Multiple sequence alignment - TraesCS4A01G029300

Loading Multiple Alignment...

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 TraesCS4A01G029300 chr4A 100.000 4320 0 0 424 4743 21453079 21457398 0.000000e+00 7978.0
1 TraesCS4A01G029300 chr4A 100.000 94 0 0 1 94 21452656 21452749 1.750000e-39 174.0
2 TraesCS4A01G029300 chr4D 93.664 4372 157 53 431 4743 445711993 445707683 0.000000e+00 6429.0
3 TraesCS4A01G029300 chr4B 93.376 4393 158 40 429 4743 557456388 557452051 0.000000e+00 6377.0
4 TraesCS4A01G029300 chr4B 96.591 88 1 2 9 94 557456531 557456444 1.380000e-30 145.0
5 TraesCS4A01G029300 chrUn 77.885 416 52 10 3774 4178 369331061 369331447 6.180000e-54 222.0
6 TraesCS4A01G029300 chrUn 85.263 190 10 10 4563 4743 369331531 369331711 3.770000e-41 180.0
7 TraesCS4A01G029300 chr2A 84.831 178 25 2 3999 4176 12175011 12175186 1.360000e-40 178.0
8 TraesCS4A01G029300 chr2D 85.294 136 7 7 4563 4694 11560573 11560699 1.390000e-25 128.0
9 TraesCS4A01G029300 chr6A 94.643 56 3 0 1339 1394 424798468 424798523 2.350000e-13 87.9


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 TraesCS4A01G029300 chr4A 21452656 21457398 4742 False 4076 7978 100.0000 1 4743 2 chr4A.!!$F1 4742
1 TraesCS4A01G029300 chr4D 445707683 445711993 4310 True 6429 6429 93.6640 431 4743 1 chr4D.!!$R1 4312
2 TraesCS4A01G029300 chr4B 557452051 557456531 4480 True 3261 6377 94.9835 9 4743 2 chr4B.!!$R1 4734
3 TraesCS4A01G029300 chrUn 369331061 369331711 650 False 201 222 81.5740 3774 4743 2 chrUn.!!$F1 969

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
37 38 0.035739 GCAGTAACACTTTCCCCCGA 59.964 55.0 0.00 0.0 0.0 5.14 F
510 513 0.390472 GCCAAGCTCGCTTACTCACT 60.390 55.0 3.53 0.0 34.5 3.41 F
1624 1689 0.533951 GTACGTGTCCCCGGATTTCT 59.466 55.0 0.73 0.0 0.0 2.52 F
2373 2438 0.320946 CAAGCAAGCAAATGGTGGGG 60.321 55.0 0.00 0.0 0.0 4.96 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1651 1716 0.673644 ACCGAAATTGTCAGCCCGAG 60.674 55.000 0.00 0.0 0.00 4.63 R
2289 2354 2.173782 ACAACACAGATTACCCACCACA 59.826 45.455 0.00 0.0 0.00 4.17 R
3601 3667 0.175989 GGTTGATCGACTCCACCTCC 59.824 60.000 12.89 0.0 36.85 4.30 R
4361 4441 1.070604 ATGGTCTCCTGGGCATATGG 58.929 55.000 4.56 0.0 0.00 2.74 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
35 36 1.534729 CAGCAGTAACACTTTCCCCC 58.465 55.000 0.00 0.00 0.00 5.40
36 37 0.036306 AGCAGTAACACTTTCCCCCG 59.964 55.000 0.00 0.00 0.00 5.73
37 38 0.035739 GCAGTAACACTTTCCCCCGA 59.964 55.000 0.00 0.00 0.00 5.14
39 40 2.423577 CAGTAACACTTTCCCCCGAAG 58.576 52.381 0.00 0.00 0.00 3.79
40 41 2.052468 AGTAACACTTTCCCCCGAAGT 58.948 47.619 0.00 0.00 37.82 3.01
510 513 0.390472 GCCAAGCTCGCTTACTCACT 60.390 55.000 3.53 0.00 34.50 3.41
515 518 1.068194 AGCTCGCTTACTCACTCACAC 60.068 52.381 0.00 0.00 0.00 3.82
516 519 1.335964 GCTCGCTTACTCACTCACACA 60.336 52.381 0.00 0.00 0.00 3.72
517 520 2.320367 CTCGCTTACTCACTCACACAC 58.680 52.381 0.00 0.00 0.00 3.82
560 565 8.915057 TTTCTCTTTCATTCAAGATTCACTCT 57.085 30.769 0.00 0.00 32.21 3.24
618 623 3.148412 GGCTACTGGCTACTAGTAGGAC 58.852 54.545 27.24 13.94 44.88 3.85
619 624 3.181441 GGCTACTGGCTACTAGTAGGACT 60.181 52.174 27.24 3.31 44.88 3.85
628 633 4.505390 GCTACTAGTAGGACTGGAGTAGGG 60.505 54.167 27.24 2.40 37.64 3.53
634 639 1.212441 AGGACTGGAGTAGGGTCGTAG 59.788 57.143 0.00 0.00 0.00 3.51
635 640 1.064832 GGACTGGAGTAGGGTCGTAGT 60.065 57.143 0.00 0.00 0.00 2.73
636 641 2.171448 GGACTGGAGTAGGGTCGTAGTA 59.829 54.545 0.00 0.00 0.00 1.82
651 656 5.579904 GGTCGTAGTATTTGGTTCTTCTTCC 59.420 44.000 0.00 0.00 0.00 3.46
678 683 0.744771 CTTGGGAAGCCGGTAAGCTC 60.745 60.000 1.90 0.00 44.11 4.09
689 694 2.106683 GTAAGCTCGCCACGGCATT 61.107 57.895 9.11 0.00 42.06 3.56
702 725 2.386935 GGCATTACCAGCCCCTCCT 61.387 63.158 0.00 0.00 46.50 3.69
783 813 3.246301 TCCCATCCTCATCAATCCTCTC 58.754 50.000 0.00 0.00 0.00 3.20
784 814 2.305343 CCCATCCTCATCAATCCTCTCC 59.695 54.545 0.00 0.00 0.00 3.71
786 816 2.109229 TCCTCATCAATCCTCTCCCC 57.891 55.000 0.00 0.00 0.00 4.81
827 859 6.509418 TCACAATCTTTGTTTATAGGGTGC 57.491 37.500 0.00 0.00 43.23 5.01
901 934 4.382541 CTTGGCCCCCTCCCAACC 62.383 72.222 0.00 0.00 37.43 3.77
945 985 4.704103 TCGACCCTGGGCTGCTCT 62.704 66.667 14.08 0.00 0.00 4.09
946 986 4.463879 CGACCCTGGGCTGCTCTG 62.464 72.222 14.08 0.00 0.00 3.35
947 987 4.792804 GACCCTGGGCTGCTCTGC 62.793 72.222 14.08 0.00 0.00 4.26
1072 1119 2.558575 CCCTCTGTCTTCTTCCTCCTGA 60.559 54.545 0.00 0.00 0.00 3.86
1075 1122 4.382901 CCTCTGTCTTCTTCCTCCTGATTG 60.383 50.000 0.00 0.00 0.00 2.67
1141 1188 1.374758 CTGTCGTGGTCCAAGAGCC 60.375 63.158 7.86 0.00 0.00 4.70
1146 1193 1.003233 GTGGTCCAAGAGCCTGGTC 60.003 63.158 0.00 0.00 37.74 4.02
1147 1194 1.461268 TGGTCCAAGAGCCTGGTCA 60.461 57.895 0.00 0.00 37.74 4.02
1306 1356 1.304217 AAGAAGAGCCGGACGGAGA 60.304 57.895 15.99 0.00 37.50 3.71
1400 1450 0.537188 ATGGACTACAGGTTGCTCCG 59.463 55.000 0.00 0.00 41.99 4.63
1446 1504 4.621991 ACATAATTCCATCTTCGTCTCCG 58.378 43.478 0.00 0.00 0.00 4.63
1472 1537 1.603802 CTGTGTGTGTGGCCTTGTTAG 59.396 52.381 3.32 0.00 0.00 2.34
1614 1679 2.880648 GTCCTCGGGTACGTGTCC 59.119 66.667 0.00 0.00 41.85 4.02
1624 1689 0.533951 GTACGTGTCCCCGGATTTCT 59.466 55.000 0.73 0.00 0.00 2.52
1651 1716 1.358046 GATTCCTCAATGCTGCGGC 59.642 57.895 11.65 11.65 39.26 6.53
1669 1734 1.982073 GCTCGGGCTGACAATTTCGG 61.982 60.000 0.00 0.00 35.22 4.30
2141 2206 1.898154 GGTGTACTCGCCCATGTCT 59.102 57.895 0.00 0.00 38.21 3.41
2209 2274 2.865119 TCTGGTCACACTAGGTACGA 57.135 50.000 0.00 0.00 0.00 3.43
2222 2287 5.520288 CACTAGGTACGATTCAAGTTCCATG 59.480 44.000 0.00 0.00 32.37 3.66
2260 2325 8.243426 GTCAACACATGCTATTTTTAATGGAGA 58.757 33.333 0.00 0.00 0.00 3.71
2279 2344 6.640518 TGGAGACAAAGTACATTATGGTCTC 58.359 40.000 15.90 15.90 45.47 3.36
2296 2361 5.928976 TGGTCTCATAAATAGATGTGGTGG 58.071 41.667 0.00 0.00 0.00 4.61
2310 2375 2.173782 TGTGGTGGGTAATCTGTGTTGT 59.826 45.455 0.00 0.00 0.00 3.32
2311 2376 2.552315 GTGGTGGGTAATCTGTGTTGTG 59.448 50.000 0.00 0.00 0.00 3.33
2315 2380 3.689649 GTGGGTAATCTGTGTTGTGATCC 59.310 47.826 0.00 0.00 0.00 3.36
2318 2383 3.370978 GGTAATCTGTGTTGTGATCCGTG 59.629 47.826 0.00 0.00 0.00 4.94
2319 2384 2.839486 ATCTGTGTTGTGATCCGTGT 57.161 45.000 0.00 0.00 0.00 4.49
2321 2386 2.209273 TCTGTGTTGTGATCCGTGTTG 58.791 47.619 0.00 0.00 0.00 3.33
2322 2387 0.660488 TGTGTTGTGATCCGTGTTGC 59.340 50.000 0.00 0.00 0.00 4.17
2323 2388 0.660488 GTGTTGTGATCCGTGTTGCA 59.340 50.000 0.00 0.00 0.00 4.08
2324 2389 1.064803 GTGTTGTGATCCGTGTTGCAA 59.935 47.619 0.00 0.00 0.00 4.08
2325 2390 1.952990 TGTTGTGATCCGTGTTGCAAT 59.047 42.857 0.59 0.00 0.00 3.56
2326 2391 2.031245 TGTTGTGATCCGTGTTGCAATC 60.031 45.455 0.59 0.00 0.00 2.67
2327 2392 2.183478 TGTGATCCGTGTTGCAATCT 57.817 45.000 0.59 0.00 0.00 2.40
2328 2393 1.805943 TGTGATCCGTGTTGCAATCTG 59.194 47.619 0.59 0.00 0.00 2.90
2329 2394 2.076100 GTGATCCGTGTTGCAATCTGA 58.924 47.619 0.59 1.86 0.00 3.27
2330 2395 2.679837 GTGATCCGTGTTGCAATCTGAT 59.320 45.455 0.59 6.80 0.00 2.90
2331 2396 2.679336 TGATCCGTGTTGCAATCTGATG 59.321 45.455 0.59 0.00 0.00 3.07
2332 2397 2.183478 TCCGTGTTGCAATCTGATGT 57.817 45.000 0.59 0.00 0.00 3.06
2373 2438 0.320946 CAAGCAAGCAAATGGTGGGG 60.321 55.000 0.00 0.00 0.00 4.96
2490 2555 2.052782 ACAAGGTTGGTCACTGTTCC 57.947 50.000 0.00 0.00 0.00 3.62
2491 2556 1.564348 ACAAGGTTGGTCACTGTTCCT 59.436 47.619 0.00 0.00 0.00 3.36
2492 2557 2.775384 ACAAGGTTGGTCACTGTTCCTA 59.225 45.455 0.00 0.00 0.00 2.94
2493 2558 3.139077 CAAGGTTGGTCACTGTTCCTAC 58.861 50.000 5.34 5.34 0.00 3.18
2494 2559 1.697982 AGGTTGGTCACTGTTCCTACC 59.302 52.381 17.79 17.79 45.28 3.18
2495 2560 1.418637 GGTTGGTCACTGTTCCTACCA 59.581 52.381 19.39 10.56 44.67 3.25
2496 2561 2.490991 GTTGGTCACTGTTCCTACCAC 58.509 52.381 0.00 0.00 41.58 4.16
2497 2562 1.796017 TGGTCACTGTTCCTACCACA 58.204 50.000 0.00 0.00 37.09 4.17
2713 2778 3.411418 GAAGGCGACGAGATGCGGA 62.411 63.158 0.00 0.00 46.49 5.54
2828 2893 2.880890 AGTAAGCAAGCACAGAACCTTG 59.119 45.455 0.00 0.00 40.97 3.61
3005 3070 2.165167 TGGAAAGCATTGCTGGAGAAG 58.835 47.619 12.82 0.00 39.62 2.85
3036 3101 2.883386 AGAGCTTGCAAACCTTCTTGAG 59.117 45.455 0.00 0.00 0.00 3.02
3076 3141 1.222661 GTGTACCGTTGGGATCCCC 59.777 63.158 28.58 12.70 45.71 4.81
3096 3161 3.987220 CCCGGAAAGCTGTAAAATTGTTG 59.013 43.478 0.73 0.00 0.00 3.33
3131 3196 5.173774 TCAGTGCTTTTGTCTTGTCATTC 57.826 39.130 0.00 0.00 0.00 2.67
3135 3200 6.532657 CAGTGCTTTTGTCTTGTCATTCTTTT 59.467 34.615 0.00 0.00 0.00 2.27
3163 3228 9.289303 CTTTACCATGTTGCAACATTACTAATC 57.711 33.333 36.41 5.90 46.95 1.75
3170 3235 3.192466 GCAACATTACTAATCGGTCGGT 58.808 45.455 0.00 0.00 0.00 4.69
3286 3351 5.006386 CAGCTAAGGATTGAACAAAGAGGT 58.994 41.667 0.00 0.00 0.00 3.85
3376 3441 1.219664 CGACAAGTATGCCGGGGAA 59.780 57.895 2.18 0.00 0.00 3.97
3424 3490 6.239600 GGAGAACTCCTGCATGGTACATTATA 60.240 42.308 12.98 0.00 45.26 0.98
3425 3491 7.527868 GGAGAACTCCTGCATGGTACATTATAT 60.528 40.741 12.98 0.00 45.26 0.86
3466 3532 7.702348 GGATATTTGCCAGATTTTGTACAGTTC 59.298 37.037 0.00 0.00 0.00 3.01
3472 3538 5.687285 GCCAGATTTTGTACAGTTCAAAGTG 59.313 40.000 5.54 5.49 36.40 3.16
3489 3555 7.715265 TCAAAGTGAACTTAGTGATCTTGTC 57.285 36.000 0.00 0.00 34.61 3.18
3601 3667 1.846782 GTCTACAGCGTATTCAGTGCG 59.153 52.381 0.00 0.00 39.08 5.34
3791 3857 6.173339 CACCCAGTGTTCAGTCATATAACTT 58.827 40.000 0.00 0.00 0.00 2.66
3929 4006 6.815142 ACATAAATGCAAGCTTCTGAATTTCC 59.185 34.615 7.50 0.00 36.24 3.13
4076 4153 2.680339 GCTTGGCTAGTTTCACAGGATC 59.320 50.000 0.00 0.00 0.00 3.36
4094 4172 7.770433 CACAGGATCCAAATAATTCAGTACAGA 59.230 37.037 15.82 0.00 0.00 3.41
4192 4272 1.211703 TCTGTTTTGCAGGTGAGGACA 59.788 47.619 0.00 0.00 45.08 4.02
4246 4326 2.591429 TGCAAGCCAGTGACCACG 60.591 61.111 0.00 0.00 36.20 4.94
4268 4348 9.410556 CCACGAAGACTCAAATTATTTCATTTT 57.589 29.630 0.00 0.00 0.00 1.82
4301 4381 8.087982 TCAAACTTCAAAGATAGCACTAACAG 57.912 34.615 0.00 0.00 0.00 3.16
4361 4441 2.161012 TGAGACAGTACGACGATCCAAC 59.839 50.000 0.00 0.00 0.00 3.77
4368 4448 1.865865 ACGACGATCCAACCATATGC 58.134 50.000 0.00 0.00 0.00 3.14
4426 4506 0.105593 ACTGCTACTGATGGCATCGG 59.894 55.000 30.04 30.04 42.09 4.18
4429 4509 1.202568 TGCTACTGATGGCATCGGAAG 60.203 52.381 36.33 24.73 37.40 3.46
4431 4511 2.035961 GCTACTGATGGCATCGGAAGTA 59.964 50.000 36.33 26.87 39.01 2.24
4448 4528 5.354234 CGGAAGTAGTGCACCAGATTATTTT 59.646 40.000 14.63 0.00 0.00 1.82
4465 4545 9.804977 AGATTATTTTCTCCCCTTCTTCATATG 57.195 33.333 0.00 0.00 0.00 1.78
4526 4606 5.523588 TCTCTCTCTCTCTCTCTCTCTCTT 58.476 45.833 0.00 0.00 0.00 2.85
4633 4753 6.715347 TTGGGGAAGAAAGAAAGAAAGAAG 57.285 37.500 0.00 0.00 0.00 2.85
4637 4757 5.048364 GGGAAGAAAGAAAGAAAGAAGGAGC 60.048 44.000 0.00 0.00 0.00 4.70
4666 4793 1.550976 TGAATGAATGCCTGCATTGCA 59.449 42.857 21.14 17.29 45.50 4.08
4671 4798 1.904771 ATGCCTGCATTGCATTGCT 59.095 47.368 28.14 10.12 46.91 3.91
4672 4799 0.179084 ATGCCTGCATTGCATTGCTC 60.179 50.000 28.14 19.03 46.91 4.26
4674 4801 1.956629 GCCTGCATTGCATTGCTCCT 61.957 55.000 28.14 0.00 43.18 3.69
4675 4802 0.102481 CCTGCATTGCATTGCTCCTC 59.898 55.000 28.14 5.83 43.18 3.71
4696 4825 8.750515 TCCTCATATCATCTATCTCATCTCAC 57.249 38.462 0.00 0.00 0.00 3.51
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 1.454295 CTGCCATGCCATGCCAGTA 60.454 57.895 7.48 0.00 0.00 2.74
1 2 2.758327 CTGCCATGCCATGCCAGT 60.758 61.111 7.48 0.00 0.00 4.00
2 3 4.221422 GCTGCCATGCCATGCCAG 62.221 66.667 11.14 11.14 0.00 4.85
4 5 4.221422 CTGCTGCCATGCCATGCC 62.221 66.667 0.00 0.00 0.00 4.40
5 6 1.669049 TTACTGCTGCCATGCCATGC 61.669 55.000 0.00 0.00 0.00 4.06
6 7 0.101759 GTTACTGCTGCCATGCCATG 59.898 55.000 0.00 0.00 0.00 3.66
7 8 0.323633 TGTTACTGCTGCCATGCCAT 60.324 50.000 0.00 0.00 0.00 4.40
35 36 2.789208 CATACCAAGCAATGCACTTCG 58.211 47.619 8.35 0.00 0.00 3.79
36 37 2.533266 GCATACCAAGCAATGCACTTC 58.467 47.619 8.35 0.00 46.19 3.01
37 38 2.660189 GCATACCAAGCAATGCACTT 57.340 45.000 8.35 0.00 46.19 3.16
424 427 3.019799 TCTCTAGGATGGTCAGTGTCC 57.980 52.381 0.00 0.00 0.00 4.02
427 430 4.222336 AGGAATCTCTAGGATGGTCAGTG 58.778 47.826 0.00 0.00 34.45 3.66
441 444 0.461693 AGCGCTTGCAGAGGAATCTC 60.462 55.000 2.64 0.00 42.66 2.75
503 506 3.517602 GTTGTGTGTGTGTGAGTGAGTA 58.482 45.455 0.00 0.00 0.00 2.59
510 513 1.078778 AGCCGTTGTGTGTGTGTGA 60.079 52.632 0.00 0.00 0.00 3.58
515 518 0.732571 AACTTGAGCCGTTGTGTGTG 59.267 50.000 0.00 0.00 0.00 3.82
516 519 1.459450 AAACTTGAGCCGTTGTGTGT 58.541 45.000 0.00 0.00 0.00 3.72
517 520 2.559998 AAAACTTGAGCCGTTGTGTG 57.440 45.000 0.00 0.00 0.00 3.82
560 565 1.280457 GAGGAGGAAGAGGGCAAGAA 58.720 55.000 0.00 0.00 0.00 2.52
618 623 4.037684 CCAAATACTACGACCCTACTCCAG 59.962 50.000 0.00 0.00 0.00 3.86
619 624 3.956199 CCAAATACTACGACCCTACTCCA 59.044 47.826 0.00 0.00 0.00 3.86
628 633 5.579904 GGGAAGAAGAACCAAATACTACGAC 59.420 44.000 0.00 0.00 0.00 4.34
634 639 4.317530 AGGGGGAAGAAGAACCAAATAC 57.682 45.455 0.00 0.00 0.00 1.89
635 640 5.083821 CAAAGGGGGAAGAAGAACCAAATA 58.916 41.667 0.00 0.00 0.00 1.40
636 641 3.903714 CAAAGGGGGAAGAAGAACCAAAT 59.096 43.478 0.00 0.00 0.00 2.32
678 683 3.876198 GCTGGTAATGCCGTGGCG 61.876 66.667 6.37 0.00 45.51 5.69
689 694 2.365635 GCAGAGGAGGGGCTGGTA 60.366 66.667 0.00 0.00 32.83 3.25
702 725 3.005539 GTGAGGAGGGCAGGCAGA 61.006 66.667 0.00 0.00 0.00 4.26
708 731 3.385384 CTGCGAGTGAGGAGGGCA 61.385 66.667 0.00 0.00 0.00 5.36
710 733 1.379176 TCTCTGCGAGTGAGGAGGG 60.379 63.158 5.66 0.00 32.78 4.30
764 794 2.305343 GGGAGAGGATTGATGAGGATGG 59.695 54.545 0.00 0.00 0.00 3.51
783 813 3.456380 TTTGATGGAAAGAAGAGGGGG 57.544 47.619 0.00 0.00 0.00 5.40
784 814 4.400567 GTGATTTGATGGAAAGAAGAGGGG 59.599 45.833 0.00 0.00 0.00 4.79
786 816 6.579666 TTGTGATTTGATGGAAAGAAGAGG 57.420 37.500 0.00 0.00 0.00 3.69
823 855 0.609131 ACTGTTGGGCTACATGCACC 60.609 55.000 0.00 0.00 46.54 5.01
946 986 3.437795 AGCGGTCATGCAGCAAGC 61.438 61.111 0.00 0.37 40.81 4.01
947 987 2.330372 ACAGCGGTCATGCAGCAAG 61.330 57.895 0.00 0.00 40.81 4.01
948 988 2.281692 ACAGCGGTCATGCAGCAA 60.282 55.556 0.00 0.00 40.81 3.91
982 1022 4.013050 CTCATTGTTCCCTTCCTTCCTTC 58.987 47.826 0.00 0.00 0.00 3.46
983 1023 3.657727 TCTCATTGTTCCCTTCCTTCCTT 59.342 43.478 0.00 0.00 0.00 3.36
1072 1119 1.251251 GCACAGGGAAACAGAGCAAT 58.749 50.000 0.00 0.00 0.00 3.56
1075 1122 1.073897 AGGCACAGGGAAACAGAGC 59.926 57.895 0.00 0.00 0.00 4.09
1141 1188 2.222027 GTTGAACCACTTCCTGACCAG 58.778 52.381 0.00 0.00 0.00 4.00
1146 1193 2.816087 CCTGATGTTGAACCACTTCCTG 59.184 50.000 0.00 0.00 0.00 3.86
1147 1194 2.711009 TCCTGATGTTGAACCACTTCCT 59.289 45.455 0.00 0.00 0.00 3.36
1335 1385 2.443203 TCGATCTTGCCCCGCCTA 60.443 61.111 0.00 0.00 0.00 3.93
1446 1504 1.963338 GCCACACACACAGGAGAGC 60.963 63.158 0.00 0.00 0.00 4.09
1480 1545 0.947244 CTGCAGGCAGTTTCGTTCTT 59.053 50.000 13.02 0.00 39.10 2.52
1481 1546 0.886490 CCTGCAGGCAGTTTCGTTCT 60.886 55.000 22.33 0.00 42.15 3.01
1482 1547 0.884704 TCCTGCAGGCAGTTTCGTTC 60.885 55.000 28.91 0.00 42.15 3.95
1637 1702 3.570638 CGAGCCGCAGCATTGAGG 61.571 66.667 0.00 0.00 46.03 3.86
1651 1716 0.673644 ACCGAAATTGTCAGCCCGAG 60.674 55.000 0.00 0.00 0.00 4.63
1904 1969 4.025401 GCCGCGTTGTTGGTCTGG 62.025 66.667 4.92 0.00 0.00 3.86
2141 2206 4.433877 GCGTGGCCGTACCCGTAA 62.434 66.667 0.00 0.00 37.83 3.18
2209 2274 4.603131 AGTACATGGCATGGAACTTGAAT 58.397 39.130 29.49 9.30 29.68 2.57
2222 2287 2.766313 TGTGTTGACAGAGTACATGGC 58.234 47.619 0.00 0.00 0.00 4.40
2279 2344 7.939039 ACAGATTACCCACCACATCTATTTATG 59.061 37.037 0.00 0.00 0.00 1.90
2289 2354 2.173782 ACAACACAGATTACCCACCACA 59.826 45.455 0.00 0.00 0.00 4.17
2296 2361 3.370978 CACGGATCACAACACAGATTACC 59.629 47.826 0.00 0.00 0.00 2.85
2310 2375 2.470983 TCAGATTGCAACACGGATCA 57.529 45.000 0.00 0.00 0.00 2.92
2311 2376 2.679837 ACATCAGATTGCAACACGGATC 59.320 45.455 0.00 0.00 0.00 3.36
2315 2380 3.818961 AGAACATCAGATTGCAACACG 57.181 42.857 0.00 0.00 0.00 4.49
2326 2391 5.238868 CCAGGCAATATCTGAAGAACATCAG 59.761 44.000 1.32 1.32 46.62 2.90
2327 2392 5.128205 CCAGGCAATATCTGAAGAACATCA 58.872 41.667 0.00 0.00 34.36 3.07
2328 2393 5.128919 ACCAGGCAATATCTGAAGAACATC 58.871 41.667 0.00 0.00 34.36 3.06
2329 2394 5.121380 ACCAGGCAATATCTGAAGAACAT 57.879 39.130 0.00 0.00 34.36 2.71
2330 2395 4.574674 ACCAGGCAATATCTGAAGAACA 57.425 40.909 0.00 0.00 34.36 3.18
2331 2396 4.439289 GCAACCAGGCAATATCTGAAGAAC 60.439 45.833 0.00 0.00 34.36 3.01
2332 2397 3.696051 GCAACCAGGCAATATCTGAAGAA 59.304 43.478 0.00 0.00 34.36 2.52
2373 2438 4.488879 GAGCCCAAATCATCAGAAACAAC 58.511 43.478 0.00 0.00 0.00 3.32
2494 2559 9.970395 AATCATAATAACCACATAGCATTTGTG 57.030 29.630 6.69 6.69 43.25 3.33
2531 2596 9.269453 TGTGATCAATTCATAAAATGCAAAACA 57.731 25.926 0.00 0.00 36.54 2.83
2537 2602 9.749490 CTTGTTTGTGATCAATTCATAAAATGC 57.251 29.630 0.00 0.00 44.07 3.56
2542 2607 7.039853 TGCCTCTTGTTTGTGATCAATTCATAA 60.040 33.333 0.00 0.00 36.54 1.90
2713 2778 2.902486 TCTCAAGCACATCTGAGTTCCT 59.098 45.455 0.00 0.00 0.00 3.36
2828 2893 3.431415 ACAAGCTTTAGGGGACAATTCC 58.569 45.455 0.00 0.00 41.95 3.01
3005 3070 0.251354 TGCAAGCTCTCACCTGATCC 59.749 55.000 0.00 0.00 0.00 3.36
3076 3141 5.040635 ACACAACAATTTTACAGCTTTCCG 58.959 37.500 0.00 0.00 0.00 4.30
3096 3161 0.239347 GCACTGATTGCCTGTGACAC 59.761 55.000 0.00 0.00 46.63 3.67
3170 3235 1.623811 ACAAGAGCTCCTCGGCTTTTA 59.376 47.619 10.93 0.00 43.20 1.52
3331 3396 3.444742 TGGTCGAGTATTTGTATGTCGGT 59.555 43.478 0.00 0.00 0.00 4.69
3376 3441 5.310409 TCTTTTCCTTCTGGTTCATGTCT 57.690 39.130 0.00 0.00 34.23 3.41
3466 3532 6.201044 ACGACAAGATCACTAAGTTCACTTTG 59.799 38.462 0.00 0.00 37.40 2.77
3472 3538 3.987868 TGCACGACAAGATCACTAAGTTC 59.012 43.478 0.00 0.00 0.00 3.01
3478 3544 0.681733 ACCTGCACGACAAGATCACT 59.318 50.000 0.00 0.00 0.00 3.41
3601 3667 0.175989 GGTTGATCGACTCCACCTCC 59.824 60.000 12.89 0.00 36.85 4.30
3791 3857 3.497763 CCAAACCCTACCTTGTCATCACA 60.498 47.826 0.00 0.00 0.00 3.58
3929 4006 4.466828 GAATGCCATTCACCGATTTATCG 58.533 43.478 12.50 5.18 42.85 2.92
4076 4153 9.396022 ACCTGTATTCTGTACTGAATTATTTGG 57.604 33.333 26.71 22.02 37.73 3.28
4094 4172 2.769663 TCAACCGGAGCATACCTGTATT 59.230 45.455 9.46 0.00 0.00 1.89
4196 4276 1.557443 CTTGTGCGTGGTTCGGAGAC 61.557 60.000 0.00 0.00 41.14 3.36
4268 4348 9.283768 TGCTATCTTTGAAGTTTGAATTCAGTA 57.716 29.630 8.41 0.00 37.91 2.74
4301 4381 1.745489 GTGCGTCATCTGGGTTCCC 60.745 63.158 0.12 0.12 0.00 3.97
4361 4441 1.070604 ATGGTCTCCTGGGCATATGG 58.929 55.000 4.56 0.00 0.00 2.74
4368 4448 4.181010 CGGCCATGGTCTCCTGGG 62.181 72.222 15.80 0.00 32.90 4.45
4426 4506 7.201652 GGAGAAAATAATCTGGTGCACTACTTC 60.202 40.741 17.98 7.51 0.00 3.01
4429 4509 5.297029 GGGAGAAAATAATCTGGTGCACTAC 59.703 44.000 17.98 0.83 0.00 2.73
4431 4511 4.273318 GGGAGAAAATAATCTGGTGCACT 58.727 43.478 17.98 0.00 0.00 4.40
4448 4528 3.114606 TGCACATATGAAGAAGGGGAGA 58.885 45.455 10.38 0.00 0.00 3.71
4465 4545 5.401550 ACAATGTTGCTATACAATGTGCAC 58.598 37.500 10.75 10.75 39.87 4.57
4633 4753 4.209866 ATTCATGGCCCCCGCTCC 62.210 66.667 0.00 0.00 34.44 4.70
4637 4757 2.043625 CATTCATTCATGGCCCCCG 58.956 57.895 0.00 0.00 0.00 5.73
4666 4793 7.974730 TGAGATAGATGATATGAGGAGCAAT 57.025 36.000 0.00 0.00 0.00 3.56
4667 4794 7.840210 AGATGAGATAGATGATATGAGGAGCAA 59.160 37.037 0.00 0.00 0.00 3.91
4668 4795 7.355890 AGATGAGATAGATGATATGAGGAGCA 58.644 38.462 0.00 0.00 0.00 4.26
4669 4796 7.503230 TGAGATGAGATAGATGATATGAGGAGC 59.497 40.741 0.00 0.00 0.00 4.70
4671 4798 7.779326 GGTGAGATGAGATAGATGATATGAGGA 59.221 40.741 0.00 0.00 0.00 3.71
4672 4799 7.781219 AGGTGAGATGAGATAGATGATATGAGG 59.219 40.741 0.00 0.00 0.00 3.86
4674 4801 7.779326 GGAGGTGAGATGAGATAGATGATATGA 59.221 40.741 0.00 0.00 0.00 2.15
4675 4802 7.560626 TGGAGGTGAGATGAGATAGATGATATG 59.439 40.741 0.00 0.00 0.00 1.78


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

AutoCloner maintained by Alex Coulton.