Multiple sequence alignment - TraesCS5B01G069500

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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 TraesCS5B01G069500 chr5B 100.000 3295 0 0 1 3295 79424757 79421463 0.000000e+00 6085.0
1 TraesCS5B01G069500 chr5B 87.290 1188 97 22 1226 2395 79562307 79561156 0.000000e+00 1308.0
2 TraesCS5B01G069500 chr5B 80.599 701 88 28 2608 3293 526680186 526680853 6.350000e-137 497.0
3 TraesCS5B01G069500 chr5B 79.509 693 80 33 2621 3295 596738522 596737874 1.400000e-118 436.0
4 TraesCS5B01G069500 chr5B 80.744 457 39 22 742 1163 79562886 79562444 8.880000e-81 311.0
5 TraesCS5B01G069500 chr5B 81.132 212 35 5 2613 2822 115631856 115632064 7.310000e-37 165.0
6 TraesCS5B01G069500 chr5A 89.261 2030 158 27 514 2522 65354553 65356543 0.000000e+00 2486.0
7 TraesCS5B01G069500 chr5A 88.259 1218 106 12 1214 2411 65360196 65361396 0.000000e+00 1423.0
8 TraesCS5B01G069500 chr5A 88.152 1207 110 13 1225 2411 65011191 65012384 0.000000e+00 1406.0
9 TraesCS5B01G069500 chr5A 86.092 719 58 13 501 1213 65359390 65360072 0.000000e+00 736.0
10 TraesCS5B01G069500 chr5A 87.194 531 44 8 1 516 65353951 65354472 1.700000e-162 582.0
11 TraesCS5B01G069500 chr5A 86.116 533 52 11 2080 2607 67317606 67318121 3.710000e-154 555.0
12 TraesCS5B01G069500 chr5A 81.638 354 36 14 816 1156 65010711 65011048 1.950000e-67 267.0
13 TraesCS5B01G069500 chr5A 83.333 114 19 0 1293 1406 65712210 65712323 4.500000e-19 106.0
14 TraesCS5B01G069500 chr5D 91.170 1846 117 17 781 2610 72613047 72614862 0.000000e+00 2464.0
15 TraesCS5B01G069500 chr5D 86.540 1211 104 25 1225 2411 72589908 72591083 0.000000e+00 1279.0
16 TraesCS5B01G069500 chr5D 91.608 429 21 11 290 711 72612627 72613047 2.200000e-161 579.0
17 TraesCS5B01G069500 chr5D 75.429 757 100 42 2611 3295 555650424 555651166 4.160000e-74 289.0
18 TraesCS5B01G069500 chr5D 84.848 297 30 2 1 286 72612175 72612467 5.380000e-73 285.0
19 TraesCS5B01G069500 chr5D 81.742 356 37 13 816 1156 72589426 72589768 4.190000e-69 272.0
20 TraesCS5B01G069500 chr5D 85.646 209 23 5 2621 2826 3502156 3501952 2.580000e-51 213.0
21 TraesCS5B01G069500 chr5D 97.436 39 0 1 2621 2658 41889083 41889045 7.630000e-07 65.8
22 TraesCS5B01G069500 chr7D 82.319 690 89 20 2621 3295 35943037 35943708 4.770000e-158 568.0
23 TraesCS5B01G069500 chr7D 86.503 326 27 13 2980 3295 42947798 42948116 3.150000e-90 342.0
24 TraesCS5B01G069500 chrUn 80.747 696 68 35 2621 3295 38665764 38666414 1.780000e-132 483.0
25 TraesCS5B01G069500 chr7B 81.183 558 69 22 2621 3164 125884881 125884346 1.830000e-112 416.0
26 TraesCS5B01G069500 chr3B 82.136 487 60 14 2825 3295 172010052 172010527 3.080000e-105 392.0
27 TraesCS5B01G069500 chr6B 88.672 256 19 4 2625 2871 25808344 25808598 1.490000e-78 303.0
28 TraesCS5B01G069500 chr2B 97.143 35 1 0 2621 2655 200645408 200645442 3.550000e-05 60.2


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 TraesCS5B01G069500 chr5B 79421463 79424757 3294 True 6085.000000 6085 100.000000 1 3295 1 chr5B.!!$R1 3294
1 TraesCS5B01G069500 chr5B 79561156 79562886 1730 True 809.500000 1308 84.017000 742 2395 2 chr5B.!!$R3 1653
2 TraesCS5B01G069500 chr5B 526680186 526680853 667 False 497.000000 497 80.599000 2608 3293 1 chr5B.!!$F2 685
3 TraesCS5B01G069500 chr5B 596737874 596738522 648 True 436.000000 436 79.509000 2621 3295 1 chr5B.!!$R2 674
4 TraesCS5B01G069500 chr5A 65353951 65361396 7445 False 1306.750000 2486 87.701500 1 2522 4 chr5A.!!$F4 2521
5 TraesCS5B01G069500 chr5A 65010711 65012384 1673 False 836.500000 1406 84.895000 816 2411 2 chr5A.!!$F3 1595
6 TraesCS5B01G069500 chr5A 67317606 67318121 515 False 555.000000 555 86.116000 2080 2607 1 chr5A.!!$F2 527
7 TraesCS5B01G069500 chr5D 72612175 72614862 2687 False 1109.333333 2464 89.208667 1 2610 3 chr5D.!!$F3 2609
8 TraesCS5B01G069500 chr5D 72589426 72591083 1657 False 775.500000 1279 84.141000 816 2411 2 chr5D.!!$F2 1595
9 TraesCS5B01G069500 chr5D 555650424 555651166 742 False 289.000000 289 75.429000 2611 3295 1 chr5D.!!$F1 684
10 TraesCS5B01G069500 chr7D 35943037 35943708 671 False 568.000000 568 82.319000 2621 3295 1 chr7D.!!$F1 674
11 TraesCS5B01G069500 chrUn 38665764 38666414 650 False 483.000000 483 80.747000 2621 3295 1 chrUn.!!$F1 674
12 TraesCS5B01G069500 chr7B 125884346 125884881 535 True 416.000000 416 81.183000 2621 3164 1 chr7B.!!$R1 543

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
547 804 0.040514 CGCTTCCGTTCACATTGCAA 60.041 50.0 0.0 0.0 0.0 4.08 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2489 2923 0.461548 TGGTGTGCAAATCGCCAAAA 59.538 45.0 5.66 0.0 41.6 2.44 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
19 20 2.472695 TTACGCTGAGCAACCAAGAT 57.527 45.000 4.88 0.00 0.00 2.40
30 31 1.541310 AACCAAGATCGGACGGCTCA 61.541 55.000 0.00 0.00 0.00 4.26
31 32 1.519455 CCAAGATCGGACGGCTCAC 60.519 63.158 0.00 0.00 0.00 3.51
48 49 1.302511 ACGAGGCGGCACATCTTTT 60.303 52.632 13.08 0.00 0.00 2.27
57 58 4.562789 GGCGGCACATCTTTTAAAAAGATC 59.437 41.667 3.07 0.00 34.96 2.75
58 59 5.402398 GCGGCACATCTTTTAAAAAGATCT 58.598 37.500 0.00 0.00 34.96 2.75
118 119 6.887002 ACTGGTCTTGTTTCTTCTTTCTTTCT 59.113 34.615 0.00 0.00 0.00 2.52
119 120 7.394641 ACTGGTCTTGTTTCTTCTTTCTTTCTT 59.605 33.333 0.00 0.00 0.00 2.52
120 121 8.122472 TGGTCTTGTTTCTTCTTTCTTTCTTT 57.878 30.769 0.00 0.00 0.00 2.52
121 122 8.585018 TGGTCTTGTTTCTTCTTTCTTTCTTTT 58.415 29.630 0.00 0.00 0.00 2.27
150 151 8.436046 TTTTGGTATTTGTACTCTGTTTACGT 57.564 30.769 0.00 0.00 0.00 3.57
169 170 2.076100 GTCAAGTGGATGATGCGAACA 58.924 47.619 0.00 0.00 0.00 3.18
171 172 1.078709 AAGTGGATGATGCGAACACG 58.921 50.000 0.00 0.00 37.16 4.49
197 198 2.816360 CGTGCATGCGATCCACCAG 61.816 63.158 14.09 0.00 0.00 4.00
216 217 3.055819 CCAGACGGAATCCTTTTCTCTCA 60.056 47.826 0.00 0.00 0.00 3.27
251 264 1.080230 CACCACAGTCTCTGCTCCG 60.080 63.158 0.00 0.00 34.37 4.63
254 267 1.662608 CACAGTCTCTGCTCCGTGT 59.337 57.895 0.00 0.00 34.37 4.49
344 513 9.683870 TTTCTTGGTACTTTTACTCCTGTTTAA 57.316 29.630 0.00 0.00 0.00 1.52
362 531 1.033746 AAGGCAAGTGGATGATGCGG 61.034 55.000 0.00 0.00 40.94 5.69
466 635 2.203167 CTCTGCTCCATGCCGCAT 60.203 61.111 0.00 0.00 42.00 4.73
468 637 0.949588 CTCTGCTCCATGCCGCATAG 60.950 60.000 5.31 1.98 42.00 2.23
547 804 0.040514 CGCTTCCGTTCACATTGCAA 60.041 50.000 0.00 0.00 0.00 4.08
699 965 6.657875 TGGATCATAATCAACACATGGTACA 58.342 36.000 0.00 0.00 36.68 2.90
700 966 6.542005 TGGATCATAATCAACACATGGTACAC 59.458 38.462 0.00 0.00 35.44 2.90
725 991 4.512944 TGAAGGCAAGATCGATGCTTATTC 59.487 41.667 20.92 20.17 43.34 1.75
735 1001 2.802816 CGATGCTTATTCTACACAGCCC 59.197 50.000 0.00 0.00 0.00 5.19
753 1019 2.418609 GCCCCCATATGTTTTCTTGTGC 60.419 50.000 1.24 0.00 0.00 4.57
755 1021 3.119029 CCCCCATATGTTTTCTTGTGCTG 60.119 47.826 1.24 0.00 0.00 4.41
761 1027 1.403679 TGTTTTCTTGTGCTGGGAACG 59.596 47.619 0.00 0.00 0.00 3.95
784 1050 4.804108 GCAGTGCCACAACATTACATTTA 58.196 39.130 2.85 0.00 0.00 1.40
818 1099 4.561326 GCAGTTGACCCAAATTAAGCATGT 60.561 41.667 0.00 0.00 0.00 3.21
858 1140 4.101790 CGTTGCACACGCCATCCC 62.102 66.667 8.15 0.00 43.37 3.85
859 1141 3.747976 GTTGCACACGCCATCCCC 61.748 66.667 0.00 0.00 37.32 4.81
893 1175 1.250840 GGCCAAAAGGCGGTTCTCAT 61.251 55.000 0.00 0.00 35.44 2.90
896 1185 2.094675 CCAAAAGGCGGTTCTCATCAT 58.905 47.619 0.00 0.00 0.00 2.45
919 1208 3.467803 ACACAGCTCAGTTTGGAACTAC 58.532 45.455 0.00 0.00 40.46 2.73
920 1209 3.118408 ACACAGCTCAGTTTGGAACTACA 60.118 43.478 0.00 0.00 40.46 2.74
932 1221 2.038557 TGGAACTACAGCTTGGAAGTCC 59.961 50.000 0.00 0.00 0.00 3.85
962 1277 8.435931 ACATATCCATACTTCTGTTGCCTATA 57.564 34.615 0.00 0.00 0.00 1.31
978 1296 3.804063 GCCTATAGCACCTTCTAGTTGGC 60.804 52.174 0.00 0.00 42.97 4.52
982 1300 2.230660 AGCACCTTCTAGTTGGCAAAC 58.769 47.619 0.00 0.00 36.47 2.93
984 1302 2.226674 GCACCTTCTAGTTGGCAAACTC 59.773 50.000 10.53 0.00 43.34 3.01
1098 1416 0.247814 GTTTCATCGCGTCATGGCTG 60.248 55.000 5.77 0.00 0.00 4.85
1165 1483 2.677037 CGGAACCCTGGTGAGTACAATC 60.677 54.545 0.00 0.00 0.00 2.67
1166 1484 2.355818 GGAACCCTGGTGAGTACAATCC 60.356 54.545 0.00 0.00 0.00 3.01
1167 1485 2.038863 ACCCTGGTGAGTACAATCCA 57.961 50.000 0.00 0.00 0.00 3.41
1168 1486 2.344592 ACCCTGGTGAGTACAATCCAA 58.655 47.619 0.00 0.00 0.00 3.53
1169 1487 2.919602 ACCCTGGTGAGTACAATCCAAT 59.080 45.455 0.00 0.00 0.00 3.16
1170 1488 3.054361 ACCCTGGTGAGTACAATCCAATC 60.054 47.826 0.00 0.00 0.00 2.67
1187 1506 3.508793 CCAATCCACCCTTCATCATATGC 59.491 47.826 0.00 0.00 0.00 3.14
1188 1507 4.404640 CAATCCACCCTTCATCATATGCT 58.595 43.478 0.00 0.00 0.00 3.79
1220 1626 5.070446 CCATGCCTGGAGTGTATCTAACTTA 59.930 44.000 0.97 0.00 46.37 2.24
1422 1842 6.534475 TTACTTACCCACATAGGTGTACTG 57.466 41.667 6.79 0.00 43.71 2.74
1468 1888 4.458989 GTGGCTGACAAAGGTTCATTCATA 59.541 41.667 0.00 0.00 0.00 2.15
1503 1923 2.023414 AAATGATCGAGCCGGCGGTA 62.023 55.000 28.82 10.75 0.00 4.02
1610 2030 0.669077 ATGGATCCTCGTCGTAGCAC 59.331 55.000 14.23 0.00 0.00 4.40
1692 2112 5.344884 GTCAGCTTAATTAACTCTCGCTCT 58.655 41.667 6.05 0.00 0.00 4.09
1763 2185 0.744874 ATGGCATGCATCTGACAAGC 59.255 50.000 21.36 0.00 37.78 4.01
1886 2308 1.644337 TCTCTAGTGTTGGGCCCTCTA 59.356 52.381 25.70 17.70 0.00 2.43
1964 2386 1.952133 GCAGACGTACACCAACGCA 60.952 57.895 0.00 0.00 46.71 5.24
2130 2552 3.627332 TACCCCGTGCCCATGAGGA 62.627 63.158 0.00 0.00 38.24 3.71
2202 2624 0.461548 GATCATGGAGCTCGGTGTCA 59.538 55.000 7.83 0.00 0.00 3.58
2372 2802 2.477863 GCAAGTCGTGGCATTGTATTCC 60.478 50.000 0.00 0.00 0.00 3.01
2387 2817 5.382664 TGTATTCCCCATTTCCTCCTTAC 57.617 43.478 0.00 0.00 0.00 2.34
2450 2882 5.779806 ATGTCCGAATCTTTACTTTGTCG 57.220 39.130 0.00 0.00 0.00 4.35
2452 2884 2.997986 TCCGAATCTTTACTTTGTCGCC 59.002 45.455 0.00 0.00 0.00 5.54
2453 2885 2.739913 CCGAATCTTTACTTTGTCGCCA 59.260 45.455 0.00 0.00 0.00 5.69
2455 2887 4.142687 CCGAATCTTTACTTTGTCGCCATT 60.143 41.667 0.00 0.00 0.00 3.16
2457 2889 6.185399 CGAATCTTTACTTTGTCGCCATTAG 58.815 40.000 0.00 0.00 0.00 1.73
2459 2891 7.412563 CGAATCTTTACTTTGTCGCCATTAGAA 60.413 37.037 0.00 0.00 0.00 2.10
2498 2932 3.214328 ACTTGTGAGTCTTTTTGGCGAT 58.786 40.909 0.00 0.00 0.00 4.58
2499 2933 3.632145 ACTTGTGAGTCTTTTTGGCGATT 59.368 39.130 0.00 0.00 0.00 3.34
2524 2958 4.918129 CATGCTCATTGGCGGCGC 62.918 66.667 26.17 26.17 34.52 6.53
2611 3110 4.445052 CGACATGTGCACAATGTTCATTTT 59.555 37.500 25.72 0.00 0.00 1.82
2672 3352 8.766994 ACGTATAAGGGTAGTATGGTCTTTTA 57.233 34.615 0.00 0.00 0.00 1.52
2673 3353 9.372189 ACGTATAAGGGTAGTATGGTCTTTTAT 57.628 33.333 0.00 0.00 0.00 1.40
2829 3962 5.405269 GCTAAAATTCAAAAAGTGGATGCGT 59.595 36.000 0.00 0.00 0.00 5.24
2832 3970 3.529634 TTCAAAAAGTGGATGCGTACG 57.470 42.857 11.84 11.84 0.00 3.67
2835 4539 1.153353 AAAAGTGGATGCGTACGTGG 58.847 50.000 17.90 0.00 0.00 4.94
2836 4540 0.672401 AAAGTGGATGCGTACGTGGG 60.672 55.000 17.90 0.00 0.00 4.61
2837 4541 1.537814 AAGTGGATGCGTACGTGGGA 61.538 55.000 17.90 0.00 0.00 4.37
2838 4542 1.143183 GTGGATGCGTACGTGGGAT 59.857 57.895 17.90 4.11 0.00 3.85
2839 4543 0.461339 GTGGATGCGTACGTGGGATT 60.461 55.000 17.90 0.00 0.00 3.01
2840 4544 1.112950 TGGATGCGTACGTGGGATTA 58.887 50.000 17.90 0.00 0.00 1.75
2866 4821 4.545823 TCGAACACAAAACCTCAATGTC 57.454 40.909 0.00 0.00 0.00 3.06
2871 4826 3.381272 ACACAAAACCTCAATGTCCACAG 59.619 43.478 0.00 0.00 0.00 3.66
2874 4829 0.251341 AACCTCAATGTCCACAGGCC 60.251 55.000 0.00 0.00 0.00 5.19
2875 4830 1.136329 ACCTCAATGTCCACAGGCCT 61.136 55.000 0.00 0.00 0.00 5.19
2878 4833 0.038166 TCAATGTCCACAGGCCTTCC 59.962 55.000 0.00 0.00 0.00 3.46
2908 4868 3.073274 ACTGGGAAGCCTACATTTCAC 57.927 47.619 0.00 0.00 0.00 3.18
2925 5645 4.466567 TTCACGTAACAATGCACTTCTG 57.533 40.909 0.00 0.00 0.00 3.02
2936 5656 7.801716 ACAATGCACTTCTGTTTTCTTACTA 57.198 32.000 0.00 0.00 0.00 1.82
2940 5660 7.859325 TGCACTTCTGTTTTCTTACTAGTTT 57.141 32.000 0.00 0.00 0.00 2.66
2941 5661 7.693952 TGCACTTCTGTTTTCTTACTAGTTTG 58.306 34.615 0.00 0.00 0.00 2.93
3156 8112 7.594758 TCATGAGCTTTTTAAAAATCGGTGAAG 59.405 33.333 13.55 1.24 0.00 3.02
3157 8113 6.801575 TGAGCTTTTTAAAAATCGGTGAAGT 58.198 32.000 13.55 0.00 0.00 3.01
3158 8114 7.262048 TGAGCTTTTTAAAAATCGGTGAAGTT 58.738 30.769 13.55 0.00 0.00 2.66
3210 8188 8.944029 TCAAATTTGTGCTTTTTCTCAAATTGA 58.056 25.926 17.47 0.00 43.45 2.57
3215 8193 7.703298 TGTGCTTTTTCTCAAATTGATGAAG 57.297 32.000 0.00 0.59 0.00 3.02
3218 8196 8.060090 GTGCTTTTTCTCAAATTGATGAAGTTG 58.940 33.333 0.00 0.00 38.28 3.16
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
30 31 0.036765 TAAAAGATGTGCCGCCTCGT 60.037 50.000 0.00 0.00 0.00 4.18
31 32 1.083489 TTAAAAGATGTGCCGCCTCG 58.917 50.000 0.00 0.00 0.00 4.63
33 34 3.572255 TCTTTTTAAAAGATGTGCCGCCT 59.428 39.130 15.24 0.00 0.00 5.52
41 42 6.308766 CGGTTGGCAGATCTTTTTAAAAGATG 59.691 38.462 30.22 21.56 37.14 2.90
48 49 2.739913 CGTCGGTTGGCAGATCTTTTTA 59.260 45.455 0.00 0.00 0.00 1.52
57 58 3.179265 CTACGCGTCGGTTGGCAG 61.179 66.667 18.63 0.00 0.00 4.85
77 78 2.773053 GTAGGGGGAGAAGGGGCC 60.773 72.222 0.00 0.00 0.00 5.80
78 79 2.073101 CAGTAGGGGGAGAAGGGGC 61.073 68.421 0.00 0.00 0.00 5.80
90 91 6.292150 AGAAAGAAGAAACAAGACCAGTAGG 58.708 40.000 0.00 0.00 42.21 3.18
136 137 4.863491 TCCACTTGACGTAAACAGAGTAC 58.137 43.478 0.00 0.00 0.00 2.73
150 151 2.076100 GTGTTCGCATCATCCACTTGA 58.924 47.619 0.00 0.00 0.00 3.02
169 170 3.049674 CATGCACGTTGCCTCCGT 61.050 61.111 7.38 0.00 44.23 4.69
171 172 4.465512 CGCATGCACGTTGCCTCC 62.466 66.667 19.57 0.00 44.23 4.30
197 198 3.799420 CGATGAGAGAAAAGGATTCCGTC 59.201 47.826 0.00 0.00 0.00 4.79
315 484 9.503399 AACAGGAGTAAAAGTACCAAGAAATAG 57.497 33.333 0.00 0.00 0.00 1.73
317 486 8.762481 AAACAGGAGTAAAAGTACCAAGAAAT 57.238 30.769 0.00 0.00 0.00 2.17
344 513 1.452651 CCGCATCATCCACTTGCCT 60.453 57.895 0.00 0.00 32.76 4.75
379 548 0.322098 TCCGTTTGGTGGATCGCATT 60.322 50.000 0.00 0.00 36.30 3.56
699 965 1.645034 CATCGATCTTGCCTTCACGT 58.355 50.000 0.00 0.00 0.00 4.49
700 966 0.302890 GCATCGATCTTGCCTTCACG 59.697 55.000 0.00 0.00 33.95 4.35
725 991 3.297134 AAACATATGGGGGCTGTGTAG 57.703 47.619 7.80 0.00 0.00 2.74
735 1001 3.119029 CCCAGCACAAGAAAACATATGGG 60.119 47.826 7.80 0.00 38.98 4.00
784 1050 2.362077 GGGTCAACTGCAAATCTGTGTT 59.638 45.455 0.00 0.00 0.00 3.32
818 1099 0.618458 GGTAGCCACATCCCACTTGA 59.382 55.000 0.00 0.00 0.00 3.02
858 1140 0.677842 GGCCGGTATATATAGGGCGG 59.322 60.000 20.53 0.00 44.66 6.13
893 1175 4.350368 TCCAAACTGAGCTGTGTAATGA 57.650 40.909 0.00 0.00 0.00 2.57
896 1185 4.150897 AGTTCCAAACTGAGCTGTGTAA 57.849 40.909 0.00 0.00 41.01 2.41
932 1221 7.095060 GGCAACAGAAGTATGGATATGTATGTG 60.095 40.741 0.00 0.00 0.00 3.21
934 1223 7.164122 AGGCAACAGAAGTATGGATATGTATG 58.836 38.462 0.00 0.00 41.41 2.39
962 1277 2.158608 AGTTTGCCAACTAGAAGGTGCT 60.159 45.455 0.42 0.00 41.81 4.40
966 1281 3.999663 CAGAGAGTTTGCCAACTAGAAGG 59.000 47.826 2.67 0.00 43.79 3.46
976 1294 1.155042 CAGTCTGCAGAGAGTTTGCC 58.845 55.000 18.89 2.22 40.81 4.52
978 1296 3.243670 TGTCTCAGTCTGCAGAGAGTTTG 60.244 47.826 24.52 15.48 41.23 2.93
982 1300 2.159212 CCATGTCTCAGTCTGCAGAGAG 60.159 54.545 18.89 20.45 41.23 3.20
984 1302 1.134759 CCCATGTCTCAGTCTGCAGAG 60.135 57.143 18.89 6.65 0.00 3.35
1098 1416 4.136978 TCCAGGAGGAGCTTCACC 57.863 61.111 0.00 0.00 39.61 4.02
1165 1483 3.508793 GCATATGATGAAGGGTGGATTGG 59.491 47.826 6.97 0.00 0.00 3.16
1166 1484 4.404640 AGCATATGATGAAGGGTGGATTG 58.595 43.478 6.97 0.00 0.00 2.67
1167 1485 4.353191 AGAGCATATGATGAAGGGTGGATT 59.647 41.667 6.97 0.00 0.00 3.01
1168 1486 3.915073 AGAGCATATGATGAAGGGTGGAT 59.085 43.478 6.97 0.00 0.00 3.41
1169 1487 3.321039 AGAGCATATGATGAAGGGTGGA 58.679 45.455 6.97 0.00 0.00 4.02
1170 1488 3.784511 AGAGCATATGATGAAGGGTGG 57.215 47.619 6.97 0.00 0.00 4.61
1220 1626 3.196469 ACGTCATCTGGAATCACACATCT 59.804 43.478 0.00 0.00 0.00 2.90
1255 1661 2.490270 CTTCCAAGGCTCCCAGGTGG 62.490 65.000 0.00 0.00 0.00 4.61
1422 1842 1.560923 ACATTCGATGTCAGTAGCGC 58.439 50.000 0.00 0.00 39.92 5.92
1551 1971 1.444724 CGTCATTACCACACGCCGA 60.445 57.895 0.00 0.00 0.00 5.54
1733 2155 5.688621 CAGATGCATGCCATTTTACATGTAC 59.311 40.000 16.68 0.00 44.43 2.90
1747 2169 1.909376 CTTGCTTGTCAGATGCATGC 58.091 50.000 11.82 11.82 34.85 4.06
1763 2185 4.034858 CAGTACCAGTTCTGCATATGCTTG 59.965 45.833 27.13 19.29 42.66 4.01
1886 2308 1.288127 GTTCACCGCCGACTGTAGT 59.712 57.895 0.00 0.00 0.00 2.73
2237 2659 1.053835 TGTCCTGAAGGCTGGTGACA 61.054 55.000 5.60 5.60 39.59 3.58
2372 2802 4.459337 GTGAACAAGTAAGGAGGAAATGGG 59.541 45.833 0.00 0.00 0.00 4.00
2447 2879 2.541556 GGTCTGAGTTCTAATGGCGAC 58.458 52.381 0.00 0.00 0.00 5.19
2448 2880 1.134367 CGGTCTGAGTTCTAATGGCGA 59.866 52.381 0.00 0.00 0.00 5.54
2449 2881 1.134367 TCGGTCTGAGTTCTAATGGCG 59.866 52.381 0.00 0.00 0.00 5.69
2450 2882 2.815478 CTCGGTCTGAGTTCTAATGGC 58.185 52.381 0.00 0.00 40.03 4.40
2488 2922 1.134699 TGGTGTGCAAATCGCCAAAAA 60.135 42.857 5.66 0.00 41.60 1.94
2489 2923 0.461548 TGGTGTGCAAATCGCCAAAA 59.538 45.000 5.66 0.00 41.60 2.44
2511 2945 3.267860 GAGAGCGCCGCCAATGAG 61.268 66.667 4.98 0.00 0.00 2.90
2524 2958 1.941734 GGCGACGCGATCTTGAGAG 60.942 63.158 15.93 0.00 0.00 3.20
2672 3352 5.104900 GCGGAGGTGGGTATATATTTCTCAT 60.105 44.000 0.00 0.00 0.00 2.90
2673 3353 4.222145 GCGGAGGTGGGTATATATTTCTCA 59.778 45.833 0.00 0.00 0.00 3.27
2681 3361 0.984230 CCATGCGGAGGTGGGTATAT 59.016 55.000 0.00 0.00 0.00 0.86
2804 3516 5.443170 CGCATCCACTTTTTGAATTTTAGCG 60.443 40.000 0.00 0.00 0.00 4.26
2820 3953 0.461339 AATCCCACGTACGCATCCAC 60.461 55.000 16.72 0.00 0.00 4.02
2829 3962 3.700539 TGTTCGAATCCTAATCCCACGTA 59.299 43.478 0.00 0.00 0.00 3.57
2832 3970 3.869065 TGTGTTCGAATCCTAATCCCAC 58.131 45.455 0.00 1.86 0.00 4.61
2835 4539 5.414765 AGGTTTTGTGTTCGAATCCTAATCC 59.585 40.000 0.00 7.07 36.13 3.01
2836 4540 6.148811 TGAGGTTTTGTGTTCGAATCCTAATC 59.851 38.462 0.00 0.00 37.31 1.75
2837 4541 6.001460 TGAGGTTTTGTGTTCGAATCCTAAT 58.999 36.000 0.00 0.00 37.31 1.73
2838 4542 5.369833 TGAGGTTTTGTGTTCGAATCCTAA 58.630 37.500 0.00 0.00 37.31 2.69
2839 4543 4.963373 TGAGGTTTTGTGTTCGAATCCTA 58.037 39.130 0.00 0.00 37.31 2.94
2840 4544 3.815809 TGAGGTTTTGTGTTCGAATCCT 58.184 40.909 0.00 1.38 38.91 3.24
2871 4826 0.404426 AGTTGGTTACCAGGAAGGCC 59.596 55.000 3.65 0.00 43.14 5.19
2874 4829 1.702957 TCCCAGTTGGTTACCAGGAAG 59.297 52.381 9.43 0.00 33.81 3.46
2875 4830 1.822425 TCCCAGTTGGTTACCAGGAA 58.178 50.000 9.43 0.00 33.81 3.36
2878 4833 1.534729 GCTTCCCAGTTGGTTACCAG 58.465 55.000 3.65 0.00 33.81 4.00
2881 4836 2.039348 TGTAGGCTTCCCAGTTGGTTAC 59.961 50.000 0.00 0.00 34.77 2.50
2908 4868 5.510671 AGAAAACAGAAGTGCATTGTTACG 58.489 37.500 8.58 0.00 34.18 3.18
2925 5645 9.712359 CAACCAGTAACAAACTAGTAAGAAAAC 57.288 33.333 0.00 0.00 35.76 2.43
3049 7984 6.072112 TCGGACAGATTGGAAAAGAAAAAG 57.928 37.500 0.00 0.00 0.00 2.27


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

AutoCloner maintained by Alex Coulton.