00 0.00 0.00 4.02
2967 3062 7.593644 ACACTTTTGTTTCAGTTCTACAAACAC 59.406 33.333 0.00 0.00 40.36 3.32
2972 3067 5.005971 TGTTTCAGTTCTACAAACACGCTAC 59.994 40.000 0.00 0.00 35.57 3.58
3001 3096 4.515191 CCTTTGTCTTTTCATTCAGGACGA 59.485 41.667 0.00 0.00 0.00 4.20
3002 3097 5.334414 CCTTTGTCTTTTCATTCAGGACGAG 60.334 44.000 0.00 0.00 0.00 4.18
3707 3811 1.755179 AATGGAATGTCAAGCTCCCG 58.245 50.000 0.00 0.00 0.00 5.14
3761 3871 4.018141 TGGAATCAAGACAAGACCATCCAT 60.018 41.667 0.00 0.00 29.93 3.41
4184 4383 0.846693 AAGGAGTTGCTTCCACCAGT 59.153 50.000 5.49 0.00 39.84 4.00
4203 4402 0.742281 TCAATCAAGAGCAGCGCCTC 60.742 55.000 2.29 4.34 0.00 4.70
4586 6301 4.036380 GGAGTGAAGACATGGTTCGTTTTT 59.964 41.667 0.00 0.00 0.00 1.94
5123 8245 0.463654 TGGCTGCACGTGAAGAACTT 60.464 50.000 28.26 0.00 0.00 2.66
5168 8290 2.089980 CCTTCCCATTGACTGCAGAAG 58.910 52.381 23.35 10.79 35.26 2.85
5551 8884 8.904099 ATATTATTTGCCTGGTAGTGAACTAC 57.096 34.615 11.44 11.44 46.09 2.73
5552 8885 4.910458 ATTTGCCTGGTAGTGAACTACT 57.090 40.909 17.71 0.00 46.06 2.57
5553 8886 4.699925 TTTGCCTGGTAGTGAACTACTT 57.300 40.909 17.71 0.00 46.06 2.24
5834 9473 2.225491 TGCTGGAATGTTAGTTTGTCGC 59.775 45.455 0.00 0.00 0.00 5.19
6015 9998 3.852939 GCAACATGCAACAATCAGTTCGA 60.853 43.478 0.00 0.00 44.26 3.71
6117 10100 7.946207 TGGAAGATTGTTTAATGCTGTGTTTA 58.054 30.769 0.00 0.00 0.00 2.01
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 1.787057 CTACTCGCCCACCGCTCTAG 61.787 65.000 0.00 0.00 36.73 2.43
1 2 1.822613 CTACTCGCCCACCGCTCTA 60.823 63.158 0.00 0.00 36.73 2.43
4 5 3.760035 CACTACTCGCCCACCGCT 61.760 66.667 0.00 0.00 36.73 5.52
5 6 3.701604 CTCACTACTCGCCCACCGC 62.702 68.421 0.00 0.00 36.73 5.68
6 7 2.490217 CTCACTACTCGCCCACCG 59.510 66.667 0.00 0.00 38.61 4.94
7 8 1.668101 CTCCTCACTACTCGCCCACC 61.668 65.000 0.00 0.00 0.00 4.61
8 9 0.966370 ACTCCTCACTACTCGCCCAC 60.966 60.000 0.00 0.00 0.00 4.61
9 10 0.622136 TACTCCTCACTACTCGCCCA 59.378 55.000 0.00 0.00 0.00 5.36
10 11 1.404748 GTTACTCCTCACTACTCGCCC 59.595 57.143 0.00 0.00 0.00 6.13
11 12 1.063764 CGTTACTCCTCACTACTCGCC 59.936 57.143 0.00 0.00 0.00 5.54
12 13 1.736681 ACGTTACTCCTCACTACTCGC 59.263 52.381 0.00 0.00 0.00 5.03
13 14 3.188048 ACAACGTTACTCCTCACTACTCG 59.812 47.826 0.00 0.00 0.00 4.18
14 15 4.762956 ACAACGTTACTCCTCACTACTC 57.237 45.455 0.00 0.00 0.00 2.59
15 16 5.334414 CGTTACAACGTTACTCCTCACTACT 60.334 44.000 0.00 0.00 46.63 2.57
16 17 4.848299 CGTTACAACGTTACTCCTCACTAC 59.152 45.833 0.00 0.00 46.63 2.73
17 18 5.034554 CGTTACAACGTTACTCCTCACTA 57.965 43.478 0.00 0.00 46.63 2.74
18 19 3.893720 CGTTACAACGTTACTCCTCACT 58.106 45.455 0.00 0.00 46.63 3.41
31 32 6.817270 TGTTTACAAGAGTCTCGTTACAAC 57.183 37.500 0.00 0.00 0.00 3.32
32 33 6.422701 CCATGTTTACAAGAGTCTCGTTACAA 59.577 38.462 0.00 0.00 0.00 2.41
33 34 5.924254 CCATGTTTACAAGAGTCTCGTTACA 59.076 40.000 0.00 0.00 0.00 2.41
34 35 5.347907 CCCATGTTTACAAGAGTCTCGTTAC 59.652 44.000 0.00 0.00 0.00 2.50
35 36 5.244402 TCCCATGTTTACAAGAGTCTCGTTA 59.756 40.000 0.00 0.00 0.00 3.18
36 37 4.039973 TCCCATGTTTACAAGAGTCTCGTT 59.960 41.667 0.00 0.00 0.00 3.85
37 38 3.576982 TCCCATGTTTACAAGAGTCTCGT 59.423 43.478 0.00 0.00 0.00 4.18
38 39 4.177026 CTCCCATGTTTACAAGAGTCTCG 58.823 47.826 0.00 0.00 0.00 4.04
39 40 4.508662 CCTCCCATGTTTACAAGAGTCTC 58.491 47.826 0.00 0.00 0.00 3.36
40 41 3.264450 CCCTCCCATGTTTACAAGAGTCT 59.736 47.826 0.00 0.00 0.00 3.24
41 42 3.610911 CCCTCCCATGTTTACAAGAGTC 58.389 50.000 0.00 0.00 0.00 3.36
42 43 2.308866 CCCCTCCCATGTTTACAAGAGT 59.691 50.000 0.00 0.00 0.00 3.24
43 44 2.357154 CCCCCTCCCATGTTTACAAGAG 60.357 54.545 0.00 0.00 0.00 2.85
44 45 1.638589 CCCCCTCCCATGTTTACAAGA 59.361 52.381 0.00 0.00 0.00 3.02
45 46 2.143876 CCCCCTCCCATGTTTACAAG 57.856 55.000 0.00 0.00 0.00 3.16
66 67 3.036075 AGAAGAAAGGCAAAAGCATGC 57.964 42.857 10.51 10.51 45.67 4.06
67 68 7.662604 ATTAAAGAAGAAAGGCAAAAGCATG 57.337 32.000 0.00 0.00 0.00 4.06
103 104 3.610040 TTCTCCAATATGCACGAGTGT 57.390 42.857 5.07 0.00 0.00 3.55
104 105 4.154015 TGTTTTCTCCAATATGCACGAGTG 59.846 41.667 0.00 0.00 0.00 3.51
105 106 4.323417 TGTTTTCTCCAATATGCACGAGT 58.677 39.130 0.00 0.00 0.00 4.18
106 107 4.944962 TGTTTTCTCCAATATGCACGAG 57.055 40.909 0.00 0.00 0.00 4.18
107 108 5.895636 ATTGTTTTCTCCAATATGCACGA 57.104 34.783 0.00 0.00 30.96 4.35
108 109 6.785191 AGTATTGTTTTCTCCAATATGCACG 58.215 36.000 0.00 0.00 37.19 5.34
115 116 9.533831 ACCTTCAATAGTATTGTTTTCTCCAAT 57.466 29.630 19.85 0.00 36.53 3.16
116 117 8.934023 ACCTTCAATAGTATTGTTTTCTCCAA 57.066 30.769 19.85 6.12 0.00 3.53
117 118 9.444600 GTACCTTCAATAGTATTGTTTTCTCCA 57.555 33.333 19.85 0.00 0.00 3.86
118 119 9.444600 TGTACCTTCAATAGTATTGTTTTCTCC 57.555 33.333 19.85 7.22 0.00 3.71
122 123 9.802039 TCCTTGTACCTTCAATAGTATTGTTTT 57.198 29.630 19.85 8.04 0.00 2.43
123 124 9.227777 GTCCTTGTACCTTCAATAGTATTGTTT 57.772 33.333 19.85 7.75 0.00 2.83
124 125 8.380099 TGTCCTTGTACCTTCAATAGTATTGTT 58.620 33.333 19.85 8.04 0.00 2.83
130 131 4.595781 TGGTGTCCTTGTACCTTCAATAGT 59.404 41.667 0.00 0.00 37.84 2.12
254 255 2.113139 ACACAACCAAGAGCCCGG 59.887 61.111 0.00 0.00 0.00 5.73
298 299 5.863935 TGTCAATGAATCGTGACTACTCTTG 59.136 40.000 15.03 0.00 43.73 3.02
310 311 6.668541 ATCTTACCTGTTGTCAATGAATCG 57.331 37.500 0.00 0.00 0.00 3.34
318 319 5.939764 AGCAGATATCTTACCTGTTGTCA 57.060 39.130 1.33 0.00 0.00 3.58
354 355 6.884832 TGGACTTATCGACATAATGTTCCTT 58.115 36.000 0.00 0.00 0.00 3.36
481 483 6.601613 ACATAACGCTCCTCCATTAATTTTGA 59.398 34.615 0.00 0.00 0.00 2.69
507 509 6.491394 TGCTCCGTTAATTTTGGATTTATCG 58.509 36.000 0.00 0.00 0.00 2.92
558 562 8.952278 CCCTTGCTTTTACTTTACACACATATA 58.048 33.333 0.00 0.00 0.00 0.86
585 589 1.036707 GGTAAAACTTGGCACCTGCA 58.963 50.000 0.00 0.00 44.36 4.41
625 635 3.391355 GCAAAGCAATGCCGATGC 58.609 55.556 10.79 10.79 44.15 3.91
631 641 0.244450 TACCTGCAGCAAAGCAATGC 59.756 50.000 8.66 0.00 45.13 3.56
632 642 2.728690 TTACCTGCAGCAAAGCAATG 57.271 45.000 8.66 0.00 45.13 2.82
633 643 3.749665 TTTTACCTGCAGCAAAGCAAT 57.250 38.095 8.66 0.00 45.13 3.56
634 644 3.749665 ATTTTACCTGCAGCAAAGCAA 57.250 38.095 8.66 0.00 45.13 3.91
635 645 3.391965 CAATTTTACCTGCAGCAAAGCA 58.608 40.909 8.66 0.00 43.35 3.91
636 646 2.738314 CCAATTTTACCTGCAGCAAAGC 59.262 45.455 8.66 0.00 0.00 3.51
637 647 4.255833 TCCAATTTTACCTGCAGCAAAG 57.744 40.909 8.66 0.00 0.00 2.77
638 648 4.679373 TTCCAATTTTACCTGCAGCAAA 57.321 36.364 8.66 7.90 0.00 3.68
639 649 4.888326 ATTCCAATTTTACCTGCAGCAA 57.112 36.364 8.66 1.02 0.00 3.91
640 650 4.402155 CCTATTCCAATTTTACCTGCAGCA 59.598 41.667 8.66 0.00 0.00 4.41
641 651 4.644685 TCCTATTCCAATTTTACCTGCAGC 59.355 41.667 8.66 0.00 0.00 5.25
642 652 5.300286 CCTCCTATTCCAATTTTACCTGCAG 59.700 44.000 6.78 6.78 0.00 4.41
687 697 1.795162 GCCATCGCTTTGAAATGACCG 60.795 52.381 0.00 0.00 0.00 4.79
993 1014 2.202756 GTGGTCGGCATCTCGTCC 60.203 66.667 0.00 0.00 38.48 4.79
1172 1193 4.069232 CCGGCTGCGAAGAGGACA 62.069 66.667 0.00 0.00 0.00 4.02
1446 1477 0.605589 CGACAGGCTCCTTCTTGACT 59.394 55.000 0.00 0.00 0.00 3.41
1510 1541 4.012721 AGACCTCGGGGCCTCCTT 62.013 66.667 0.00 0.00 35.63 3.36
1520 1551 0.646381 CGTACTCTCGTCAGACCTCG 59.354 60.000 0.00 0.00 0.00 4.63
1521 1552 1.928503 CTCGTACTCTCGTCAGACCTC 59.071 57.143 0.00 0.00 0.00 3.85
1621 1652 2.898472 ATCCCCACTTCCTCCTCCCG 62.898 65.000 0.00 0.00 0.00 5.14
1752 1783 1.749634 TCTTCTTCCGATTCCTCCGAC 59.250 52.381 0.00 0.00 0.00 4.79
1877 1923 0.598065 CCCTTCAAACTTCCGCTTGG 59.402 55.000 0.00 0.00 0.00 3.61
2034 2080 3.749064 TCCGAGCTGGACTGCGAC 61.749 66.667 0.00 0.00 43.74 5.19
2052 2098 0.891373 CTTTCTCGTCCTCCTCTGCA 59.109 55.000 0.00 0.00 0.00 4.41
2067 2113 0.591659 GAGGCGGTGGTTTGTCTTTC 59.408 55.000 0.00 0.00 0.00 2.62
2158 2204 0.320374 TCATCGGCGTTTTGTCCTCT 59.680 50.000 6.85 0.00 0.00 3.69
2193 2239 4.717629 CTCGTCGCCGTTCTGCCA 62.718 66.667 0.00 0.00 35.01 4.92
2253 2299 4.157120 ATTCCGCCGGGTTCCTCG 62.157 66.667 1.90 0.00 33.83 4.63
2362 2408 1.780309 TCCTTCTTTCTTTGCCCTCCA 59.220 47.619 0.00 0.00 0.00 3.86
2416 2462 3.551496 CTGCGGGGAAGTCCTTGCA 62.551 63.158 13.76 13.76 41.86 4.08
2478 2524 4.821589 CGCCTCGGAGGAACCAGC 62.822 72.222 27.95 9.74 37.67 4.85
2581 2627 2.685380 AGGGGCGTCCAGAGGAAG 60.685 66.667 9.07 0.00 38.24 3.46
2582 2628 3.003173 CAGGGGCGTCCAGAGGAA 61.003 66.667 9.07 0.00 38.24 3.36
2967 3062 2.969628 AGACAAAGGGATCAGTAGCG 57.030 50.000 0.00 0.00 0.00 4.26
2972 3067 6.349944 CCTGAATGAAAAGACAAAGGGATCAG 60.350 42.308 0.00 0.00 0.00 2.90
3001 3096 1.117994 TTCATGCTCATCGCTCTCCT 58.882 50.000 0.00 0.00 40.11 3.69
3002 3097 1.945387 TTTCATGCTCATCGCTCTCC 58.055 50.000 0.00 0.00 40.11 3.71
3377 3481 2.539476 CCAGTTTTGTCACTTGCCAAC 58.461 47.619 0.00 0.00 0.00 3.77
3378 3482 1.134848 GCCAGTTTTGTCACTTGCCAA 60.135 47.619 0.00 0.00 30.76 4.52
3382 3486 1.594518 CGACGCCAGTTTTGTCACTTG 60.595 52.381 0.00 0.00 32.91 3.16
3707 3811 2.039084 ACTGGAACTGAGGACATGGAAC 59.961 50.000 0.00 0.00 0.00 3.62
3741 3851 7.121759 CAGTTTATGGATGGTCTTGTCTTGATT 59.878 37.037 0.00 0.00 0.00 2.57
3761 3871 4.080356 CCATGATCCTTGGAGACCAGTTTA 60.080 45.833 6.00 0.00 36.26 2.01
4184 4383 0.742281 GAGGCGCTGCTCTTGATTGA 60.742 55.000 7.64 0.00 0.00 2.57
4203 4402 0.835941 CCTTCATCCTCCTCCACCTG 59.164 60.000 0.00 0.00 0.00 4.00
4373 5701 2.011122 TCTGACGAGGAAGAGGGTTT 57.989 50.000 0.00 0.00 0.00 3.27
4586 6301 1.476488 TCGCAAAGACGGATGATCTCA 59.524 47.619 0.00 0.00 0.00 3.27
5123 8245 6.072508 GGAGAATCTGCACAAACATGTCTTTA 60.073 38.462 0.00 0.00 33.73 1.85
5168 8290 8.718102 TTCCACTTACAAGATTGAGCTATAAC 57.282 34.615 0.00 0.00 0.00 1.89
5834 9473 2.363788 TCAAATCTGAAGACGGACCG 57.636 50.000 13.61 13.61 33.97 4.79


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

AutoCloner maintained by Alex Coulton.