Multiple sequence alignment - TraesCS2B01G442100

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 TraesCS2B01G442100 chr2B 100.000 2537 0 0 1 2537 634643014 634645550 0.000000e+00 4686
1 TraesCS2B01G442100 chr2B 92.786 499 33 3 1049 1547 776645725 776645230 0.000000e+00 719
2 TraesCS2B01G442100 chr3A 97.614 1006 22 2 46 1049 37195935 37194930 0.000000e+00 1724
3 TraesCS2B01G442100 chr6B 97.154 1019 25 4 33 1047 29864494 29863476 0.000000e+00 1718
4 TraesCS2B01G442100 chr6B 97.237 941 24 2 109 1047 679575363 679576303 0.000000e+00 1592
5 TraesCS2B01G442100 chr6B 97.237 941 24 2 109 1047 679606221 679607161 0.000000e+00 1592
6 TraesCS2B01G442100 chr6B 97.062 885 24 2 109 991 679590775 679591659 0.000000e+00 1489
7 TraesCS2B01G442100 chr6B 78.333 180 19 9 1671 1849 33038621 33038781 5.780000e-17 99
8 TraesCS2B01G442100 chr1A 95.976 1019 23 5 33 1047 71427163 71426159 0.000000e+00 1639
9 TraesCS2B01G442100 chr3B 93.032 1019 39 8 33 1047 131530111 131529121 0.000000e+00 1459
10 TraesCS2B01G442100 chr7A 97.486 716 13 5 9 720 686665898 686665184 0.000000e+00 1218
11 TraesCS2B01G442100 chr7A 97.582 703 7 5 9 707 696177581 696176885 0.000000e+00 1195
12 TraesCS2B01G442100 chr7A 91.952 497 39 1 1048 1543 151328062 151327566 0.000000e+00 695
13 TraesCS2B01G442100 chrUn 97.730 705 14 2 17 720 400835846 400836549 0.000000e+00 1212
14 TraesCS2B01G442100 chr5D 89.890 821 40 14 1048 1829 515094262 515093446 0.000000e+00 1016
15 TraesCS2B01G442100 chr5D 94.779 498 25 1 1048 1545 515039622 515039126 0.000000e+00 774
16 TraesCS2B01G442100 chr7B 93.889 540 30 2 509 1047 403034154 403034691 0.000000e+00 811
17 TraesCS2B01G442100 chr7B 91.200 500 44 0 1048 1547 113445503 113445004 0.000000e+00 680
18 TraesCS2B01G442100 chr5A 95.984 498 19 1 1048 1545 643312011 643311515 0.000000e+00 808
19 TraesCS2B01G442100 chr2D 95.391 499 23 0 1048 1546 534129441 534129939 0.000000e+00 795
20 TraesCS2B01G442100 chr2D 91.583 499 41 1 1048 1546 534122970 534123467 0.000000e+00 688
21 TraesCS2B01G442100 chr2D 85.816 564 34 12 1991 2537 534130402 534130936 7.930000e-155 556
22 TraesCS2B01G442100 chr2D 89.688 320 30 2 1671 1990 534130043 534130359 3.040000e-109 405
23 TraesCS2B01G442100 chr3D 92.555 497 28 2 1048 1544 594958330 594957843 0.000000e+00 704


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 TraesCS2B01G442100 chr2B 634643014 634645550 2536 False 4686.000000 4686 100.000000 1 2537 1 chr2B.!!$F1 2536
1 TraesCS2B01G442100 chr3A 37194930 37195935 1005 True 1724.000000 1724 97.614000 46 1049 1 chr3A.!!$R1 1003
2 TraesCS2B01G442100 chr6B 29863476 29864494 1018 True 1718.000000 1718 97.154000 33 1047 1 chr6B.!!$R1 1014
3 TraesCS2B01G442100 chr6B 679575363 679576303 940 False 1592.000000 1592 97.237000 109 1047 1 chr6B.!!$F2 938
4 TraesCS2B01G442100 chr6B 679606221 679607161 940 False 1592.000000 1592 97.237000 109 1047 1 chr6B.!!$F4 938
5 TraesCS2B01G442100 chr6B 679590775 679591659 884 False 1489.000000 1489 97.062000 109 991 1 chr6B.!!$F3 882
6 TraesCS2B01G442100 chr1A 71426159 71427163 1004 True 1639.000000 1639 95.976000 33 1047 1 chr1A.!!$R1 1014
7 TraesCS2B01G442100 chr3B 131529121 131530111 990 True 1459.000000 1459 93.032000 33 1047 1 chr3B.!!$R1 1014
8 TraesCS2B01G442100 chr7A 686665184 686665898 714 True 1218.000000 1218 97.486000 9 720 1 chr7A.!!$R2 711
9 TraesCS2B01G442100 chr7A 696176885 696177581 696 True 1195.000000 1195 97.582000 9 707 1 chr7A.!!$R3 698
10 TraesCS2B01G442100 chrUn 400835846 400836549 703 False 1212.000000 1212 97.730000 17 720 1 chrUn.!!$F1 703
11 TraesCS2B01G442100 chr5D 515093446 515094262 816 True 1016.000000 1016 89.890000 1048 1829 1 chr5D.!!$R2 781
12 TraesCS2B01G442100 chr7B 403034154 403034691 537 False 811.000000 811 93.889000 509 1047 1 chr7B.!!$F1 538
13 TraesCS2B01G442100 chr2D 534129441 534130936 1495 False 585.333333 795 90.298333 1048 2537 3 chr2D.!!$F2 1489

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
571 593 0.839853 AGGAGAAACCAGGAGCTGCT 60.84 55.0 0.0 0.0 42.04 4.24 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1955 2057 0.033504 GTCGGCTTCAAGACCAGTGA 59.966 55.0 0.0 0.0 0.0 3.41 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
571 593 0.839853 AGGAGAAACCAGGAGCTGCT 60.840 55.000 0.00 0.00 42.04 4.24
619 641 1.217882 CCGTCGGCATAGATTTCCAC 58.782 55.000 0.00 0.00 0.00 4.02
836 859 3.321967 GGAAAACAACGCCGACGA 58.678 55.556 0.00 0.00 43.93 4.20
1086 1109 0.984230 AATTTCAGGTCGAGGAGGCA 59.016 50.000 0.00 0.00 0.00 4.75
1186 1209 3.370104 GACTCCAAGATCCTCTCCAAGA 58.630 50.000 0.00 0.00 0.00 3.02
1240 1263 4.323477 CCAAACCGGCCGACTCCA 62.323 66.667 30.73 0.00 0.00 3.86
1278 1301 1.901085 CTCCACCACCTCTACTGCC 59.099 63.158 0.00 0.00 0.00 4.85
1324 1347 0.944311 GAGCTTTGACGCCGAGTTCA 60.944 55.000 0.00 0.00 0.00 3.18
1339 1362 2.231478 GAGTTCATCAAGGTCGACCAGA 59.769 50.000 35.00 29.86 38.89 3.86
1340 1363 2.632996 AGTTCATCAAGGTCGACCAGAA 59.367 45.455 35.00 24.42 38.89 3.02
1413 1436 1.546476 CTCGACCTTACTTGCCAGACT 59.454 52.381 0.00 0.00 0.00 3.24
1434 1457 1.133790 GTTGCAGACATGATCAAGGGC 59.866 52.381 0.00 1.99 0.00 5.19
1541 1564 4.524328 CCAGTGGGCTTTTGAGTAGAAAAT 59.476 41.667 0.00 0.00 0.00 1.82
1546 1601 7.724061 AGTGGGCTTTTGAGTAGAAAATAGAAA 59.276 33.333 0.00 0.00 0.00 2.52
1609 1675 4.037089 TCGTATGTCGCTGCCTTTTCTATA 59.963 41.667 0.00 0.00 39.67 1.31
1615 1681 2.405357 CGCTGCCTTTTCTATATCGTCG 59.595 50.000 0.00 0.00 0.00 5.12
1634 1700 3.073678 TCGTAGTGCTAGTGGTCGTAAA 58.926 45.455 0.00 0.00 0.00 2.01
1641 1707 6.273825 AGTGCTAGTGGTCGTAAATATTCTG 58.726 40.000 0.00 0.00 0.00 3.02
1647 1713 5.657302 AGTGGTCGTAAATATTCTGGAGTCT 59.343 40.000 0.00 0.00 0.00 3.24
1652 1718 7.167136 GGTCGTAAATATTCTGGAGTCTAAACG 59.833 40.741 0.00 0.00 0.00 3.60
1657 1723 3.996150 TTCTGGAGTCTAAACGTCGTT 57.004 42.857 4.40 4.40 0.00 3.85
1667 1733 2.867456 AAACGTCGTTTATTCCTGCG 57.133 45.000 21.29 0.00 33.70 5.18
1668 1734 1.787012 AACGTCGTTTATTCCTGCGT 58.213 45.000 4.40 0.00 0.00 5.24
1720 1822 1.375551 AGTGGACGTTTTGCTTCGTT 58.624 45.000 0.00 0.00 40.39 3.85
1728 1830 5.103290 ACGTTTTGCTTCGTTACATCATT 57.897 34.783 0.00 0.00 36.93 2.57
1736 1838 5.291858 TGCTTCGTTACATCATTCTTAGCTG 59.708 40.000 0.00 0.00 0.00 4.24
1760 1862 6.072783 TGTGATTTATGCGTGTGATTTGAGAA 60.073 34.615 0.00 0.00 0.00 2.87
1768 1870 6.038985 TGCGTGTGATTTGAGAAATTTTTGA 58.961 32.000 0.00 0.00 0.00 2.69
1770 1872 6.019961 GCGTGTGATTTGAGAAATTTTTGACA 60.020 34.615 0.00 0.00 0.00 3.58
1854 1956 5.172934 GCATGATTTTCATTTGGCTTCAGA 58.827 37.500 0.00 0.00 34.28 3.27
1858 1960 7.177832 TGATTTTCATTTGGCTTCAGATCAT 57.822 32.000 0.00 0.00 0.00 2.45
1870 1972 5.357878 GGCTTCAGATCATATTTTGTGACCA 59.642 40.000 0.00 0.00 0.00 4.02
1884 1986 3.073678 TGTGACCATTGGAATCTCAACG 58.926 45.455 10.37 0.00 0.00 4.10
1912 2014 2.648724 GCATTTGTCCATCGCGCG 60.649 61.111 26.76 26.76 0.00 6.86
1916 2018 2.852495 ATTTGTCCATCGCGCGGAGT 62.852 55.000 31.69 13.88 31.65 3.85
1955 2057 3.564053 TTGTTTCGGGTTACAGGTCTT 57.436 42.857 0.00 0.00 0.00 3.01
1968 2070 2.771943 ACAGGTCTTCACTGGTCTTGAA 59.228 45.455 0.00 0.00 40.23 2.69
1972 2074 1.151668 CTTCACTGGTCTTGAAGCCG 58.848 55.000 0.00 0.00 42.58 5.52
1986 2088 4.410400 GCCGACCAGGTCCCCAAG 62.410 72.222 14.46 0.00 43.70 3.61
2008 2152 2.491022 GGCGCCGAGAGACAGGTAT 61.491 63.158 12.58 0.00 0.00 2.73
2014 2158 1.331138 CCGAGAGACAGGTATGACGAC 59.669 57.143 0.00 0.00 0.00 4.34
2040 2184 4.351938 CCCGACGTCCGTGCTCAA 62.352 66.667 10.58 0.00 36.31 3.02
2097 2250 1.571919 GAGCGCCGTCATTCAGTATT 58.428 50.000 2.29 0.00 0.00 1.89
2101 2254 2.034001 GCGCCGTCATTCAGTATTGTAC 60.034 50.000 0.00 0.00 0.00 2.90
2158 2311 4.020307 TCAAGCATGTGACATTCCACTAGA 60.020 41.667 0.00 0.00 37.89 2.43
2161 2314 4.019860 AGCATGTGACATTCCACTAGAACT 60.020 41.667 0.00 0.00 37.29 3.01
2166 2319 5.773176 TGTGACATTCCACTAGAACTACTCA 59.227 40.000 0.00 0.00 37.29 3.41
2167 2320 6.437477 TGTGACATTCCACTAGAACTACTCAT 59.563 38.462 0.00 0.00 37.29 2.90
2171 2324 7.036220 ACATTCCACTAGAACTACTCATTTCG 58.964 38.462 0.00 0.00 37.29 3.46
2220 2375 4.141274 TGTGATGGACATTATTCCGGGATT 60.141 41.667 0.00 0.00 38.69 3.01
2221 2376 4.455877 GTGATGGACATTATTCCGGGATTC 59.544 45.833 0.00 0.00 38.69 2.52
2225 2380 2.737252 GACATTATTCCGGGATTCGCTC 59.263 50.000 0.00 0.00 37.59 5.03
2233 2388 1.409412 CGGGATTCGCTCATAACTCG 58.591 55.000 0.00 0.00 0.00 4.18
2287 2442 4.290155 CAAAACACAAACTAATGCGCTCT 58.710 39.130 9.73 0.00 0.00 4.09
2288 2443 3.542712 AACACAAACTAATGCGCTCTG 57.457 42.857 9.73 0.00 0.00 3.35
2289 2444 2.766313 ACACAAACTAATGCGCTCTGA 58.234 42.857 9.73 0.00 0.00 3.27
2290 2445 2.738846 ACACAAACTAATGCGCTCTGAG 59.261 45.455 9.73 0.00 0.00 3.35
2291 2446 2.094894 CACAAACTAATGCGCTCTGAGG 59.905 50.000 9.73 0.00 0.00 3.86
2292 2447 1.063174 CAAACTAATGCGCTCTGAGGC 59.937 52.381 9.73 8.77 0.00 4.70
2293 2448 0.462759 AACTAATGCGCTCTGAGGCC 60.463 55.000 9.73 0.00 0.00 5.19
2294 2449 1.144716 CTAATGCGCTCTGAGGCCA 59.855 57.895 9.73 0.92 0.00 5.36
2295 2450 1.153369 TAATGCGCTCTGAGGCCAC 60.153 57.895 9.73 0.00 0.00 5.01
2296 2451 1.617018 TAATGCGCTCTGAGGCCACT 61.617 55.000 9.73 0.00 0.00 4.00
2297 2452 3.677284 ATGCGCTCTGAGGCCACTG 62.677 63.158 9.73 2.33 0.00 3.66
2298 2453 4.074526 GCGCTCTGAGGCCACTGA 62.075 66.667 5.01 7.67 0.00 3.41
2299 2454 2.659016 CGCTCTGAGGCCACTGAA 59.341 61.111 5.01 0.00 0.00 3.02
2300 2455 1.447489 CGCTCTGAGGCCACTGAAG 60.447 63.158 5.01 1.66 0.00 3.02
2301 2456 1.078567 GCTCTGAGGCCACTGAAGG 60.079 63.158 5.01 0.00 0.00 3.46
2319 2474 3.208747 AGGTGTTTTGGACCTACAGTG 57.791 47.619 0.00 0.00 42.35 3.66
2330 2485 3.508793 GGACCTACAGTGCTACTTGTGTA 59.491 47.826 0.00 0.00 33.19 2.90
2331 2486 4.380655 GGACCTACAGTGCTACTTGTGTAG 60.381 50.000 0.00 0.00 46.59 2.74
2332 2487 4.150359 ACCTACAGTGCTACTTGTGTAGT 58.850 43.478 7.40 0.00 45.84 2.73
2333 2488 4.587684 ACCTACAGTGCTACTTGTGTAGTT 59.412 41.667 7.40 0.00 45.84 2.24
2334 2489 4.923871 CCTACAGTGCTACTTGTGTAGTTG 59.076 45.833 7.40 4.76 45.84 3.16
2335 2490 4.402056 ACAGTGCTACTTGTGTAGTTGT 57.598 40.909 5.31 5.25 45.84 3.32
2343 2498 6.821665 TGCTACTTGTGTAGTTGTTTCTCTTT 59.178 34.615 5.31 0.00 45.84 2.52
2348 2503 8.448615 ACTTGTGTAGTTGTTTCTCTTTTGTAC 58.551 33.333 0.00 0.00 31.29 2.90
2352 2507 7.903431 GTGTAGTTGTTTCTCTTTTGTACAGTG 59.097 37.037 0.00 0.00 0.00 3.66
2363 2518 5.756347 TCTTTTGTACAGTGCTACGTTCATT 59.244 36.000 0.00 0.00 0.00 2.57
2366 2521 4.373527 TGTACAGTGCTACGTTCATTTGT 58.626 39.130 0.00 4.83 0.00 2.83
2389 2544 3.555966 ACTGTCTTCTTTTCCCCAAGTG 58.444 45.455 0.00 0.00 0.00 3.16
2390 2545 2.294512 CTGTCTTCTTTTCCCCAAGTGC 59.705 50.000 0.00 0.00 0.00 4.40
2391 2546 1.613925 GTCTTCTTTTCCCCAAGTGCC 59.386 52.381 0.00 0.00 0.00 5.01
2392 2547 1.216678 TCTTCTTTTCCCCAAGTGCCA 59.783 47.619 0.00 0.00 0.00 4.92
2393 2548 2.158325 TCTTCTTTTCCCCAAGTGCCAT 60.158 45.455 0.00 0.00 0.00 4.40
2394 2549 2.397044 TCTTTTCCCCAAGTGCCATT 57.603 45.000 0.00 0.00 0.00 3.16
2395 2550 1.969923 TCTTTTCCCCAAGTGCCATTG 59.030 47.619 0.00 0.00 0.00 2.82
2409 2564 3.449737 GTGCCATTGGACCTACAGTACTA 59.550 47.826 6.95 0.00 0.00 1.82
2424 2579 6.295039 ACAGTACTACGTTTGAACAATTGG 57.705 37.500 10.83 0.00 0.00 3.16
2504 2665 5.918011 GCTAGCTAGCTGTTACTAGTCATTG 59.082 44.000 33.71 0.00 45.62 2.82
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 4.263572 CACCACCACCTCCGCCAA 62.264 66.667 0.00 0.00 0.00 4.52
4 5 4.329545 CCACCACCACCACCTCCG 62.330 72.222 0.00 0.00 0.00 4.63
5 6 2.292785 AAACCACCACCACCACCTCC 62.293 60.000 0.00 0.00 0.00 4.30
6 7 0.396556 AAAACCACCACCACCACCTC 60.397 55.000 0.00 0.00 0.00 3.85
7 8 0.686112 CAAAACCACCACCACCACCT 60.686 55.000 0.00 0.00 0.00 4.00
8 9 1.681486 CCAAAACCACCACCACCACC 61.681 60.000 0.00 0.00 0.00 4.61
10 11 2.060980 GCCAAAACCACCACCACCA 61.061 57.895 0.00 0.00 0.00 4.17
11 12 2.818841 GCCAAAACCACCACCACC 59.181 61.111 0.00 0.00 0.00 4.61
12 13 2.415426 CGCCAAAACCACCACCAC 59.585 61.111 0.00 0.00 0.00 4.16
13 14 2.835431 CCGCCAAAACCACCACCA 60.835 61.111 0.00 0.00 0.00 4.17
14 15 2.519780 TCCGCCAAAACCACCACC 60.520 61.111 0.00 0.00 0.00 4.61
15 16 2.561037 CCTCCGCCAAAACCACCAC 61.561 63.158 0.00 0.00 0.00 4.16
19 20 2.203422 CCACCTCCGCCAAAACCA 60.203 61.111 0.00 0.00 0.00 3.67
342 363 5.886715 TCATTTGACAGCATTTCAAAACG 57.113 34.783 10.34 6.41 44.14 3.60
715 738 4.810790 CCGTCGGCATAGATTTCTATCTT 58.189 43.478 0.00 0.00 41.38 2.40
759 782 3.612681 CAGGGGACGACACGTGGT 61.613 66.667 21.57 9.01 41.37 4.16
814 837 0.031857 TCGGCGTTGTTTTCCGTCTA 59.968 50.000 6.85 0.00 43.35 2.59
1186 1209 3.452474 GCTTCTTGCAGTACTCGATGAT 58.548 45.455 0.00 0.00 42.31 2.45
1264 1287 3.391382 GGCGGCAGTAGAGGTGGT 61.391 66.667 3.07 0.00 0.00 4.16
1290 1313 2.492090 CTCTTGAGGTCCTCGGCG 59.508 66.667 14.34 0.00 32.35 6.46
1324 1347 1.002087 GGTGTTCTGGTCGACCTTGAT 59.998 52.381 33.39 0.00 36.82 2.57
1339 1362 1.550976 GATGAGGTCGAAGAGGGTGTT 59.449 52.381 0.00 0.00 36.95 3.32
1340 1363 1.187087 GATGAGGTCGAAGAGGGTGT 58.813 55.000 0.00 0.00 36.95 4.16
1413 1436 2.439409 CCCTTGATCATGTCTGCAACA 58.561 47.619 0.00 4.56 43.51 3.33
1434 1457 1.127343 GGATCTCCTCTGGGGTCTTG 58.873 60.000 0.00 0.00 36.25 3.02
1443 1466 1.859302 AAGTCTTGCGGATCTCCTCT 58.141 50.000 0.00 0.00 0.00 3.69
1511 1534 0.853530 AAAAGCCCACTGGTTCTCCT 59.146 50.000 0.00 0.00 32.32 3.69
1541 1564 9.485206 AAGAAAACACGAATACTAAGCTTTCTA 57.515 29.630 3.20 0.00 32.01 2.10
1572 1627 5.074134 CGACATACGATGATACGAAGTCTC 58.926 45.833 0.00 0.00 43.01 3.36
1609 1675 1.669779 GACCACTAGCACTACGACGAT 59.330 52.381 0.00 0.00 0.00 3.73
1615 1681 7.378995 CAGAATATTTACGACCACTAGCACTAC 59.621 40.741 0.00 0.00 0.00 2.73
1634 1700 5.831702 ACGACGTTTAGACTCCAGAATAT 57.168 39.130 0.00 0.00 0.00 1.28
1641 1707 5.287992 CAGGAATAAACGACGTTTAGACTCC 59.712 44.000 29.64 29.64 40.58 3.85
1647 1713 3.121611 CACGCAGGAATAAACGACGTTTA 59.878 43.478 29.39 29.39 41.32 2.01
1652 1718 4.260091 GGTAATCACGCAGGAATAAACGAC 60.260 45.833 0.00 0.00 0.00 4.34
1657 1723 4.081365 TCACAGGTAATCACGCAGGAATAA 60.081 41.667 0.00 0.00 0.00 1.40
1720 1822 8.777413 GCATAAATCACAGCTAAGAATGATGTA 58.223 33.333 0.00 0.00 0.00 2.29
1728 1830 4.329801 CACACGCATAAATCACAGCTAAGA 59.670 41.667 0.00 0.00 0.00 2.10
1736 1838 5.868257 TCTCAAATCACACGCATAAATCAC 58.132 37.500 0.00 0.00 0.00 3.06
1831 1933 5.172934 TCTGAAGCCAAATGAAAATCATGC 58.827 37.500 0.00 0.00 37.15 4.06
1854 1956 8.543293 AGATTCCAATGGTCACAAAATATGAT 57.457 30.769 0.00 0.00 0.00 2.45
1858 1960 7.574779 CGTTGAGATTCCAATGGTCACAAAATA 60.575 37.037 0.00 0.00 31.28 1.40
1870 1972 0.729116 CTGCGCGTTGAGATTCCAAT 59.271 50.000 8.43 0.00 0.00 3.16
1884 1986 3.179265 CAAATGCTGCTGCTGCGC 61.179 61.111 23.38 19.66 43.34 6.09
1912 2014 1.381165 AACAAACACACGCCCACTCC 61.381 55.000 0.00 0.00 0.00 3.85
1916 2018 0.603569 AAACAACAAACACACGCCCA 59.396 45.000 0.00 0.00 0.00 5.36
1920 2022 4.370212 CGAAACAAAACAACAAACACACG 58.630 39.130 0.00 0.00 0.00 4.49
1922 2024 3.741344 CCCGAAACAAAACAACAAACACA 59.259 39.130 0.00 0.00 0.00 3.72
1955 2057 0.033504 GTCGGCTTCAAGACCAGTGA 59.966 55.000 0.00 0.00 0.00 3.41
2006 2150 3.218974 GGGGGAGAAGGTCGTCATA 57.781 57.895 0.00 0.00 0.00 2.15
2033 2177 1.563173 GGACAACGACGTTGAGCAC 59.437 57.895 39.13 26.15 45.28 4.40
2131 2284 3.827876 TGGAATGTCACATGCTTGAATGT 59.172 39.130 6.60 0.00 41.50 2.71
2158 2311 9.099454 CCTAATTAAGAAGCGAAATGAGTAGTT 57.901 33.333 0.00 0.00 0.00 2.24
2161 2314 7.788026 TCCCTAATTAAGAAGCGAAATGAGTA 58.212 34.615 0.00 0.00 0.00 2.59
2171 2324 7.606839 AGGCGTATTAATCCCTAATTAAGAAGC 59.393 37.037 11.82 11.82 46.58 3.86
2225 2380 2.425312 ACTGGTGAGAGCTCGAGTTATG 59.575 50.000 15.13 0.00 0.00 1.90
2293 2448 6.711569 CTGTAGGTCCAAAACACCTTCAGTG 61.712 48.000 14.27 0.00 46.67 3.66
2294 2449 3.201266 TGTAGGTCCAAAACACCTTCAGT 59.799 43.478 0.00 0.00 41.95 3.41
2295 2450 3.815401 CTGTAGGTCCAAAACACCTTCAG 59.185 47.826 10.10 10.10 46.69 3.02
2296 2451 3.201266 ACTGTAGGTCCAAAACACCTTCA 59.799 43.478 0.00 0.00 41.95 3.02
2297 2452 3.564225 CACTGTAGGTCCAAAACACCTTC 59.436 47.826 0.00 0.00 41.95 3.46
2298 2453 3.551846 CACTGTAGGTCCAAAACACCTT 58.448 45.455 0.00 0.00 41.95 3.50
2299 2454 2.748465 GCACTGTAGGTCCAAAACACCT 60.748 50.000 0.00 0.00 46.60 4.00
2300 2455 1.607148 GCACTGTAGGTCCAAAACACC 59.393 52.381 0.00 0.00 0.00 4.16
2301 2456 2.572290 AGCACTGTAGGTCCAAAACAC 58.428 47.619 0.00 0.00 0.00 3.32
2330 2485 5.648092 AGCACTGTACAAAAGAGAAACAACT 59.352 36.000 0.00 0.00 0.00 3.16
2331 2486 5.880341 AGCACTGTACAAAAGAGAAACAAC 58.120 37.500 0.00 0.00 0.00 3.32
2332 2487 6.237996 CGTAGCACTGTACAAAAGAGAAACAA 60.238 38.462 0.00 0.00 0.00 2.83
2333 2488 5.233476 CGTAGCACTGTACAAAAGAGAAACA 59.767 40.000 0.00 0.00 0.00 2.83
2334 2489 5.233689 ACGTAGCACTGTACAAAAGAGAAAC 59.766 40.000 0.00 0.00 0.00 2.78
2335 2490 5.353938 ACGTAGCACTGTACAAAAGAGAAA 58.646 37.500 0.00 0.00 0.00 2.52
2343 2498 4.812091 ACAAATGAACGTAGCACTGTACAA 59.188 37.500 0.00 0.00 0.00 2.41
2348 2503 3.494626 AGTCACAAATGAACGTAGCACTG 59.505 43.478 0.00 0.00 36.31 3.66
2352 2507 3.741344 AGACAGTCACAAATGAACGTAGC 59.259 43.478 2.66 0.00 36.31 3.58
2363 2518 3.053991 TGGGGAAAAGAAGACAGTCACAA 60.054 43.478 2.66 0.00 0.00 3.33
2366 2521 3.202151 ACTTGGGGAAAAGAAGACAGTCA 59.798 43.478 2.66 0.00 0.00 3.41
2389 2544 3.490419 CGTAGTACTGTAGGTCCAATGGC 60.490 52.174 5.39 0.00 0.00 4.40
2390 2545 3.698040 ACGTAGTACTGTAGGTCCAATGG 59.302 47.826 5.39 0.00 41.94 3.16
2391 2546 4.978083 ACGTAGTACTGTAGGTCCAATG 57.022 45.455 5.39 0.00 41.94 2.82
2392 2547 5.477984 TCAAACGTAGTACTGTAGGTCCAAT 59.522 40.000 5.39 0.00 45.00 3.16
2393 2548 4.826733 TCAAACGTAGTACTGTAGGTCCAA 59.173 41.667 5.39 0.00 45.00 3.53
2394 2549 4.397420 TCAAACGTAGTACTGTAGGTCCA 58.603 43.478 5.39 0.00 45.00 4.02
2395 2550 5.157067 GTTCAAACGTAGTACTGTAGGTCC 58.843 45.833 5.39 0.00 45.00 4.46
2396 2551 5.762045 TGTTCAAACGTAGTACTGTAGGTC 58.238 41.667 5.39 0.00 45.00 3.85
2397 2552 5.772825 TGTTCAAACGTAGTACTGTAGGT 57.227 39.130 5.39 0.00 45.00 3.08
2398 2553 7.359765 CCAATTGTTCAAACGTAGTACTGTAGG 60.360 40.741 5.39 0.00 45.00 3.18
2399 2554 7.359765 CCCAATTGTTCAAACGTAGTACTGTAG 60.360 40.741 5.39 0.00 45.00 2.74
2400 2555 6.424509 CCCAATTGTTCAAACGTAGTACTGTA 59.575 38.462 5.39 0.00 45.00 2.74
2401 2556 5.237779 CCCAATTGTTCAAACGTAGTACTGT 59.762 40.000 5.39 0.00 45.00 3.55
2402 2557 5.334569 CCCCAATTGTTCAAACGTAGTACTG 60.335 44.000 5.39 0.00 45.00 2.74
2409 2564 2.621526 GAGACCCCAATTGTTCAAACGT 59.378 45.455 4.43 0.00 0.00 3.99
2424 2579 0.620556 TTGCCAATGGAGAGAGACCC 59.379 55.000 2.05 0.00 0.00 4.46
2452 2613 3.802139 TGCTTCAGTACAACTTCGACAAG 59.198 43.478 0.00 0.00 35.50 3.16
2456 2617 3.067601 TGAGTGCTTCAGTACAACTTCGA 59.932 43.478 0.00 0.00 32.87 3.71
2497 2658 8.034804 GGAAATAATTAAGCAACCACAATGACT 58.965 33.333 0.00 0.00 0.00 3.41
2504 2665 6.027749 CGACAGGAAATAATTAAGCAACCAC 58.972 40.000 0.00 0.00 0.00 4.16


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

AutoCloner maintained by Alex Coulton.