Multiple sequence alignment - TraesCS1B01G329300

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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 TraesCS1B01G329300 chr1B 100.000 3039 0 0 1 3039 555292518 555295556 0.000000e+00 5613
1 TraesCS1B01G329300 chr1B 87.852 568 54 6 2472 3039 605475065 605475617 0.000000e+00 652
2 TraesCS1B01G329300 chr1D 88.049 2435 169 55 3 2426 412021892 412024215 0.000000e+00 2772
3 TraesCS1B01G329300 chr1A 88.398 1267 77 26 3 1242 508526080 508527303 0.000000e+00 1461
4 TraesCS1B01G329300 chr1A 87.634 1027 81 28 1270 2282 508527303 508528297 0.000000e+00 1151
5 TraesCS1B01G329300 chr2B 88.376 585 50 7 2472 3039 714797756 714797173 0.000000e+00 688
6 TraesCS1B01G329300 chr2B 87.565 579 54 8 2472 3039 583527651 583527080 0.000000e+00 654
7 TraesCS1B01G329300 chr2B 85.763 590 58 12 2472 3037 737485100 737484513 4.340000e-168 601
8 TraesCS1B01G329300 chr7B 87.973 582 53 7 2472 3037 57696707 57696127 0.000000e+00 671
9 TraesCS1B01G329300 chr3D 86.783 575 59 10 2472 3039 13251629 13252193 2.570000e-175 625
10 TraesCS1B01G329300 chr3D 85.217 575 68 11 2472 3038 174069311 174068746 2.630000e-160 575
11 TraesCS1B01G329300 chr3B 86.644 584 55 10 2472 3039 480369743 480370319 2.570000e-175 625
12 TraesCS1B01G329300 chr3B 85.455 220 32 0 1337 1556 566835209 566834990 2.360000e-56 230
13 TraesCS1B01G329300 chrUn 86.207 580 61 11 2472 3039 238885302 238884730 7.200000e-171 610
14 TraesCS1B01G329300 chr2D 83.562 219 36 0 1340 1558 192156799 192156581 3.970000e-49 206


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 TraesCS1B01G329300 chr1B 555292518 555295556 3038 False 5613 5613 100.000 1 3039 1 chr1B.!!$F1 3038
1 TraesCS1B01G329300 chr1B 605475065 605475617 552 False 652 652 87.852 2472 3039 1 chr1B.!!$F2 567
2 TraesCS1B01G329300 chr1D 412021892 412024215 2323 False 2772 2772 88.049 3 2426 1 chr1D.!!$F1 2423
3 TraesCS1B01G329300 chr1A 508526080 508528297 2217 False 1306 1461 88.016 3 2282 2 chr1A.!!$F1 2279
4 TraesCS1B01G329300 chr2B 714797173 714797756 583 True 688 688 88.376 2472 3039 1 chr2B.!!$R2 567
5 TraesCS1B01G329300 chr2B 583527080 583527651 571 True 654 654 87.565 2472 3039 1 chr2B.!!$R1 567
6 TraesCS1B01G329300 chr2B 737484513 737485100 587 True 601 601 85.763 2472 3037 1 chr2B.!!$R3 565
7 TraesCS1B01G329300 chr7B 57696127 57696707 580 True 671 671 87.973 2472 3037 1 chr7B.!!$R1 565
8 TraesCS1B01G329300 chr3D 13251629 13252193 564 False 625 625 86.783 2472 3039 1 chr3D.!!$F1 567
9 TraesCS1B01G329300 chr3D 174068746 174069311 565 True 575 575 85.217 2472 3038 1 chr3D.!!$R1 566
10 TraesCS1B01G329300 chr3B 480369743 480370319 576 False 625 625 86.644 2472 3039 1 chr3B.!!$F1 567
11 TraesCS1B01G329300 chrUn 238884730 238885302 572 True 610 610 86.207 2472 3039 1 chrUn.!!$R1 567

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
420 433 0.175531 GGATTTTTGGTGCCCGGATG 59.824 55.0 0.73 0.0 0.0 3.51 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2399 2453 0.606401 ATGACCCCGTGACTTTGCAG 60.606 55.0 0.0 0.0 0.0 4.41 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
59 60 2.722201 CGTGTACAGCTCCTCCCCC 61.722 68.421 0.00 0.00 0.00 5.40
173 174 2.158900 CGCCTCTCTCTCTCTCTCTCTT 60.159 54.545 0.00 0.00 0.00 2.85
182 183 5.011090 TCTCTCTCTCTCTTTCTCTCTCG 57.989 47.826 0.00 0.00 0.00 4.04
183 184 3.531538 TCTCTCTCTCTTTCTCTCTCGC 58.468 50.000 0.00 0.00 0.00 5.03
184 185 3.055458 TCTCTCTCTCTTTCTCTCTCGCA 60.055 47.826 0.00 0.00 0.00 5.10
185 186 3.006940 TCTCTCTCTTTCTCTCTCGCAC 58.993 50.000 0.00 0.00 0.00 5.34
186 187 2.088423 TCTCTCTTTCTCTCTCGCACC 58.912 52.381 0.00 0.00 0.00 5.01
187 188 0.805614 TCTCTTTCTCTCTCGCACCG 59.194 55.000 0.00 0.00 0.00 4.94
188 189 0.800300 CTCTTTCTCTCTCGCACCGC 60.800 60.000 0.00 0.00 0.00 5.68
189 190 1.080501 CTTTCTCTCTCGCACCGCA 60.081 57.895 0.00 0.00 0.00 5.69
190 191 1.347817 CTTTCTCTCTCGCACCGCAC 61.348 60.000 0.00 0.00 0.00 5.34
191 192 2.765250 TTTCTCTCTCGCACCGCACC 62.765 60.000 0.00 0.00 0.00 5.01
262 264 1.377612 GGTAACCACCCGCTTTCCT 59.622 57.895 0.00 0.00 39.11 3.36
420 433 0.175531 GGATTTTTGGTGCCCGGATG 59.824 55.000 0.73 0.00 0.00 3.51
424 437 1.175983 TTTTGGTGCCCGGATGTGAC 61.176 55.000 0.73 0.00 0.00 3.67
432 445 1.366111 CCCGGATGTGACGCGATTTT 61.366 55.000 15.93 0.00 0.00 1.82
454 467 1.068832 CTCGATTTCGCGTTCGTGGA 61.069 55.000 21.30 8.06 39.60 4.02
455 468 1.068832 TCGATTTCGCGTTCGTGGAG 61.069 55.000 21.30 3.83 39.60 3.86
456 469 1.342082 CGATTTCGCGTTCGTGGAGT 61.342 55.000 5.77 0.00 36.96 3.85
462 475 1.579932 GCGTTCGTGGAGTCTGAGA 59.420 57.895 0.00 0.00 0.00 3.27
469 482 1.249407 GTGGAGTCTGAGAAGTCGGT 58.751 55.000 0.00 0.00 0.00 4.69
489 502 1.144716 TGGATGAGGCGATCTGTGC 59.855 57.895 0.00 0.00 0.00 4.57
513 526 1.334160 TTAGTTGTCGGCTGGTCAGA 58.666 50.000 1.65 0.00 0.00 3.27
521 534 1.610673 GGCTGGTCAGACTCTGGGA 60.611 63.158 6.20 0.00 32.39 4.37
522 535 1.594310 GCTGGTCAGACTCTGGGAC 59.406 63.158 6.20 0.00 31.51 4.46
598 613 1.126846 GGTTGTTCTCGCGATCTGTTG 59.873 52.381 10.36 0.00 0.00 3.33
602 617 1.014044 TTCTCGCGATCTGTTGTGCC 61.014 55.000 10.36 0.00 0.00 5.01
623 638 5.183331 TGCCAGAACTCCGTATATAGCTTAG 59.817 44.000 0.00 0.00 0.00 2.18
624 639 5.393243 GCCAGAACTCCGTATATAGCTTAGG 60.393 48.000 0.00 0.00 0.00 2.69
629 644 7.670559 AGAACTCCGTATATAGCTTAGGTTGAT 59.329 37.037 0.00 0.00 0.00 2.57
667 682 2.561419 TGGGAGAACTTGGTCTCGTTAG 59.439 50.000 9.27 0.00 44.30 2.34
671 686 2.067013 GAACTTGGTCTCGTTAGTGGC 58.933 52.381 0.00 0.00 0.00 5.01
672 687 1.339097 ACTTGGTCTCGTTAGTGGCT 58.661 50.000 0.00 0.00 0.00 4.75
700 715 2.670905 TGGTTAGATGCGTCGATTTGTG 59.329 45.455 0.00 0.00 0.00 3.33
705 720 1.922135 ATGCGTCGATTTGTGGCACC 61.922 55.000 16.26 0.00 36.31 5.01
762 777 7.901029 AGAGTTTCATCTCTGTTCATCTGTTA 58.099 34.615 0.00 0.00 42.36 2.41
763 778 8.370940 AGAGTTTCATCTCTGTTCATCTGTTAA 58.629 33.333 0.00 0.00 42.36 2.01
765 780 6.951256 TTCATCTCTGTTCATCTGTTAACG 57.049 37.500 0.26 0.00 0.00 3.18
767 782 5.185056 TCATCTCTGTTCATCTGTTAACGGA 59.815 40.000 19.19 19.19 38.38 4.69
770 785 5.060662 TCTGTTCATCTGTTAACGGAGAG 57.939 43.478 21.19 15.95 36.35 3.20
771 786 4.082190 TCTGTTCATCTGTTAACGGAGAGG 60.082 45.833 21.19 11.44 36.35 3.69
772 787 3.576982 TGTTCATCTGTTAACGGAGAGGT 59.423 43.478 21.19 3.02 34.27 3.85
773 788 4.174762 GTTCATCTGTTAACGGAGAGGTC 58.825 47.826 21.19 8.07 34.27 3.85
774 789 3.698289 TCATCTGTTAACGGAGAGGTCT 58.302 45.455 21.19 1.93 34.27 3.85
776 791 2.872732 TCTGTTAACGGAGAGGTCTGT 58.127 47.619 13.25 0.00 44.85 3.41
779 794 4.008330 CTGTTAACGGAGAGGTCTGTAGA 58.992 47.826 8.90 0.00 41.85 2.59
785 800 3.283751 CGGAGAGGTCTGTAGATCTGTT 58.716 50.000 5.18 0.00 35.24 3.16
788 803 4.707448 GGAGAGGTCTGTAGATCTGTTGAA 59.293 45.833 5.18 0.00 35.24 2.69
812 835 2.961522 TTCGTTTTGGTCGATGAAGC 57.038 45.000 0.00 0.00 37.18 3.86
814 837 1.798223 TCGTTTTGGTCGATGAAGCTG 59.202 47.619 0.00 0.00 32.30 4.24
821 844 1.134670 GGTCGATGAAGCTGCTAGGTT 60.135 52.381 0.90 1.09 38.85 3.50
826 849 0.685097 TGAAGCTGCTAGGTTTCGGT 59.315 50.000 0.90 0.00 35.86 4.69
827 850 1.337823 TGAAGCTGCTAGGTTTCGGTC 60.338 52.381 0.90 0.00 35.86 4.79
856 889 2.038837 GTACCTGGTTTGCCTCGGC 61.039 63.158 3.84 0.00 42.35 5.54
866 901 2.670934 GCCTCGGCCCTGCATATG 60.671 66.667 0.00 0.00 34.56 1.78
894 929 7.962934 TTCACTTGTTATTTGTTTCTCAACG 57.037 32.000 0.00 0.00 35.40 4.10
899 934 9.498307 ACTTGTTATTTGTTTCTCAACGTTTAG 57.502 29.630 0.00 0.00 35.40 1.85
925 962 7.707464 GTCATCATTTATTGAATGGCATGTGAA 59.293 33.333 0.00 0.00 44.30 3.18
1067 1104 1.230324 GCCTTCGGTATGCTTCCATC 58.770 55.000 0.00 0.00 32.85 3.51
1068 1105 1.475034 GCCTTCGGTATGCTTCCATCA 60.475 52.381 0.00 0.00 32.85 3.07
1069 1106 2.213499 CCTTCGGTATGCTTCCATCAC 58.787 52.381 0.00 0.00 32.85 3.06
1070 1107 2.158900 CCTTCGGTATGCTTCCATCACT 60.159 50.000 0.00 0.00 32.85 3.41
1071 1108 2.890808 TCGGTATGCTTCCATCACTC 57.109 50.000 0.00 0.00 32.85 3.51
1081 1118 2.336945 TCCATCACTCACATCCATGC 57.663 50.000 0.00 0.00 0.00 4.06
1214 1254 5.378292 TGAGTGTAGTCAGTCACTTGATC 57.622 43.478 2.19 0.00 45.55 2.92
1226 1266 7.335422 GTCAGTCACTTGATCATCCTAAACAAT 59.665 37.037 0.00 0.00 0.00 2.71
1231 1271 7.121168 TCACTTGATCATCCTAAACAATGGTTC 59.879 37.037 0.00 0.00 35.82 3.62
1251 1291 0.323451 GGTGTTCAATCTGGTCCCCC 60.323 60.000 0.00 0.00 0.00 5.40
1253 1293 1.075536 GTGTTCAATCTGGTCCCCCTT 59.924 52.381 0.00 0.00 0.00 3.95
1255 1295 2.225017 TGTTCAATCTGGTCCCCCTTTC 60.225 50.000 0.00 0.00 0.00 2.62
1286 1327 5.164620 TCATGTTGCTCATCTTGACCTTA 57.835 39.130 0.00 0.00 34.09 2.69
1315 1356 3.276857 CATGAGCTCTGCCTACATGTTT 58.723 45.455 16.19 0.00 33.83 2.83
1316 1357 2.977914 TGAGCTCTGCCTACATGTTTC 58.022 47.619 16.19 0.00 0.00 2.78
1562 1603 3.165875 GAGCTAGGCCAGGTATGATACA 58.834 50.000 5.01 0.00 34.30 2.29
1610 1657 3.334583 TTCTCTGCCTGATGTTGGTAC 57.665 47.619 0.00 0.00 0.00 3.34
1625 1672 8.590204 TGATGTTGGTACACTGACTAGAATTTA 58.410 33.333 0.00 0.00 39.29 1.40
1626 1673 9.431887 GATGTTGGTACACTGACTAGAATTTAA 57.568 33.333 0.00 0.00 39.29 1.52
1629 1676 8.709646 GTTGGTACACTGACTAGAATTTAACTG 58.290 37.037 0.00 0.00 39.29 3.16
1694 1742 4.680407 TGCTACTTTCCTAGTCCAGGTAA 58.320 43.478 0.00 0.00 45.71 2.85
1697 1745 5.890419 GCTACTTTCCTAGTCCAGGTAACTA 59.110 44.000 0.00 0.00 45.71 2.24
1698 1746 6.550481 GCTACTTTCCTAGTCCAGGTAACTAT 59.450 42.308 0.00 0.00 45.71 2.12
1699 1747 7.069702 GCTACTTTCCTAGTCCAGGTAACTATT 59.930 40.741 0.00 0.00 45.71 1.73
1721 1769 3.515502 TCGACTTCTCCCAAGATGAACAT 59.484 43.478 0.00 0.00 32.42 2.71
1763 1811 7.474398 AATGTTTCTGTGACTGATCATATCG 57.526 36.000 0.00 0.00 37.14 2.92
1886 1934 4.815269 CCGGCTCTTCTCTATATTGAAGG 58.185 47.826 12.18 6.85 39.85 3.46
1919 1967 0.882927 TATATTGCCGCCCGCTTGTC 60.883 55.000 0.00 0.00 38.78 3.18
1954 2003 2.753989 TGATGCAAGTTGTGTTGTCG 57.246 45.000 4.48 0.00 0.00 4.35
1981 2030 1.586422 ATTATGCTGCTGCTGTACCG 58.414 50.000 17.00 0.00 40.48 4.02
2018 2068 2.959516 TGTCTAAGATGTTGCCGACTG 58.040 47.619 0.00 0.00 0.00 3.51
2096 2147 0.109919 TCGTTGTCGTGATCGTGGAG 60.110 55.000 0.00 0.00 38.33 3.86
2097 2148 1.674611 CGTTGTCGTGATCGTGGAGC 61.675 60.000 0.00 0.00 38.33 4.70
2098 2149 0.388649 GTTGTCGTGATCGTGGAGCT 60.389 55.000 0.00 0.00 38.33 4.09
2145 2196 1.020861 CCTAATGTGCTGCGTGCTGA 61.021 55.000 2.69 0.00 43.37 4.26
2185 2236 3.124921 CGATTCTTGGCCCGCGTT 61.125 61.111 4.92 0.00 0.00 4.84
2219 2270 0.872021 GTAGTCGGCAGAAGCATCCG 60.872 60.000 0.00 0.00 44.61 4.18
2225 2276 2.046023 CAGAAGCATCCGGGCACA 60.046 61.111 0.00 0.00 35.83 4.57
2228 2279 0.539438 AGAAGCATCCGGGCACAAAA 60.539 50.000 0.00 0.00 35.83 2.44
2235 2286 1.403814 TCCGGGCACAAAACAAATCA 58.596 45.000 0.00 0.00 0.00 2.57
2236 2287 1.757118 TCCGGGCACAAAACAAATCAA 59.243 42.857 0.00 0.00 0.00 2.57
2294 2346 2.548920 CCGCTAAGGGGAAGCTTATCTG 60.549 54.545 0.00 0.00 37.91 2.90
2296 2348 3.181465 CGCTAAGGGGAAGCTTATCTGAA 60.181 47.826 0.00 0.00 37.85 3.02
2303 2355 2.224066 GGAAGCTTATCTGAAGGCGCTA 60.224 50.000 7.64 0.00 0.00 4.26
2333 2385 3.270877 CTGTAGTTAACCATGTGCTCCC 58.729 50.000 0.88 0.00 0.00 4.30
2334 2386 2.277084 GTAGTTAACCATGTGCTCCCG 58.723 52.381 0.88 0.00 0.00 5.14
2335 2387 0.676782 AGTTAACCATGTGCTCCCGC 60.677 55.000 0.88 0.00 0.00 6.13
2336 2388 1.743623 TTAACCATGTGCTCCCGCG 60.744 57.895 0.00 0.00 39.65 6.46
2399 2453 6.585322 AGCAAAACTACAGAACGTATAGTCAC 59.415 38.462 0.00 0.00 0.00 3.67
2403 2457 4.698780 ACTACAGAACGTATAGTCACTGCA 59.301 41.667 0.00 0.00 39.22 4.41
2426 2480 1.134560 GTCACGGGGTCATCTACTGTC 59.865 57.143 0.00 0.00 0.00 3.51
2427 2481 1.005569 TCACGGGGTCATCTACTGTCT 59.994 52.381 0.00 0.00 0.00 3.41
2428 2482 2.240414 TCACGGGGTCATCTACTGTCTA 59.760 50.000 0.00 0.00 0.00 2.59
2429 2483 2.358267 CACGGGGTCATCTACTGTCTAC 59.642 54.545 0.00 0.00 0.00 2.59
2430 2484 2.241685 ACGGGGTCATCTACTGTCTACT 59.758 50.000 0.00 0.00 0.00 2.57
2431 2485 2.619177 CGGGGTCATCTACTGTCTACTG 59.381 54.545 0.00 0.00 0.00 2.74
2432 2486 3.684697 CGGGGTCATCTACTGTCTACTGA 60.685 52.174 0.00 0.00 0.00 3.41
2433 2487 4.279145 GGGGTCATCTACTGTCTACTGAA 58.721 47.826 0.00 0.00 0.00 3.02
2434 2488 4.098196 GGGGTCATCTACTGTCTACTGAAC 59.902 50.000 0.00 0.00 0.00 3.18
2435 2489 4.951094 GGGTCATCTACTGTCTACTGAACT 59.049 45.833 0.00 0.00 0.00 3.01
2436 2490 5.066764 GGGTCATCTACTGTCTACTGAACTC 59.933 48.000 0.00 0.00 0.00 3.01
2437 2491 5.648526 GGTCATCTACTGTCTACTGAACTCA 59.351 44.000 0.00 0.00 0.00 3.41
2439 2493 6.596106 GTCATCTACTGTCTACTGAACTCAGA 59.404 42.308 13.61 0.00 46.59 3.27
2440 2494 6.821160 TCATCTACTGTCTACTGAACTCAGAG 59.179 42.308 13.61 0.00 46.59 3.35
2441 2495 4.938832 TCTACTGTCTACTGAACTCAGAGC 59.061 45.833 13.61 1.75 46.59 4.09
2442 2496 3.491342 ACTGTCTACTGAACTCAGAGCA 58.509 45.455 13.61 5.68 46.59 4.26
2443 2497 4.085733 ACTGTCTACTGAACTCAGAGCAT 58.914 43.478 13.61 0.00 46.59 3.79
2444 2498 4.157656 ACTGTCTACTGAACTCAGAGCATC 59.842 45.833 13.61 0.00 46.59 3.91
2515 2570 4.308458 CGTGGGTCCGCCTTGTCA 62.308 66.667 0.00 0.00 34.45 3.58
2535 2590 1.733041 CGAGTCGAGCGCCTTTTCA 60.733 57.895 6.73 0.00 0.00 2.69
2547 2602 1.535226 GCCTTTTCACGCCGTTTCTTT 60.535 47.619 0.00 0.00 0.00 2.52
2548 2603 2.804647 CCTTTTCACGCCGTTTCTTTT 58.195 42.857 0.00 0.00 0.00 2.27
2550 2605 3.430931 CTTTTCACGCCGTTTCTTTTCA 58.569 40.909 0.00 0.00 0.00 2.69
2558 2614 3.732471 CGCCGTTTCTTTTCACTTTTCCA 60.732 43.478 0.00 0.00 0.00 3.53
2559 2615 4.177783 GCCGTTTCTTTTCACTTTTCCAA 58.822 39.130 0.00 0.00 0.00 3.53
2573 2630 0.699577 TTCCAACACTCCCCTCCCAA 60.700 55.000 0.00 0.00 0.00 4.12
2576 2633 1.638589 CCAACACTCCCCTCCCAATTA 59.361 52.381 0.00 0.00 0.00 1.40
2591 2648 2.238898 CCAATTACTCCTTTCCTCCCGT 59.761 50.000 0.00 0.00 0.00 5.28
2740 2819 2.175811 GGCATGTCAAACGCCGAC 59.824 61.111 0.00 0.00 35.79 4.79
2785 2864 3.515286 GCCGTCATCTCCGACCGA 61.515 66.667 0.00 0.00 31.91 4.69
2797 2876 3.692406 GACCGACGGAACAGGGCT 61.692 66.667 23.38 0.00 0.00 5.19
2803 2882 4.069232 CGGAACAGGGCTCTCGCA 62.069 66.667 0.00 0.00 38.10 5.10
2918 3016 2.764637 GAATCCCCTGGCAACCACGT 62.765 60.000 0.00 0.00 0.00 4.49
3033 3138 4.765273 GGTTCAACCCAAACATCACTTTT 58.235 39.130 0.00 0.00 30.04 2.27
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
7 8 2.100879 GATTCCCTCCGACCCATCCG 62.101 65.000 0.00 0.00 0.00 4.18
59 60 2.079170 TATGCAGAGAGAGGGACAGG 57.921 55.000 0.00 0.00 0.00 4.00
60 61 2.364970 CCTTATGCAGAGAGAGGGACAG 59.635 54.545 0.00 0.00 0.00 3.51
61 62 2.392662 CCTTATGCAGAGAGAGGGACA 58.607 52.381 0.00 0.00 0.00 4.02
62 63 1.069978 GCCTTATGCAGAGAGAGGGAC 59.930 57.143 0.00 0.00 40.77 4.46
63 64 1.418334 GCCTTATGCAGAGAGAGGGA 58.582 55.000 0.00 0.00 40.77 4.20
173 174 2.258591 GTGCGGTGCGAGAGAGAA 59.741 61.111 0.00 0.00 0.00 2.87
262 264 0.032952 CGCGGATTTAATCGGGGAGA 59.967 55.000 19.52 0.00 42.54 3.71
351 355 0.320073 CTCCGGAAACACTAACCGCA 60.320 55.000 5.23 0.00 44.45 5.69
432 445 1.123576 CACGAACGCGAAATCGAGAAA 59.876 47.619 29.28 0.00 41.67 2.52
454 467 0.962489 CCACACCGACTTCTCAGACT 59.038 55.000 0.00 0.00 0.00 3.24
455 468 0.959553 TCCACACCGACTTCTCAGAC 59.040 55.000 0.00 0.00 0.00 3.51
456 469 1.546029 CATCCACACCGACTTCTCAGA 59.454 52.381 0.00 0.00 0.00 3.27
462 475 1.296715 GCCTCATCCACACCGACTT 59.703 57.895 0.00 0.00 0.00 3.01
469 482 0.176449 CACAGATCGCCTCATCCACA 59.824 55.000 0.00 0.00 0.00 4.17
489 502 1.296056 CCAGCCGACAACTAAACCGG 61.296 60.000 0.00 0.00 44.34 5.28
513 526 5.251700 ACCAAGATAAGAAATGTCCCAGAGT 59.748 40.000 0.00 0.00 0.00 3.24
548 563 9.687210 GATCCGTAAAAATAATAATTCCCCAAC 57.313 33.333 0.00 0.00 0.00 3.77
560 575 6.988622 ACAACCATCGATCCGTAAAAATAA 57.011 33.333 0.00 0.00 0.00 1.40
562 577 5.646360 AGAACAACCATCGATCCGTAAAAAT 59.354 36.000 0.00 0.00 0.00 1.82
598 613 3.256136 AGCTATATACGGAGTTCTGGCAC 59.744 47.826 0.00 0.00 37.78 5.01
602 617 6.821031 ACCTAAGCTATATACGGAGTTCTG 57.179 41.667 0.00 0.00 37.78 3.02
623 638 3.491934 CGAACGAATCGCATCAACC 57.508 52.632 1.15 0.00 45.89 3.77
667 682 2.507407 TCTAACCATTTCCCAGCCAC 57.493 50.000 0.00 0.00 0.00 5.01
671 686 2.614057 GACGCATCTAACCATTTCCCAG 59.386 50.000 0.00 0.00 0.00 4.45
672 687 2.639065 GACGCATCTAACCATTTCCCA 58.361 47.619 0.00 0.00 0.00 4.37
700 715 3.945434 CGAGATGCGCATGGTGCC 61.945 66.667 30.76 13.17 41.12 5.01
705 720 0.602106 AGGAATCCGAGATGCGCATG 60.602 55.000 30.76 13.79 39.11 4.06
734 749 4.543590 TGAACAGAGATGAAACTCTCCC 57.456 45.455 0.00 0.00 44.18 4.30
762 777 3.283751 CAGATCTACAGACCTCTCCGTT 58.716 50.000 0.00 0.00 0.00 4.44
763 778 2.240160 ACAGATCTACAGACCTCTCCGT 59.760 50.000 0.00 0.00 0.00 4.69
765 780 4.274147 TCAACAGATCTACAGACCTCTCC 58.726 47.826 0.00 0.00 0.00 3.71
767 782 5.184864 CAGTTCAACAGATCTACAGACCTCT 59.815 44.000 0.00 0.00 0.00 3.69
768 783 5.047660 ACAGTTCAACAGATCTACAGACCTC 60.048 44.000 0.00 0.00 0.00 3.85
769 784 4.835615 ACAGTTCAACAGATCTACAGACCT 59.164 41.667 0.00 0.00 0.00 3.85
770 785 5.140747 ACAGTTCAACAGATCTACAGACC 57.859 43.478 0.00 0.00 0.00 3.85
771 786 6.129062 CGAAACAGTTCAACAGATCTACAGAC 60.129 42.308 0.00 0.00 32.89 3.51
772 787 5.920840 CGAAACAGTTCAACAGATCTACAGA 59.079 40.000 0.00 0.00 32.89 3.41
773 788 5.692204 ACGAAACAGTTCAACAGATCTACAG 59.308 40.000 0.00 0.00 32.89 2.74
774 789 5.597806 ACGAAACAGTTCAACAGATCTACA 58.402 37.500 0.00 0.00 32.89 2.74
776 791 7.406553 CAAAACGAAACAGTTCAACAGATCTA 58.593 34.615 0.00 0.00 32.89 1.98
779 794 5.105917 ACCAAAACGAAACAGTTCAACAGAT 60.106 36.000 0.00 0.00 32.89 2.90
785 800 3.001414 TCGACCAAAACGAAACAGTTCA 58.999 40.909 0.00 0.00 36.84 3.18
788 803 3.199677 TCATCGACCAAAACGAAACAGT 58.800 40.909 0.00 0.00 42.80 3.55
812 835 0.741221 GCCTGACCGAAACCTAGCAG 60.741 60.000 0.00 0.00 0.00 4.24
814 837 0.107654 ATGCCTGACCGAAACCTAGC 60.108 55.000 0.00 0.00 0.00 3.42
821 844 0.616395 TACCCTCATGCCTGACCGAA 60.616 55.000 0.00 0.00 0.00 4.30
851 884 2.670934 GCCATATGCAGGGCCGAG 60.671 66.667 14.18 0.00 46.15 4.63
856 889 2.062971 AGTGAAAGCCATATGCAGGG 57.937 50.000 0.00 0.00 44.83 4.45
866 901 6.978080 TGAGAAACAAATAACAAGTGAAAGCC 59.022 34.615 0.00 0.00 0.00 4.35
894 929 9.754382 ATGCCATTCAATAAATGATGACTAAAC 57.246 29.630 0.00 0.00 46.54 2.01
899 934 7.204604 TCACATGCCATTCAATAAATGATGAC 58.795 34.615 0.00 0.00 46.54 3.06
925 962 3.553508 GCTGCACAAAATCACAACATCCT 60.554 43.478 0.00 0.00 0.00 3.24
1067 1104 1.471287 CAACAGGCATGGATGTGAGTG 59.529 52.381 2.31 0.00 0.00 3.51
1068 1105 1.830279 CAACAGGCATGGATGTGAGT 58.170 50.000 2.31 0.00 0.00 3.41
1069 1106 0.454600 GCAACAGGCATGGATGTGAG 59.545 55.000 2.31 0.00 43.97 3.51
1070 1107 2.570365 GCAACAGGCATGGATGTGA 58.430 52.632 2.31 0.00 43.97 3.58
1081 1118 6.255020 GCATTTATTTCATGAGAAGCAACAGG 59.745 38.462 0.00 0.00 34.71 4.00
1184 1223 5.179555 GTGACTGACTACACTCAAATTTCCC 59.820 44.000 0.00 0.00 34.65 3.97
1214 1254 3.756434 ACACCGAACCATTGTTTAGGATG 59.244 43.478 10.66 8.20 36.58 3.51
1226 1266 1.142060 ACCAGATTGAACACCGAACCA 59.858 47.619 0.00 0.00 0.00 3.67
1231 1271 2.854522 GGGACCAGATTGAACACCG 58.145 57.895 0.00 0.00 0.00 4.94
1278 1319 6.607600 AGAGCTCATGTACATACTAAGGTCAA 59.392 38.462 24.95 0.00 0.00 3.18
1286 1327 3.303938 AGGCAGAGCTCATGTACATACT 58.696 45.455 17.77 6.48 0.00 2.12
1330 1371 4.082125 CAGCAAAAGGATCTACAAAGGGT 58.918 43.478 0.00 0.00 0.00 4.34
1331 1372 4.335416 TCAGCAAAAGGATCTACAAAGGG 58.665 43.478 0.00 0.00 0.00 3.95
1562 1603 4.722700 ATTGAAGCACGGCCGGCT 62.723 61.111 31.76 29.81 45.15 5.52
1610 1657 6.646653 TGCAGACAGTTAAATTCTAGTCAGTG 59.353 38.462 0.00 0.00 0.00 3.66
1625 1672 2.775890 CTGAATGACCTGCAGACAGTT 58.224 47.619 17.39 10.71 42.81 3.16
1626 1673 1.610102 GCTGAATGACCTGCAGACAGT 60.610 52.381 17.39 14.12 42.81 3.55
1629 1676 1.736681 GAAGCTGAATGACCTGCAGAC 59.263 52.381 17.39 9.61 34.07 3.51
1694 1742 4.956700 TCATCTTGGGAGAAGTCGAATAGT 59.043 41.667 0.00 0.00 35.07 2.12
1697 1745 4.020218 TGTTCATCTTGGGAGAAGTCGAAT 60.020 41.667 0.00 0.00 35.07 3.34
1698 1746 3.323691 TGTTCATCTTGGGAGAAGTCGAA 59.676 43.478 0.00 0.00 35.07 3.71
1699 1747 2.897326 TGTTCATCTTGGGAGAAGTCGA 59.103 45.455 0.00 0.00 35.07 4.20
1704 1752 8.054572 TGATAAATGATGTTCATCTTGGGAGAA 58.945 33.333 12.94 0.00 35.76 2.87
1708 1756 8.857098 AGAATGATAAATGATGTTCATCTTGGG 58.143 33.333 12.94 0.00 35.76 4.12
1709 1757 9.678941 CAGAATGATAAATGATGTTCATCTTGG 57.321 33.333 12.94 0.00 39.69 3.61
1763 1811 2.866156 GCCTTTGCAAAACAGAAAGGAC 59.134 45.455 13.84 2.16 45.93 3.85
1868 1916 7.548780 GCCTTATGCCTTCAATATAGAGAAGAG 59.451 40.741 15.07 8.68 42.95 2.85
1886 1934 6.403636 GGCGGCAATATATATATGCCTTATGC 60.404 42.308 27.73 24.51 42.98 3.14
1919 1967 2.663879 GCATCAAGCAAGACACAGTTCG 60.664 50.000 0.00 0.00 44.79 3.95
1954 2003 2.818432 AGCAGCAGCATAATAATCAGGC 59.182 45.455 3.17 0.00 45.49 4.85
1981 2030 7.217200 TCTTAGACAAACCATACTGATATGCC 58.783 38.462 0.00 0.00 37.46 4.40
2018 2068 6.492254 AGCCAAACGATACGGATTTTTATTC 58.508 36.000 0.00 0.00 0.00 1.75
2096 2147 2.990514 ACGAACAACCAAACAAACAAGC 59.009 40.909 0.00 0.00 0.00 4.01
2097 2148 4.323336 CAGACGAACAACCAAACAAACAAG 59.677 41.667 0.00 0.00 0.00 3.16
2098 2149 4.023107 TCAGACGAACAACCAAACAAACAA 60.023 37.500 0.00 0.00 0.00 2.83
2185 2236 2.669113 CGACTACGGATCCGACAAAACA 60.669 50.000 39.55 13.82 42.83 2.83
2219 2270 4.893608 ACCTATTGATTTGTTTTGTGCCC 58.106 39.130 0.00 0.00 0.00 5.36
2225 2276 5.240623 TGTCTGCGACCTATTGATTTGTTTT 59.759 36.000 6.30 0.00 0.00 2.43
2228 2279 3.937814 TGTCTGCGACCTATTGATTTGT 58.062 40.909 6.30 0.00 0.00 2.83
2251 2303 1.087501 TGGTCTCAGATGACTCGTCG 58.912 55.000 0.00 0.00 37.16 5.12
2294 2346 1.874466 GTGTCGAGCTAGCGCCTTC 60.874 63.158 13.17 2.15 36.60 3.46
2296 2348 2.752238 AGTGTCGAGCTAGCGCCT 60.752 61.111 13.17 0.91 36.60 5.52
2303 2355 2.889045 TGGTTAACTACAGTGTCGAGCT 59.111 45.455 0.00 0.00 0.00 4.09
2333 2385 3.476646 CTGAGAGCAGTGCACGCG 61.477 66.667 19.20 3.53 37.37 6.01
2334 2386 1.018226 AATCTGAGAGCAGTGCACGC 61.018 55.000 19.20 20.97 42.84 5.34
2335 2387 0.997932 GAATCTGAGAGCAGTGCACG 59.002 55.000 19.20 7.77 42.84 5.34
2336 2388 1.338484 TGGAATCTGAGAGCAGTGCAC 60.338 52.381 19.20 9.40 42.84 4.57
2338 2390 2.105006 TTGGAATCTGAGAGCAGTGC 57.895 50.000 7.13 7.13 42.84 4.40
2339 2391 2.414481 CGTTTGGAATCTGAGAGCAGTG 59.586 50.000 0.00 0.00 42.84 3.66
2340 2392 2.037772 ACGTTTGGAATCTGAGAGCAGT 59.962 45.455 0.00 0.00 42.84 4.40
2341 2393 2.693069 ACGTTTGGAATCTGAGAGCAG 58.307 47.619 0.00 0.00 43.67 4.24
2342 2394 2.839486 ACGTTTGGAATCTGAGAGCA 57.161 45.000 0.00 0.00 0.00 4.26
2343 2395 5.351465 TGATTAACGTTTGGAATCTGAGAGC 59.649 40.000 18.34 0.00 32.01 4.09
2344 2396 6.968131 TGATTAACGTTTGGAATCTGAGAG 57.032 37.500 18.34 0.00 32.01 3.20
2345 2397 7.278646 CAGATGATTAACGTTTGGAATCTGAGA 59.721 37.037 24.66 9.00 41.35 3.27
2347 2399 6.878923 ACAGATGATTAACGTTTGGAATCTGA 59.121 34.615 30.11 13.72 41.35 3.27
2399 2453 0.606401 ATGACCCCGTGACTTTGCAG 60.606 55.000 0.00 0.00 0.00 4.41
2403 2457 2.233922 CAGTAGATGACCCCGTGACTTT 59.766 50.000 0.00 0.00 0.00 2.66
2426 2480 3.953612 AGGAGATGCTCTGAGTTCAGTAG 59.046 47.826 6.53 6.63 44.12 2.57
2427 2481 3.698539 CAGGAGATGCTCTGAGTTCAGTA 59.301 47.826 6.53 0.00 44.12 2.74
2428 2482 2.496871 CAGGAGATGCTCTGAGTTCAGT 59.503 50.000 6.53 0.00 44.12 3.41
2429 2483 3.167921 CAGGAGATGCTCTGAGTTCAG 57.832 52.381 6.53 2.69 45.08 3.02
2455 2509 2.672996 CCGTTCTGCCTGTTGGGG 60.673 66.667 0.00 0.00 35.12 4.96
2456 2510 2.672996 CCCGTTCTGCCTGTTGGG 60.673 66.667 0.00 0.00 38.36 4.12
2457 2511 2.672996 CCCCGTTCTGCCTGTTGG 60.673 66.667 0.00 0.00 0.00 3.77
2458 2512 3.365265 GCCCCGTTCTGCCTGTTG 61.365 66.667 0.00 0.00 0.00 3.33
2510 2565 2.126850 CGCTCGACTCGCTGACAA 60.127 61.111 0.00 0.00 0.00 3.18
2531 2586 2.420722 AGTGAAAAGAAACGGCGTGAAA 59.579 40.909 15.70 0.00 0.00 2.69
2535 2590 3.431856 GAAAAGTGAAAAGAAACGGCGT 58.568 40.909 6.77 6.77 0.00 5.68
2547 2602 2.243736 AGGGGAGTGTTGGAAAAGTGAA 59.756 45.455 0.00 0.00 0.00 3.18
2548 2603 1.850345 AGGGGAGTGTTGGAAAAGTGA 59.150 47.619 0.00 0.00 0.00 3.41
2550 2605 1.145119 GGAGGGGAGTGTTGGAAAAGT 59.855 52.381 0.00 0.00 0.00 2.66
2558 2614 2.576648 GAGTAATTGGGAGGGGAGTGTT 59.423 50.000 0.00 0.00 0.00 3.32
2559 2615 2.197465 GAGTAATTGGGAGGGGAGTGT 58.803 52.381 0.00 0.00 0.00 3.55
2573 2630 2.829023 TGACGGGAGGAAAGGAGTAAT 58.171 47.619 0.00 0.00 0.00 1.89
2576 2633 1.555533 GAATGACGGGAGGAAAGGAGT 59.444 52.381 0.00 0.00 0.00 3.85
2591 2648 2.127869 CGAGCGGGAGGGAGAATGA 61.128 63.158 0.00 0.00 0.00 2.57
2628 2687 1.080025 GCGTACTTCTTCGGTGGCT 60.080 57.895 0.00 0.00 0.00 4.75
2740 2819 0.250513 GCTGTACTTCCACCCTCCAG 59.749 60.000 0.00 0.00 0.00 3.86
2797 2876 2.047274 CGGGCCTTCTTTGCGAGA 60.047 61.111 0.84 0.00 0.00 4.04
2803 2882 1.164041 CGTTGTCACGGGCCTTCTTT 61.164 55.000 0.84 0.00 43.16 2.52
2907 3005 1.890041 GTACTGCACGTGGTTGCCA 60.890 57.895 18.88 5.11 42.25 4.92


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

AutoCloner maintained by Alex Coulton.